8
Graduate Program in Biochemistry & Cell Biology
Graduate Program in Biochemistry & Cell Biology
2 www.gsbs.uth.edu/biochemistry-and-cell-biology
The Biochemistry and Cell Biology (BCB) Graduate Program is a rigorous interdisciplinary graduate program that focuses on understand-ing the fundamental basis of life and disease at the molecular and cellular levels. Our faculty apply biochemistry and cell biology approaches to understand fundamental mechanisms gov-erning almost all types of biological processes and systems including neurobiology, cancer biology, immunol-ogy, physiology, and pharmacology. Graduates of this program will have extensive training
traversing from single molecules to human disease pathogenesis. Our well-funded faculty and student teams collaborate to make high-impact discoveries relevant to human health.
The BCB program has faculty from over 25 depart-ments and divisions from both UTHealth and MD Anderson, leading to a truly interdisciplinary training environment. In addition to formal classroom and laboratory training, students participate in enriching activities including seminar series, research workshops, and an annual off-campus retreat as well as social and community service events. The BCB program provides an exceptional training environment that effec-tively prepares students for the next steps in their careers.
Throughout their training, all BCB students receive full financial support for tuition and fees as well as a stipend. In addition, BCB students are highly competitive for fellowships, awards, and travel scholarships to present their work at scientific meetings and workshops.
Poster session at annual retreat
PROGRAM OVERVIEW
Tristen Tellman, Ph.D. student One of the best things about BCB is the diversity in research that our program represents. From structural modeling to cell signaling, you will walk out of this program with a wealth of knowledge to propel you into your future.
Cardiomyocyte
Co-localization of A-kinase anchor protein with two populations of nociceptive sensory neurons in rat dorsal root ganglia.
Cover images, clockwise from top left:
Lipid phase separation in giant plasma membrane vesicles
Ras proteins in plasma membrane
Astrocytic processes (in orange) surround blood vessels (in blue); Sytox green labels non-specified cell nuclei
Ki67 staining of mouse mammary gland
Defense of Morayo Adebiyi, Ph.D.
Ashabari Mukherjee, Ph.D. student I’d like to say how happy I am to have found a small community within GSBS. Not only are the students extremely welcoming and friendly, the faculty and administration are also the most ap-proachable of any department I worked in. It is so easy to get help for anything in the BCB program, research related otherwise, all you have to do is ask.
3www.gsbs.uth.edu/biochemistry-and-cell-biology
The interdisciplinary nature of the BCB program creates a unique environment that exposes students to a wide range of research subjects and approaches and compels students to think about research problems from different perspectives. Ultimately this provides students with an added breadth of knowledge that can benefit their future careers. Students in BCB also benefit from a very high faculty to student ratio. BCB faculty have an “open door” policy and encourage students to stop by and discuss technical challenges, progress on their thesis project, or career development. Because our program comprises faculty and research staff with diverse expertise, BCB students have a tremendous opportunity to gain conceptual and technical help as their projects inevitably take them in exciting, unexpected directions.
The BCB program maintains a collegial and relaxed atmosphere that is conducive to student learning. The program provides students with many opportunities for interac-tion and feedback from their fellow students, including student-only break rooms, student-run lunches, and student-only social outings to local eateries and bars.
The BCB Graduate Program is proud that our students actively participate in program management through the Biochemistry and Cell Biology Student Orga-nization (BCBSO), serving on program standing committees and forming ad hoc committees to organize recruitment, the annual retreat and other events. Student leadership activities include inviting guest speakers, honoring program faculty,
assisting the BCB faculty in orientation and recruitment initiatives, participating in community service activities, and organizing social activities to promote interactions among students and between students and faculty. The BCB Director provides strong support to the BCBSO, especially in fostering the students’ skills in manage-ment and fiscal matters, often seeking input and help from the students on all aspects of program governance.
BCB STUDENT SUCCESSMany BCB students are successful in obtaining fellowships from both intramural and extramural sources. Most students also obtain scholarships through the GSBS. BCB students also receive many awards for research excellence such as the McGovern Medical School Deans’ Scholarship Award, the Presidents’ Award, McGovern
Award for Presentations, as well as travel fellowships. These awards provide stu-dents with records of achievement and a degree of independence that enormously
benefits their careers. BCB students often publish their work in high impact journals and such as Nature, Cell, Proceedings of the National Academy of Sciences, and Current Biology, to name a few. The average BCB student time to graduate with a Ph.D. is five years, faster than the average time to gradu-ation in GSBS and nationally. After graduation, BCB students are extremely competitive for postdoctoral fellowships at prestigious universities nation-wide. Many BCB students also find success in non-academic career paths.
BCB STUDENT LIFE
Sporting activities at the retreat
Journal covers highlighting faculty research
Immunohistochemical detection of a prostate cancer lesion. Prostate biopsy tissue derived from a patient suspected of having cancer was stained for AMACR (red), p63/basal cells (brown) and counterstained with hematoxylin (blue). Positive staining for AMACR in epithelial cells combined with loss of p63/basal cell staining and enlarged nuclei indicate the presence of a malignant lesion compared to normal/benign glands that can be observed in the periphery of the image.
www.gsbs.uth.edu/biochemistry-and-cell-biology4
Course requirements for program students are designed to accommodate the diversity of the research environments in which Program students will be trained. BCB students can expect to finish all of the required didactic courses in the first year of study. The second year of study will focus on electives specific to your field of interest. The second year is also when BCB students take the qualifying examination. In BCB the qualifying examination is “on topic.” The written component is a grant application based upon your thesis project, which is then orally defended. We encourage submission of this grant to funding agencies after the successful defense of the proposal.
BCB COURSE REQUIREMENTSFall Year 1GS21 1017 Foundations of Biomedical Research GS21 1051 Ethical Dimensions Biomedical Sciences GS00 1514 Tutorial Research Experience
Spring Year 1GS03 1023 Current Methods in Biochemistry and Cell BiologyGS13 1024 Molecular Basis of Cell Signaling GS00 1514 Tutorial Research Experience
Summer Year 1GS03 1111 Scientific Writing for Grant Proposals (Any GSBS-approved writing course may be substituted in a different semester, prior to candidacy exam)
GS00 1520 Research in Biomedical Science (Required for all BCB students every semester)
Fall Year 2GS04 1751 Design and Delivery of Advanced Research Seminar Course GS12 1051 Seminars in Life Sciences (Required for all BCB students every semester)GS12 1011 BCB Research in Progress (Required for all BCB students every semester)
Spring Year 2Take candidacy exam.Take two 1-unit electives (Any elective approved for credit by GSBS, including approved courses around TMC)
Years 3+GS12 1011 BCB Research in ProgressGS00 1520 Research in Biomedical Science
CURRICULUM
Dhananjay Thakur, Ph.D.
2015 graduate, Zhu lab
The best thing is the breadth of science: from atoms to behavior!
Calcium mobilization
Skeletal muscle fibers with different metabolic and endurance capacity
Cory Wilson, center, with Deans Michael Blackburn, Ph.D., left, and Michelle Barton, Ph.D., receiving the GSBS Student Research Day Poster Session bonus award for first-year students.
www.gsbs.uth.edu/biochemistry-and-cell-biology 5
Student LuncheonsBCB students participate in monthly, student-only lunch meetings that provide opportunities for discussion and feedback on a myriad of subjects, including thesis research, presentations for thesis committee meetings, prepa-ration for candidacy exams, or even interesting journal articles.
Research Seminars and WorkshopsBCB students are required to attend weekly scientific seminars presented by faculty from within the Texas Medi-cal Center and research institutions nationwide. All students also partici-pate in a one-credit course called BCB Research in Progress, which is a forum for students, postdoctoral fellows and occasionally faculty to present their current work in a 45-minute seminar. The setting is informal and intended to generate insightful discussion. Students receive feedback on their work dur-ing the seminar and on their presentation style afterward, with the goal of improving their public speaking skills.
Annual BCB RetreatsThe BCB program spon-sors an annual retreat in the Texas countryside to provide students with the chance to present their work and unwind.
Over the span of two days, students and faculty participate in both scientific and social activities designed to foster communication and scientific interac-tions. This annual event is a favorite activity of students and faculty.
Travel AwardsThe BCB program offers travel awards to all students to enable attendance of at least one scientific meeting or workshop per year. Participation in a scientific conference is an important part of student education. It provides the student with an opportunity to interact with scientists from around the world and gain exposure to new ways of thinking about research problems.
PROGRAM ACTIVITIES
Annual retreat
Megan Livingston, Ph.D. student I love that BCB is a supportive network of students and faculty, who are always available to you for assistance and advice.
Nuclear defects caused by Net1 overexpression
Student luncheon presentation
6 www.gsbs.uth.edu/biochemistry-and-cell-biology
Houston is the fourth largest city in the United States with an ethnically diverse and dynamic population. We enjoy a low cost of living compared to other large U.S. metropolitan areas, and the diverse economy of Houston offers a wide array of job opportunities for spouses and family members. As the cultural center of the Southwest, Hous-ton is home to the world-renowned Houston Ballet, the Houston Grand Opera, the Houston Symphony, the Tony Award-winning Alley Theatre and the Theater Under the Stars, which presents Broadway-quality musicals in the fabulous Hobby Center for the Performing Arts. If museums are more your interest, the Museum of Fine Arts, the Contemporary Arts Museum, the Menil Collection, the Museum of Natural Science, and the Children’s Museum are all within a mile of the Texas Medical Center. Houston is located 50 miles from the Gulf of Mexico and enjoys a sub-tropical climate that enables year-round outdoor activities. Houston is also home to major league sports teams such as the Astros, Texans, Rockets, and Dynamo. The low cost of living, mild climate, wealth of cultural and entertainment activities, and friendly people combine to make Houston a great place to live.
GSBS students generally live near the Texas Medical Center, either in student housing or in affordable nearby housing. The university maintains a recreation center near the student apartments with an Olympic-size swimming pool. The university is adjacent to Rice Village, which offers a wide variety of shopping and dining opportunities.
The BCB program is based in labs at the McGovern Medical School and MD Anderson Cancer Center, in the heart of the Texas Medical Center (TMC). The TMC includes over 20 academic institutions and hospitals, all within walking distance, including Baylor College of Medicine, the Texas Heart Institute, and Rice University. This unique concentration of institutions provides a wealth of opportunities for seminars and collaboration.
HOW TO APPLYStudents interested in the BCB program must first apply to the GSBS. Once accepted, students join a program at the end of their first year. Applications to the GSBS are accepted from Septem-ber 1st through January 4th. Qualified applicants are interviewed from January to April, and admitted applicants begin school in August of that year.
Early applications are encouraged. gsbs.uth.edu/admissions
HOUSTON LIVING
Randi Fitzgibbon, Ph.D. 2017 graduate, Berdeaux labI greatly benefited from discussions with other BCB students and professors outside of my exact field of study as this has widened my scientific perspective and has helped me develop skills for communicating my findings to a broad audience.
2018 Commencement
TEXAS MEDICAL CENTER
Texas Medical Center
Xenopus cilia
2017 Lab Coat Ceremony
Jun-ichi Abe, Ph.D. Posttranslational modifications in cardio-oncology
Askar Akimzhanov, Ph.D.Dynamic lipidation of signaling proteins
Joseph Alcorn, Ph.D.Surfactant protein regulation and function
Hesham M. Amin, M.D.Signal transduction; apoptosis; cell cycle; cytokines
Michael Andreeff, M.D., Ph.D.Apoptosis regulation, leukemia and tumor stem cells, microenvironment, leukemia signaling, mesenchymal stem cell gene therapy
Jennifer M. Bailey, Ph.D.Gastroenterology, hepatology and nutrition
Blaine Bartholomew, Ph.D.ATP-dependent chromatin remodelers and transcription regulation
Venkata Lokesh Battula, Ph.D.Stem cells in cancer, tumor-stroma interactions in cancer progression
Andrew J. Bean, Ph.D. Molecular mechanisms of endocytic protein sorting
Rebecca Berdeaux, Ph.D.Signaling in muscle metabolism and regeneration
Xiaohong Bi, Ph.D. Translational application of optical spectroscopy and imaging
Michael R. Blackburn, Ph.D. Adenosine signaling and chronic lung disease
Darren F. Boehning, Ph.D.Cell death signaling in disease
Mikhail V. Bogdanov, Ph.D.Lipochaperones lipid-assisted protein folding and topogenesis
Ghislain Breton, Ph.D.Mapping the circadian clock network in zebrafish
L. Maximilian Buja, M.D. Myocardial cell injury, myocardial ischemia, atherosclerosis and cardiomyopathies
Jeffrey Chang, Ph.D.Cell signaling and genomics in cancer
Zheng (Jake) Chen, Ph.D. Small-molecule probes for chronobiology and medicine
Xiaodong Cheng Ph.D.Molecular coupling of DNA modification and histone methylation
Xiaodong Cheng, Ph.D. cAMP-mediated cell signaling and drug discovery
Shane Cunha, Ph.D.Membrane specialization in cardiac cells
Radbod Darabi, M.D., Ph.D.Using stem cells and gene editing to treat skeletal muscle disorders
Pramod Dash, Ph.D.Formation and impairment of memory
Catherine Denicourt, Ph.D.Regulation of cell growth in normal and cancer cells
Carmen W. Dessauer, Ph.D.Mechanisms of cyclic AMP signaling in heart and chronic pain models
Burton F. Dickey, M.D.Airway mucin secretion
William Dowhan, Ph.D.Structure, assembly and function of cell membrane components
Guangwei Du, Ph.D.Lipid signaling and metabolism
Kristin L. Eckel-Mahan, Ph.D.Role of the circadian clock in health and disease
Holger K. Eltzschig, M.D., Ph.D. Acute organ injury—lungs, heart, and kidney
Scott E. Evans, M.D.Mechanisms of inducible microbial resistance in the lung epithelium
Mary (Cindy) Farach- Carson, Ph.D.Extracellular matrix, 3D tissue and tumor engineering
Daniel E. Frigo, Ph.D.Molecular endocrinology, signal transduction and cancer metabolism
Jeffrey A. Frost, Ph.D.Signal transduction, cell proliferation and cancer
Alemayehu A. Gorfe, Ph.D.Biophysics of lipid-modified signaling proteins
John P. Hagan, Ph.D.MicroRNAs and their post-transcriptional regulators in developmental and cancer biology
Leng Han, Ph.D.High-throughput technologies in complex diseases
John F. Hancock, M.D., Ph.D.Roles of Ras proteins in cellular signaling
John R. Horton, Ph.D. Structural biology; epigenetic mechanisms; drug design
Johnny Huard, Ph.D.Orthopaedic surgery; regenerative medicine; adult muscle derived stem cells
Junichi Iwata, D.D.S., Ph.D.Membrane trafficking and cellular metabolism
Roger Janz, Ph.D.Synaptic vesicle proteins as regulators of neurotransmitter release
Vasanthi Jayaraman, Ph.D.Structure and function of glutamate receptors
Jianping Jin, Ph.D.Genes involved in ubiquitylation and DNA damage responses
Nicholas Justice, Ph.D.The role of stress in Alzheimer’s disease pathogenesis
Harry Karmouty-Quintana, Ph.D.Mechanisms of pulmonary hypertension associated with chronic lung diseases
F. Kurtis Kasper, Ph.D. Biomaterial-based solutions for craniofacial challenges
Rodney E. Kellems, Ph.D.Angiotensin receptors, autoantibodies and disease; Inflammation, autoimmunity and hypertension.
Melvin E. Klegerman, Ph.D.Molecular targeting of nanoparticulate formulations
Bruce C. Kone, M.D.Epigenetics of epithelial ion transport
Anna Konovalova, Ph.D.Biogenesis of bacterial cell surfaces
Jian Kuang, Ph.D. Cell cycle control, regulation of G2/M transition, phosphoregulation of protein functions, anti-mitotic cancer therapy, regulation of ESCRT-mediated processes by the adaptor protein ALIX
Richard J. Kulmacz, Ph.D.Mammalian cytochrome b561 family of proteins
Jonathan M. Kurie, M.D.Retinoid-induced prevention of lung carcinogenesis
Cheng Chi Lee, Ph.D. Molecular connectivity of the core circadian clock mechanism and other cellular pathways
Dung-Fang Lee, Ph.D. iPSC disease modelling, cancer pathological mechanisms
Ilya Levental, Ph.D.Membrane dynamics and signaling
Wenbo Li, Ph.D. Enhancers, noncoding RNAs and 3D Genome Control
Yi-Ping Li, Ph.D.Signaling mechanism of striate muscle remodeling
Lenard M. Lichtenberger, Ph.D.Mechanism of peptic ulcer disease
Tao Lin, D.V.M.Bacteria pathogenesis, host-pathogen interaction, function genetics
David S. Loose, Ph.D.Biomarkers of endometrial cancer, Wnt signaling
Chai-An Mao, Ph.D.Genetic regulatory network for RGC development; RGC subtypes; mitochondria biogenesis in retinal development and diseases
Emil Martin, Ph.D.Regulation of NO/cGMP signaling in health and disease
Pawel K. Mazur, Ph.D.Next-generation mouse models to dissect cancer progression and CAR-T development
Diana Milewicz, M.D., Ph.D. Genetically triggered vascular disease: thoracic aneurysms, aortic dissections, pediatric onset strokes
Rachel Miller, Ph.D.Wnt signaling in kidney development and disease
Steven W. Millward, Ph.D.Novel molecular scaffolds to develop targeted imaging probes for cancer
Kevin A. Morano, Ph.D.Protein folding and proteostasis in yeast
Ines Moreno-Gonzalez, Ph.D.Risk factors and molecular mechanisms of Alzheimer’s disease
Naoki Nakayama, Ph.D. Pluripotent stem cell biology and joint cartilage regeneration
Vihang Narkar, Ph.D.Transcriptional regulation of muscle function
John O’Brien, Ph.D.Mechanisms of electrical synapse regulation in the vertebrate CNS
Oleh M. Pochynyuk, Ph.D. Renal ion channels in health and disease
John A. Putkey, Ph.D.Structural and molecular basis of calcium signaling
Christophe P. Ribelayga, Ph.D.Circadian signaling in the retina
Irina I. Serysheva, Ph.D.Structure and function of integral membrane proteins
Ann-Bin Shyu, Ph.D.Global regulation of mammalian mRNA fate
Min Sup Song, Ph.D.Molecular pathogenesis of cancer, aging, and metabolic disorder
Claudio Soto, Ph.D.Role of protein misfolding and aggregation in neurodegenerative diseases and design of novel strategies for therapy and diagnosis
John L. Spudich, Ph.D.Structure and function of microbial rhodopsins and optogenetics
Kai Sun, Ph.D. Fat tissue remodeling in obesity and diabetes
Heinrich Taegtmeyer, M.D., Ph.D.Metabolic regulation of cardiac gene expression
John A. Tainer, Ph.D.DNA repair mechanisms, inhibitors, and cancer biology
Ba-Bie Teng, Ph.D. Molecular genetics and pathogenesis of cardiovascular diseases
Roopa Thapar, Ph.D.Structural Bbiology, RNA-protein interactions, RNA
Kartik Venkatachalam, Ph.D.Signal transduction in the nervous system
Edgar T. Walters, Ph.D.Mechanisms of persistent pain and nociceptive memory
Rick A. Wetsel, Ph.D. Inflammation and stem cell therapeutics
Ching On Wong, Ph.D.Endo-lysosomes in immune and neuronal cell biology
Wendy A. Woodward, M.D., Ph.D.Stromal cells in inflammatory breast cancer
Jiaqian Wu, Ph.D. Stem/neural cell fate, neurotrauma, bioinformatics
Yang Xia, M.D., Ph.D.Hypertension, preeclampsia, priapism, chronic kidney disease and blood disorders (sickle cell disease)
Wa Xian, Ph.D. Stem cell mediated lung regeneration, evolution and resistance of lethal epithelial cancers, patient-specific models of inflammatory diseases
Jiusheng Yan, Ph.D.Ion channels, calcium signaling, pain and cancer
Liuqing Yang, Ph.D.Long noncoding RNA, breast cancer, tumor immunosurveillance and immunotherapy
Seung-Hee (Sally) Yoo, Ph.D.Circadian rhythm: from genes to behavior
Lei Zheng, Ph.D.Molecular mechanisms of Ca2+ homeostasis and lipid metabolism
Yong Zhou, Ph.D.Membrane mechanics, membrane protein lateral segregation and signal transduction
Michael Zhu, Ph.D.Structure, function, and physiological roles of calcium permeable channels in mammalian cells
Eva M. Zsigmond, Ph.D.Developmental biology, stem cell biology, genetically- engineered animal models
7
FACULTY
Dr. Rebecca Berdeaux, Program Director
Department of Integrative Biology and Pharmacology
The McGovern Medical School
Dr. Ilya Levental, Program Co-Director
Department of Integrative Biology and Pharmacology
The McGovern Medical School
Amanda Williamson, Program Coordinator
MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
GRADUATE PROGRAM IN BIOCHEMISTRY & CELL BIOLOGY
BCB: INNOVATIVE MODEL SYSTEMS AND COLLABORATIVE APPROACHESBCB faculty and students utilize a wide range of animal and cell-based systems for their research. Common animal model systems include yeast, fruit fly, zebrafish, mice, and rats, as well as less common models such as snails and squid. Cell-based approaches often leverage the state-of-the-art Center for Advanced Microscopy, a Nikon Center of Excellence within the Department of Integrative Biology and Pharmacology. BCB labs are very interactive and often work together to achieve unique solutions to research questions. Moreover, faculty and students within BCB enjoy networking opportunities through participation in topic-focused research groups throughout the Texas Medical Center.
Model of Ras protein dimerization Artistic rendering of a fly brain
Dr. Dessauer and Ph.D. student Tanya Baldwin Brittany Jewell, UT System’s new student regent for 2018-2019, and her advisor is Dung-Fang Lee, Ph.D.
State-of-the-art imaging facility
