Fall 2020 courses
BIO/MOL/BCH 395J MOLECULAR BIOLOGY
Prof. Russell, TTh 9:30-11 am. Explore how genomes are maintained, propagated, and converted to functional RNAs and proteins. Understand the primary literature that has led to key advances in these research areas and the experimental approaches that are currently being used to forge new advances. Appreciate the current frontiers in these areas and explore the boundaries; what questions have known or hypothesized answers, and what questions remain to be answered by the next group of researchers and students.
MOL 290C INTRO BIOSTATS/COMPUT ANLY-WB
Prof. Iyer, M 9:30-11:30 am. This course will introduce first year Ph.D. students in the ICMB graduate programs to the basic concepts and practices of statistics, programming, quantitative data analysis and data visualization as they apply to research in biochemistry, cell and molecular biology, and microbiology. Quantitative data analysis skills are increasingly critical in these research fields, so this course is intended to provide the foundation for developing these skills and prepare for more advanced coursework. Students will learn in an interactive, hands-on manner using the widely used languages R and Python, and build up to executing an independent data analysis project working in teams.
MOL 190C RSPNSBLE CONDUCT OF RSRCH-WB
Prof. Iyer, W 10-11 am. This course will provide formal training in the ethical and responsible conduct of research in the disciplines represented in the ICMB graduate programs. Such training is required for researchers funded by training grants and federal fellowship awards, but is also vital for trainees embarking on their careers in scientific research. The class will be taught by a team of faculty with experience in research training and mentorship, using a discussion and case-study based approach. The topics covered will include professional development of trainees, research misconduct, conflicts of interest, collaborations, mentor/mentee responsibilities, authorship and publication, peer-review, data management, animal and human subject research, as well as contemporary ethical issues such as racism and inequity in science.
BIO 391 GRANT WRITING/PRES SKILLS-WB
Prof. Paull, M 2-5 pm. In this class, students will be guided through the development and preparation of a detailed proposal of their dissertation research goals. Emphasis will be placed on critical evaluation of research aims, methodology, and communication skills. Students will engage in intensive in-class peer review during the development of their proposals and they will present their completed proposals orally as short talks. This class is designed for second-year doctoral students preparing for their qualifying exams and is strictly limited to students in the Cell and Molecular Biology, Microbiology, and Biochemistry graduate programs.
BIO 391 GRANT WRITING/PRES SKILLS-WB
Prof. A. Johnson, M 3-6 pm. In this class, students will be guided through the development and preparation of a detailed proposal of their dissertation research goals. Emphasis will be placed on critical evaluation of research aims, methodology, and communication skills. Students will engage in intensive in-class peer review during the development of their proposals and they will present their completed proposals orally as short talks. This class is designed for second-year doctoral students preparing for their qualifying exams and is strictly limited to students in the Cell and Molecular Biology, Microbiology, and Biochemistry graduate programs.
BIO 381K CELL/MOL BASES OF NEUR DEV-WB
Prof. Agarwalla, TTh 9:30-11 am. This course examines the cellular and molecular bases of brain development with an emphasis on birth defects and potential therapies. This highly interactive class carries a writing flag and focuses on how to analyze, present and write scientific papers using innovative assignments and feedback from the instructor as well as peers.
BIO 388M PLANT MOLECULAR BIOLOGY-WB
Prof. Mehdy, TTh 3:30-5 pm. We’ll investigate the cellular and molecular bases of major physiological processes in plants, emphasizing characteristics unique to plant lineages while also covering mechanisms common with other eukaryotes. Our studies will pair molecular regulation with resulting adaptive advantages for the whole organism, with emphasis on important contemporary areas such as climate change, limitations to photosynthesis, and pathogen defense. Applications of genetic technologies to improve crops and provide better stewardship to ecosystems will also be discussed. Students in the graduate section will carry out an extra writing or oral presentation project.
BIO 391P ADVANCED VIROLOGY
Prof. Sullivan, MW 11-12:30 pm. My version of BIO391 "Advanced Virology" covers the basics of molecular virology with an emphasis that successful completion of the course results in a useful real-world product, typically a review article manuscript of publication quality, relevant to the student’s thesis or dissertation research, that incorporates the principles of virology (as a discipline and/or tool). The goal is to learn the principles of virology without emphasis on regurgitation/memorization and apply them (even if only via the thinnest of connections) to the students’ own research. It is expected that the final written document or project is suitable to be included in the Introduction section of the students dissertation or thesis and/or be submitted for peer review publication. In the end, the goal is a useful and fun experience that provides a deep molecular understanding of virology and a critical perspective on the workings of science. The course is open to students of any discipline and examples of students who have taken this course include those with research projects involving: viruses, the host response to pathogens, public health, immunology, cell-to-cell communication, new molecular technologies labs and government policy.
BIO 394L IMMUNOLOGY-WB
Prof.Ehrlich, TTh 2-3:30 pm. Bio394L is a comprehensive introductory immunology course for advanced undergraduates and graduate students. We will discuss innate immunity, the molecular basis of T cell and B cell antigen recognition, hematopoiesis and the development of lymphocytes, and cellular and humoral immune responses. We will touch on immunodeficiency, autoimmunity, immunotherapy and vaccination as well. Learning how the immune system works is extremely relevant to understanding host responses to SARS-CoV-2, the betacoronavirus causing the COVID-19 pandemic. Throughout synchronous class sessions, we will discuss how our growing understanding of the immune system relates to SARS-CoV-2 and other human diseases.
BIO 394M BACTRL BEHAV/SIGNALING MECH-WB
Prof. Harshey, TTh 9:30-11 am. Advanced studies in how bacteria perceive their environment and communicate with each other. Topics include chemotaxis and motility, morphogenesis and development, distinguishing self from non-self, secretion and virulence, photo-sensing and quorum sensing, and biofilms.
BIO 394M TUMOR BIOLOGY-WB
Prof. Huibregste, MWF 10-11 am. This course explores the biology, genetics and biochemistry of human tumors, with an emphasis on causes, diagnosis, and treatment of cancer. Core concepts will be explored in cancer pathology, treatment modalities (including immunotherapy, epidemiology, and the genetics and biochemistry of oncoproteins and tumor suppressors. The characteristic features of malignant tumors will be emphasized - including metastatic behavior, genomic instability, angiogenesis, cell cycle regulation, and evasion of apoptosis – as well as how these differ from normal cells and benign tumors. There will be a strong emphasis on the biochemical functions of cancer-related proteins and enzymes and treatment modalities. The events in the experimental history of cancer biology will be emphasized to illustrate how we have come to our current understanding.
BIO 381P ADVANCED PLANT PHYSIOLOGY-WB
Prof. Clark, TTh 2-3:30 pm. Utilizing recently published discoveries, the course aims to convey an up-to-date knowledge of important information and concepts in the broad field of plant physiology. This course highlights aspects of plant growth, development, cell signaling, and stress responses that are very similar to these processes in animals, but will also illustrate unique aspects of plants that are fascinating and exemplify the diversity of life strategies on earth. Course helps students develop critical thinking skills in evaluating current literature, data interpretation, and methods for solving key questions in the field. Writing a final paper on a current research topic in plant physiology provides students the opportunity to learn more in an area of interest not covered in detail during the course as well as improve their writing skills.
BIO 395L LAB STUDIES MOLECULAR BIO-WB
Prof. Mehdy, W 11-12 pm; 1-5 pm . We’ll analyze original research on a contemporary biological system. Our course will emphasize experimental design, how the methods work, data analysis, and troubleshooting which will help you build skills in thinking about research projects generally. Secondly, you will become a better writer as we work closely with you on 3 reports written in the style of articles published in scientific journals, with some modifications. Students in the graduate section will work with the instructors outside of class hours to develop an extra analytical project that is mutually decided upon, guided by the student’s research interests.
spring 2021 courses
BCH 387D BIOPHYS MTHDS
Prof. Jason McLellan. This course will focus on the theory and application of physical methods used in biochemistry and molecular biology, with a major emphasis on macromolecular structure determination by X-ray crystallography and cryo-electron microscopy. Other topics include surface plasmon resonance, isothermal titration calorimetry, and biolayer interferometry. The couse will provide students with the knowledge to design structural and biophysical studies to maximize data quality and avoid pitfalls, as well as to analyze and critique metrics used to validate structural results found in the primary literature. Much of the learning is expected to occur during lectures, with supplemental learning occurring via online content.
BCH 394P BIOINFORMATICS
Prof. Marcotte. An introduction to systems biology and bioinformatics, emphasizing quantitative analysis of high-throughput biological data, and covering typical data, data analysis, and computer algorithms. Topics will include introductory probability and statistics, basics of Python programming, protein and nucleic acid sequence analysis, genome sequencing and assembly, proteomics, synthetic biology, analysis of large-scale gene expression data, data clustering, biological pattern recognition, and gene and protein networks.
BCH 394 STRUC FUNC OF PROT NUC ACIDS
Prof. K. Johnson. This course is designed to give students the tools they need to be successful in a career in research in biochemistry and related disciplines by building a strong foundation to understand structure/function relationships in biological macromolecules. We begin with the fundamentals of the structure of proteins and nucleic acids, their pathways of folding, structure prediction, and the limitations of viewing dynamic molecules from static snapshots. Although we will start with a review of basic structure, we will rapidly progress to a deeper understanding of the forces that govern the structures and functions through their dynamics. All of biological activity is based upon structural changes induced by interactions with other molecules and such responses are time dependent. Therefore, we will work hard to develop a new way of thinking about dynamics. Here the ability to visualize the time-dependence of changes in structures and reactants is a skill that must be mastered through concentrated effort. Learning is facilitated by computer simulation of reaction kinetics, which provides the basis to learn kinetics but also gives the most robust and comprehensive methods of fitting data to test models. This course places additional demands on the student to work to understand the material based upon the lectures and the reading assignments. Expect a larger than average workload.
BIO 395F GENETICS
Prof. Miller. This course will focus on modern molecular genetic concepts and the scientific process, with analyses involving genetic mechanisms in biological systems and disease. The course consists of lectures covering these topics and reading/discussing primary literature relevant to these concepts. This course aims to expose students to genetic concepts while developing the skills to read and evaluate the data and papers that have been instrumental in providing the foundation for modern molecular genetics. The course will culminate with the students developing and writing their own independent research proposal involving primarily genetic topics and methodologies. Students will have the opportunity to evaluate proposals and will be required to present their own project in a class presentation. These exercises are aimed at developing independent thinking, research, communication and presentation skills that are essential for conducting scientific research, disseminating your findings to the scientific community and obtaining funding to support your research (i.e. NSF/NIH predoctoral fellowships). Bio395 goes beyond just learning modern genetics and techniques, aiming to provide students with additional skills that can be utilized in careers involving scientific research, writing and communication.
BIO 395G BIOCHEMISTRY
Prof. Xhemalce. This graduate-level course is designed for students interested in dissecting biological problems at the molecular level, and in the tools and methods that drive the process of discovery. This is an interactive class comprising lectures, case studies, in-depth analysis of original research papers, and student-led oral presentations.
BIO 395H CELL BIOLOGY
Prof. Wallingford. This course will involve an in-depth immersion in the current scientific literature exploring how basic cell biological processes (vesicle trafficking, cytoskeletal remodeling, etc.) contribute to the physiology of organisms, how fundamental molecular mechanisms drive cellular and subcellular behaviors, and how these mechanisms go awry in the course of human disease.
BIO 395M ADVANCED MICROBIOLOGY
Prof.Davies. In-depth study of microbiology topics. Students read original research papers in addtion to text assignments. Three lecture hours a week for one semester. Graduate standing, and consent of instructor and graduate advisor. Additional prerequisites vary with the topic.
BIO 381K DEV/PLASTICITY OF NERVOUS SYS
Prof. Agarwalla. This course examines the cellular and molecular bases of brain development with an emphasis on birth defects and potential therapies. This highly interactive class carries a writing flag and focuses on how to analyze, present and write scientific papers using innovative assignments and feedback from the instructor as well as peers.
BIO 395L LAB STUDIES MOLECULAR BIO-WB
Prof. Mehdy. We’ll analyze original research on a contemporary biological system. Our course will emphasize experimental design, how the methods work, data analysis, and troubleshooting which will help you build skills in thinking about research projects generally. Secondly, you will become a better writer as we work closely with you on 3 reports written in the style of articles published in scientific journals, with some modifications. Students in the graduate section will work with the instructors outside of class hours to develop an extra analytical project that is mutually decided upon, guided by the student’s research interests.
BIO 391P ADVANCED VIROLOGY
Prof. Dudley. This course focuses on the molecular biology and pathogenesis of animal viruses including those that cause polio, COVID-19, influenza, rabies, arthritis, and AIDS. Viruses are the ultimate parasites that depend on their hosts for reproduction, yet use mechanisms for replication that have provided tremendous insights into cell biology, immunology, and cancer. Approximately 9% of the human genome is comprised of viral sequences, so viruses are “us”. From immunodeficiency to leukemia to gene therapy, open your eyes to the tiny domains of these fascinating organisms.
BIO 394L IMMUNOLOGY-WB
Prof. Ippolito. This course will serve as a general introduction to the immune system and will survey its fundamental concepts: innate versus adaptive immunity, cellular and humoral immunity, autoimmunity, cancer, and vaccination. Current advances in the therapeutic intervention of immunologic diseases (i.e. immunotherapy) will also be discussed.
