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Graduate Courses All 600-level courses are open to undergraduates with permission. 020.601 Current Research in Bioscience Instructors: Staff Fall, 1 credit 020.637 Genomes and Development This course covers the genetic analysis of development, model developmental systems, cell determination, organization of tissues and organs, cell motility and recognition, and sexual reproduction. Instructors: Van Doren, Spradling, Halpern, Bortvin Spring, 3 hours 020.668 Advanced Molecular Biology An advanced course in organization and function of eukaryotic and prokaryotic genes, including discussion of techniques to analyze gene structure and transcription. Prerequisite: 020.665. Instructor: Schleif Fall, 3 hours 020.674 Graduate Biophysical Students interested in pursuing biophysical research, who have taken undergraduate physical chemistry, may opt to take a two semester series in Molecular Biophysics (250.-689-690). This course will provide an overview of protein and nucleic acid structure, fundamentals of thermodynamics and kinetics, ligand binding, folding and stability of macromolecules, and the principles of biophysical methods such as fluorescence spectroscopy, NMR, and X-ray crystallography. Similar topics are covered in the two-semester series, but with greater emphasis on mathematical and quantitative analysis. Students wishing to pursue this option should consult with faculty. Instructors: Woodson, Bowman, Brand, Hill Spring, 3 hours 020.686 Advanced Cell Biology All aspects of cell biology are reviewed and updated in this intensive course through critical evaluation and discussion of the current scientific literature. Topics include protein trafficking, membrane dynamics, cytoskeleton, signal transduction, cell cycle control, extracellular matrix, and the integration of these processes in cells of the immune system. Open to graduate students and advanced undergraduates by permission of the instructor. Instructors: Staff Fall, 3 hours 020.699 Responsible Conduct in Research (INTERSESSION) The Johns Hopkins Departments of Biology, Biophysics, Chemistry and Carnegie Institution are committed to promoting the highest ethical standards amoun our administration, faculty members, and students. Therefore, all trainees and training faculty are required to attend the discussions series, Responsible Conduct of Research. The two week series meets for 6 two hour sessions and will be offered every January. Graduate students must attend the discussion series during their first year of study. Science has come under increased scrutiny and scientific misconduct has become a public issue regularly addressed in the media. Against the background of public skepticism, each university must make a visible commitment to responsible conduct of research. We believe that this is best accomplished by case-based discussions involving both trainees and faculty who are active investigators. In addition to general information, such as Honor in Science, participants will be expected to read related handouts sent to them before each session. Copies of the material contained in the suggested reading list will also be available. Through the use of pre/post testing and presentation evaluations, the course will respond to the specific needs of trainees and faculty. Instructors: Staff Intersession Elective Courses 020.606 Molecular Evolution A history of life on earth has been recorded in the DNA of organisms that live today. But what language is it and how can we read that history? This course introduces basic principles of molecular evolution plus a wide array of methodologies used to interpret molecular sequence data. Many interesting studies of gene and genome evolution will be covered as examples of this burgeoning area of research. This fun and popular course now includes computer labs that will enable students to obtain first-hand experience in this exciting field of research. Instructor: Cunningham Spring - odd years 020.612 Introduction to the Human Brain This course explores the outstanding problem of biology; how knowledge is represented in the brain. Relating insights from cognitive psychology and systems neuroscience with formal theories of learning and memory, topics include (1) anatomical and functional relations of cerebral cortex, basal ganglia, limbic system, thalamus, cerebellum, and spinal cord; (2) cortical anatomy and physiology including laminar/columnar organization, intrinsic cortical circuit, hierarchies of cortical areas; (3) activity-dependent synaptic mechanism; (4) functional brain imaging; (5) logicist and connectist theories of cognition; and (6) relation of mental representations and natural language. Instructor: Hedgecock Spring 020.613 Biology Science Writing Students will learn how to write abstracts and grant proposals, organize scientific manuscripts and thesis dissertations by writing and rewriting about their own research and editing other students’ work. Focus will be on structure, substance, accessibility, and clarity of writing. Instructor: Audrey Huang Spring 020.614 Signaling in Development and Disease An advanced undergraduate level seminar on current topics on signal transduction mechanisms underlying neuronal morphology, development and function. The proper functioning of the nervous system relies on the establishment of precise neuronal circuits through a developmental program including proliferation, neuronal migration, axonal growth and neuronal survival. This course pertains to the extracellular cues and downstream neuronal signaling pathways that coordinate these key events during neuronal development. The course will also cover the role of aberrant signaling mechanisms in neuronal degeneration and disease. Instructor: Kuruvilla Fall 020.615 Communication Between Cells: The Synapse as Model System All cells inform neighbors of their own activities. That act of communication frequently requires the formation of cell junctions across which information can pass. One of the best studied of the means of communication between cells is the synapse between neurons. This course examines the synapse in depth. both as a means to look at the nature of neuronal comunication and as a model for communication across cells of all types. Lectures on the physiology, structure, biochemistry and cell biology of synapses will be used as an introduction to the function of synapses in learning and memory and the effect on synapses of drugs and disease. Prerequisites: Biochemistry (020.305) & Cell Biology (020.306) or Cellular Molecular Neuroscience (080.301) Instructor: Kirkwood 020.616 (N) Planets, Life and the Universe This multidisciplinary course explores the origins of life, planets' formation, Earth's evolution, extrasolar planets, habitable zones, life in extreme environments, the search for life in the Universe, space missions and planetary protection. Prerequisites: Three upper level (300+) courses in sciences (Biophysics, Biology, Chemistry, Physics, Astronomy, Math, or Computer Science). Instructors: DiRuggiero, Norman 020.620 Stem Cells This course consists of introductory lectures given by faculty members, followed by student presentations in the form of seminars. The introductory part will cover the basic knowledge about stem cells, such as: What features make cells qualified as stem cells? What are the unique cellular and molecular properties of stem cells? How do stem cells maintain their identities? What are the mechanisms underlying stem cell differentiation and reprogramming? What are the therapeutic applications of stem cells? The student seminar will be based on selected literatures by the faculty. A summary mini-review paper is required for a chosen topic at the end of the semester. Instructor: Chen Spring - even years 020.629 Principles of Cancer Biology Lectures include recent findings in tumor genetics, cancer pathways, invasions and metastasis and cancer therapies. Instructor: Huang Spring 020.630 Human Genetics This course will examine the growing impact of human genetics on the biological sciences, on law and medicine, and on our understanding of human origins. Topics include structure and evolution of the human genome, genetic and physical mapping of human chromosomes, molecular genetics of inherited diseases and forensic genetics. Instructor: Hedgecock Fall - even years 020.634 Chromatin and Gene Expression An advanced course in molecular genetics covering various aspects of gene expression, including the structure of the nucleosome, effects of chromatin on transcription of eukaryotic genes, mechanisms of enhancer function, and the role of nuclear organization on gene expression. The course will consist of lectures as well as presentations of current papers by the students. Instructors: Moudrianakis, Beemon Fall - even years, 2 credits 020.638 Regulation and Mechanisms of the Cell Cycle The great progress in eukaryotic cell cycle research in the past decade was made possible by a unique synergism between different modern biological approaches (genetic, cell biological, biochemical, and developmental). These approaches will be highlighted in this course. We will cover the mechanisms the cell employs to carry out its duplication cycle, such as DNA replication, mitotic spindle function, and cytokinesis, as well as the regulatory mechanisms that govern these processes. The relationship of cell cycle biology to the cancer problem will receive special attention. Prerequisites: 020.305, 020.306, and 020.330, or the equivalent. Instructor: Hoyt Spring - even years 020.643 643 Viruses and Anti-Virals Viral infections are a major health problem to the entire world. The human and economic cost to society is tremendous; however, for many of these diseases no effective cures are available. Viral infections like HIV/AIDS, hepatitis C, herpes, HPV, SARS, avian flu, west nile virus, dengue not only affect or threaten people in the developing world but also in the most developed regions of the planet. Currently, fewer than 30 antivirals have been approved by the FDA, most of which specifically target HIV/AIDS. This course will discuss current strategies and approaches for the development of new anti-virals using a molecular and thermodynamic point of view. Instructors: Beemon, Freire Spring 020.644 RNA A graduate seminar course that will explore RNA from Its beginning in the primordial RNA world to its present-day roles in gene regulation in bacteria, mammals, and viruses. Topics will include: The early RNA world, Riboswitches, Ribozymes, evolution of protein synthesis, splicing, telomerase, RNA interference, microRNAs, long non-coding RNAs, Viral non-coding RNAs, and RNA therapeutics. Grad students only. Undergrads with permission of instructor. Instructor: Beemon Spring 020.646 Biological Spectroscopy This course provides a theoretical background for fluorescence spectroscopy and demonstrates how fluorescence can be used to advantage to address important problems in biochemistry, biophysics, molecular biology, and cell biology. Instructor: Brand Fall - even years, 2 hours 020.650 Eukaryotic Molecular Biology The field of molecular biology is fundamental for those interested in modern biological research and medicine. In this course students examine DNA, RNA and protein synthesis (i.e., the "central dogma" of molecular biology) in molecular detail, as well as how these processes are regulated and interrelated. There is significant examination of molecular structure-function relationships, with particular emphasis on RNA synthesis and processing and chromosomal organization, nucleosome regulation and epigenetics. Modern and fundamental experimental techniques and concepts are explored in detail. Students will learn how to use some genome databases and bioinformatics tools available online to improve their molecular biology research skills and knowledge. Readings are both from scientific journals as well as a textbook that includes interactive online content. Students enrolled in 020.650 will have additional assignments compared to those enrolled in 020.380. Instructors: Zappulla, Moudrianakis and Beemon Fall, one 1.5-hour and one 2.5-hour session per week 020.666 Biological Thermodynamics An in-depth discussion of thermodynamics, statistical thermodynamics and their applications to the conformational equilibrium and the interactions of biological macromolecules with other macromolecules and small molecular weight ligands. Graduate Students and Seniors with permission of Instructor. Instructor: Freire Fall - 2 hours 020.668 Advanced Molecular Biology An advanced course in organization and function of eukaryotic and prokaryotic genes, including discussion of techniques to analyze gene structure and transcription. Prerequisite: 020.665. Instructor: Schleif Fall, 3 hours 020.670 (N) Emerging Strategies and Applications in Biomedical Research Up-to-date primary literature manuscripts related to new discoveries and new strategies that are allowing scientists to make amazing progress in biomedical research will be presented. Examples include: labeling neurons with up to 90 different colors to trace their circuitry, evolution studies in glowing bacteria, detecting several viruses on a single chip and using fiber optics and channel rhodopsin to induce sleep. Students should be interested in reading primary literature research papers and discussing them in class. Instructor: Hattar Spring - 3 hours 020.679 Advanced Biological Microscopy This course is intended to build upon the basic skills students acquired in the previous course. Students will be required to work on actual ongoing research projects. The course will emphasize the integration and use of various light and electron microscopic techniques and their application to various research related questions. The course will have primarily a practical “hands-on” component; but will also include theoretical considerations as students will read, analyze, and discuss current journal articles. Prerequisites: Introduction to Biological Electron Microscopy and approval of the instructor. Instructor: McCaffery Spring - even years 020.684 Fundamentals of Drug Discovery and Development The creation and implementation of new approaches to the drug discovery and development process is a very active area of research. Currently, only one compound out of 5,000 that enter preclinical studies becomes a drug. Moreover, the development process is time consuming, lasting more than ten years on average. The rate of failure is extremely high. It has become evident that this field is in urgent need of revolutionary changes. This course will cover drug discovery issues ranging from the identification of hits to their optimization as drug candidates. Current as well as novel and proposed approaches aimed at accelerating discovery, potency optimization, selectivity, pharmacokinetics and other drug properties will be discussed. Grad students only Instructor: Freire Fall 020.731 Critical Thinking in Biology (formerly Molecular Morphogenesis) In this course, students will critically analyze modern and seminal primary research papers in molecular, cellular and developmental biology. This analysis will emphasize the logic and experimental design of a selected set of outstanding research publications from diverse fields. Points of view of authors and reviewers will be actively considered. Graduate students enrolled will develop the skills needed to efficiently understand and critique the rapidly expanding literature and growing diversity of biological research methods. In preparation for each class, all course participants will be expected to very thoroughly read and analyze the two assigned papers. Instructors will facilitate highly interactive discussions in the first third of the course sessions. Subsequently, individual students will present assigned papers to lead the discussion for the remainder of the semester. Students presenting papers will submit a written synopsis/summary of the paper in advance. Biology Ph.D. students, second year and above. Prerequisites: 020.637, 020.668, 020.674, and 020.686 Instructors: Bortvin, Ingolia and Zappulla Fall, 2 hours 020.735 Seminar: Membrane Trafficking The Membrane Trafficking seminar course consists of several weeks of lectures and discussions led by the professors discussing key background concepts in the field of Membrane Trafficking. Class meetings during the final weeks of the course are seminars on current topics in Membrane Trafficking, led by the students. Over the course of the semester, students will learn about the methods and logic of experiment design, model building and hypothesis testing, gain exposure to and skills in reading and summarizing scientific literature, and get experience with preparing and delivering an effective oral presentation. Instructors: Wendland, McCaffery Fall - odd years 020.738 Seminar: Biological Spectroscopy We will discuss important recent and classical papers in biological spectroscopy with an emphasis on steady-state and nanosecond time-resolved fluorescence. Topics will include FRET, fluorescence anisotropy and single molecule fluorescence. We will discuss photophysics and applications of spectroscopy to studies of proteins, membranes and nucleic acids. Instructor: Brand Spring - even years 020.739 Seminar: Topics in Biochemistry Minireviews taken from the Journal of Biological Chemistry. Students select a topic of their choice from the "Compendium of Minireviews" for the current year, and present it before the class for discussion. Instructor: Bessman Spring, 2 hours 020.753 Methods & Logic in Modern Biology The purpose of this course is to gain experience in critical thinking about the logic and methods used in modern biological research. The main approach will be the critical reading, presentation, and discussion of primary research papers, and the preparation and presentation of a research proposal. It is held once a week on the NIH Bethesda campus. Grad students only. Prerequisites: 020.637, 020.668, 020.674 and 020.686 Instructors: Lichten, Cohen-Fix Fall - odd years 020.801-802 Research on Biological Problems Independent research for the Ph.D. dissertation. Instructors: Staff 020.823-826 Introduction to Biological Research Training in techniques of biological research in research laboratories. Open to first-year biology graduate students only. Instructors: Staff 250.685 Proteins and Nucleic Acids The structure of proteins, DNA, and RNA and their functions in living systems. Experimental and theoretical approaches to macromolecules, including modeling, simulating, and visualizing three-dimensional structures. Instructors: Woodson, Bowman, Lecomte Fall 250.689 Physical Chemistry of Biological Macromolecules Introduction to the principles, methods, and approaches employed in the study of the energetics of proteins and nucleic acids, with emphasis in understanding the relationship between structure, energy, dynamics and biological function. Topics include classical, chemical, and statistical thermodynamics, kinetics, theory of ligand binding, and conformational equilibria. Instructor: Garcia-Moreno Fall, 3 hours 250.690 Methods in Molecular Biophysics Introduction to the methods employed in the study of energetics, structure, and function of biological macromolecules. Topics include optical spectroscopy, transport methods, NMR, X-ray crystallography. Course emphasizes theoretical understanding and practical knowledge through problem solving and literature discussion. Prerequisites, highly recommended: Proteins and Nucleic Acids (250.685) and Physical Chemistry of Biological Macromolecules (250.689), Calculus (110.108/109), or equivalent course work. Instructors: Bowman, Staff Spring Students may also take courses on other campuses with permission of the Director of the Graduate Program. School of Medicine (Course Listings) The School of Public Health (Course Listings) DISCLAIMER- Information on this page should be confirmed by the Registar's Office, the Department of Biology, or the course instructor. Information on this page is for the added assistance of students. It is not intended to replace official JHU publications. Mistakes should be reported to the CMDB Webmaster.
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