Biology & Biomedical Sciences

BBS 5011 Ethics & Research Science

This course prepares DBBS graduate students to analyze and address ethical and professional issues across the range of their professional roles and responsibilities. The primary goals are for students to recognize complex situational dynamics and ethical issues and to develop professional and ethical problem-solving skills. The course examines ethical challenges related to research design and data collection, management, ownership, security, sharing, analysis, interpretation, and reporting while providing practical guidance on these issues. The course also examines the fundamentals of the broader research environment, including principles of ethics in genetics and human and animal subjects research, regulatory issues in biological and biomedical research, publication and authorship, and collaboration in science.

Credit 1 unit.

Typical periods offered: Spring Half B, Spring Half A, Spring, Spring Intersession, Summer

BBS 5014 Biotech Industry Innovators

Late one Friday afternoon in April 1976, the late venture capitalist Robert Swanson met with biochemist Herb Boyer, PhD, at his UCSF lab. Swanson had requested 10 minutes of Boyer's time; when the meeting ended, three hours later, the foundations had been laid for the formation of Genentech, the first biotechnology company, and the beginnings of the biotechnology industry. This course, The Basics of Bio-Entrepreneurship, investigates issues and choices that inventor/scientists encounter when considering the applications and commercialization of early stage scientific discoveries. This course is intended for anyone interested in working in the medical device, life-, bio-, or pharma-sciences industries as a founder, scientist, entrepreneur, manager, consultant, or investor. It focuses on the decision processes and issues that researchers and their business partners face when considering how a discovery might best be moved from academia to successful commercialization.

Credit 3 units.

Typical periods offered: Fall, Spring

BBS 5053 Immunobiology I

Immunobiology I is taught by the faculty members of the Immunology Program. This course covers in depth modern immunology and are based on Janeway's Immunobiology 10th Edition textbook. The topics include: basic concepts in immunology, innate immunity: the first lines of defense, the induce responses of innate immunity, antigen recognition by B-cell and T-cell receptors, the generation of lymphocyte antigen receptors, antigen presentation to T lymphocytes and signaling through immune system receptors. 

Credit 4 units.

Typical periods offered: Fall

BBS 5054 Immunobiology II

Immunobiology II is taught by the faculty members of the Immunology Program. This course covers in depth modern immunology and are based on Janeway's Immunobiology 10th Edition textbook. The topics include: the development and survival of lymphocytes, T cell-mediated immunity, the humoral immune response, dynamics of adaptive immunity, the mucosal immune system, failures of host defense mechanisms, allergy and allergic diseases, autoimmunity and transplantation, and manipulation of the immune response. 

Credit 4 units.

Typical periods offered: Spring

BBS 5068 Fundamentals of Molecular Cell Biology

This is a core course for incoming graduate students in Cell and Molecular Biology programs to learn about research and experimental strategies used to dissect molecular mechanisms that underlie cell structure and function, including techniques of protein biochemistry. Enrolling students should have backgrounds in cell biology and biochemistry. The format is two lectures and one small group discussion section per week. Discussion section focuses on original research articles.

Credit 4 units.

Typical periods offered: Fall

BBS 5075 Introduction to Coding and Statistical Thinking for Genetics and Genomics

This course is designed for first-year DBBS students who have had little to no prior experience in programming or statistics. The course will cover common statistical practices and concepts in the life sciences, such as error bars, summary statistics, probability and distributions, and hypothesis testing. The class will also teach students basic programming skills for statistical computation, enabling them to retrieve and analyze small and large data sets from online databases and other sources.

Credit 2 units.

Typical periods offered: Fall

BBS 5084 Single Molecule Biophysics Journal Club

Molecular motors in the cell harness chemical energy to generate mechanical work in a host of processes including cell motility, DNA replication and repair, cell division, transcriptional regulation, and intracellular transport. The purpose of this course is to discuss recent advances in the field of molecular motors. Special emphasis will be placed on understanding and critically evaluating single molecule studies. The course will consist of both journal club presentations and small group discussions.

Credit 1 unit.

Typical periods offered: Spring

BBS 5098 Graduate Research Fundamentals

This course introduces first-year Ph.D. students to the foundational skills, knowledge, and habits of mind required of successful independent biological scientists: 1) Social dynamics in the scientific research enterprise 2) Epistemology and ethics of bioresearch methods 3) Development and communication of research questions and results 4) Interdisciplinary scientific thinking. Class sessions and homework introduce these topics; major assignments prompt student to connect them with the broader scope of graduate training in lab rotations, course work, and interdisciplinary scientific seminars. the interactive, student-driven class structure facilitates autodidactic development while integrating small group activities and peer mentoring from advanced DBBS students.

Credit 0.5 units.

Typical periods offered: Fall

BBS 5123 Experimental Hematopoiesis Journal Club

Journal club in which papers that describe significant advances in the field of experimental hematopoiesis are discussed. Students are expected to present one paper per semester and attend the weekly (1 hour) session.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5137 TriMED: Membrane Excitability and Disease

TriMED consists of seminars , work-in-progress talks and journal club presentations. It meets Monday lunchtime (1-2pm, with lunch provided) from Jan - end April and from Sept - end November (1 credit each semester). Any student signed up for credit has to attend regularly and make one half hour presentation (either of their own research, or of a paper). The attendees are a mix of students, post-docs and faculty, but the goal is for trainee experience. The course is designed to fulfil interest in membrane proteins or signaling, ion channels, electrophysiology, neurobiology or excitability more broadly.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5138 Journal Club for the Molecular Mechanism of Aging

Why do we age? What causes aging? How is our life span determined? This journal club will address such fundamental, but challenging questions of aging and longevity. Recent studies on aging and longevity are now unveiling regulatory mechanisms of the complex biological phenomenon. We'll cover the latest progress in this exciting field and stimulate discussions on a variety of topics including aging-related diseases. One hour of paper presentation or research talk and discussion per every two weeks. Registered students are expected to have at least one presentation for 1 unit credit.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5146 Principles and Applications of Biological Imaging

Principles and Applications of Biological Imaging will introduce the interdisciplinary nature of the imaging sciences and conduct a comprehensive survey of the array of interrelated topics that define biological imaging. The course will cover the basics of the optical, magnetic resonance, CT, SPECT and PET imaging modalities, and microscopy, while focusing on applications of imaging to different disease states, such as oncology, neurology, cardiology and pulmonary diseases.

Credit 3 units.

Typical periods offered: Fall

BBS 5147 Contrast Agents for Biological Imaging

Contrast Agents in Biological Imaging will build the chemistry foundations for the design and use of contrast agents in imaging applications such as nuclear medicine, magnetic resonance imaging (MRI) and optical imaging. The course will include lectures on the design of radiopharmaceuticals for gamma scintigraphy and positron emission tomography, MRI contrast agents and agents for optical imaging, including bioluminescence and fluorescence microscopy. One year of general chemistry, one semester of organic chemistry required.

Credit 3 units.

Typical periods offered: Spring

BBS 5148 Metabolism Journal Club

The purpose of the Metabolism Journal Club is to introduce the graduate students to advanced topics spanning the biochemistry, cell biology and genetics of cellular and whole body metabolism.  Under the guidance of the course directors, students will select recent topical articles for discussion in the weekly journal club.  Students will be expected to provide a succinct introduction to the topic and lead discussion of the data presented in the journal article.  Students will be evaluated on the basis of their presentation and their participation in the seminar throughout the semester.  

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5152 Rad Journal Club (Regeneration, Aging, and Development)

Focuses on developing a dialog around current topics in developmental and regenerative biology at the molecular, cellular and systems levels.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5191 Pathobiology of Human Disease States

Three human disease states will be discussed in detail. Topics will include background clinical and epidemiological information, followed by a detailed examination of the molecular and cellular events that underlie the disease state. Examples of pertinent topics include Alzheimer's disease, AIDS, leukemia, cystic fibrosis, sickle cell anemia, diabetes, etc.

Credit 2 units.

Typical periods offered: Fall

BBS 5192 Cancer Biology Journal Club

This journal club covers current papers in molecular oncology, cancer genetics and contemporary molecular biology. Presentations will be given by students, post-docs and faculty, then discussed.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5196 Special Emphasis Pathway in Cancer Biology

This course is designed to present pre- and postdoctoral trainees with an organized educational format to explore major contemporary topics in cancer biology. The elective will provide an integrated view of cancer research including basic science, translational science, and clinical investigation. Approximately 60 minutes will be devoted to a didactic presentation by a faculty member with interaction by the participants. The remaining 30 minutes will be used to discuss a pivotal research paper from this field, preselected by the faculty member. Outside reading (30-60 min/week) will be required.

Credit 2 units.

Typical periods offered: Spring

BBS 5201 Membrane Protein Biophysics Journal Club

Cells are encapsulated by lipid bilayers providing a physical barrier for the passage of charged molecules and ions in and out of the cell. the proteins that reside within this layer of oil are called membrane proteins, and they act as the molecular gatekeepers, controlling the passage of ions, nutrients, waste products and signaling elements, across cell membranes. This journal club focuses on examining key literature in the field that investigates how membrane proteins fold, adopt certain structures, and how they function inside of the strange environment of the lipid membrane. The papers will be selected from biophysical studies that combine new and notable research with key historical work, for a broad perspective of the science being conducted in this complex and emerging field. Special emphasis will be placed on emerging topics, such as regulation of protein function by lipid composition, membrane protein synthesis and folding, cutting-edge developments in membrane biophysics. The course will consist of both journal club presentations, as well as small group discussions in the form of chalk-talks.

Credit 1 unit.

Typical periods offered: Spring

BBS 5217 Special Topics in Microbial Pathogenesis

Primarily for graduate and MSTP students, this course involves oral presentation and discussion of current research articles on pathogenic microorganisms (bacteria, viruses, parasites, and fungi). Discussion will include design of specific aims for research proposals. Emphasis will be on literature that addresses the cellular and molecular basis of host-pathogen interactions. Students are expected to prepare all articles covered and to participate actively in each discussion. Class meets twice per week for 1.5 hours each.

Credit 2 units.

Typical periods offered: Spring

BBS 5224 Molecular, Cell and Organ Systems

This course will introduce Ph.D. and MSTP students to fundamental problems in cell and molecular biology at the systems level. The course is divided into 5 themes: 1) microbial systems; 2) organ development and repair; 3) cardiovascular system and disease; 4) tumor & host systems; and 5) metabolic systems and disease. Topics within each theme highlight current research concepts, questions, approaches and findings at the molecular, cellular and physiological levels. Students will write an original research grant proposal on a topic of their choosing in one of the 5 themes. Students will critique proposals anonymously in an NIH-like study section.

Credit 3 units.

Typical periods offered: Spring

BBS 5235 Genetics Journal Club

This journal club will be focused on the Genetics department seminar series. Students will present one or a few recent papers by the seminar speaker scheduled for that week. Students will provide a brief written evaluation (on a form that will be provided) of their peers' presentations, and the faculty advisors will meet with each student after the presentation to provide feedback.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5255 Experimental Skeletal Biology Journal Club

The journal club, which meets weekly, focuses on cellular and molecular biology of the skeleton. Emphasis is placed on gaining insights into normal skeletal homeostasis as well as systemic disorders of bone. Papers presented for review are selected from the most competitive journals. Participants are encouraged to think outside of the box and discuss novel molecular discoveries that may impact bone cell function.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5272 Advanced Topics in Immunology

This course uses a journal club format to discuss contemporary issues in the cell and molecular biology of the immune system. Discussions focus on the use of current approaches to analyze the cellular and molecular basis of immunity. Topics include mechanisms of antigenic specificity, diversity, cell communication, differentiation, activation, and effector activity.

Credit 2 units.

Typical periods offered: Fall

BBS 5282 Chromatin Structure and Gene Expression

This special topics course will use Epigenetics ed. By Allis, Jenuwein, Reinberg, and Caparros (2007, Cold Spring Harbor Laboratory Press) as the organizing text. Each week a faculty member will provide a background lecture on an important topic or model system, and a student will present and lead discussion of a paper from the current scientific literature related to the previous week's background lecture. Topics to be considered will include background on chromatin structure, histone modifications and histone variants; epigenetic regulation in yeast, other fungi, ciliates, flies, mammals and plants; dosage compensation in different systems; DNA methylation and imprinting in mammals; stem cells, nuclear transplantation and reprogramming; and the epigenetics of cancer and other human diseases (some variation in topics in different years). Students enrolled in the course will be required to present one paper and to come prepared to each session, with a question for discussion.

Credit 2 units.

Typical periods offered: Spring

BBS 5284 Current Research in Chromatin, Epigenetics and Nuclear Organization

This journal club considers papers from the current literature on chromatin structure and function, with an emphasis on regulation of transcription, epigenetics and genomics. Presentations are given by students, postdocs and faculty, with discussion by all. Students enrolled for credit are expected to attend regularly, and to present a minimum of one paper during the term, with consultation and critique from the faculty.

Credit 1 unit.

Typical periods offered: Spring

BBS 5285 Current Topics in Human and Mammalian Genetics

This course aims to provide both biologists and those with mathematical backgrounds with a basis in mammalian genetics. The course will include the following modules: Nucleic acid biochemistry; Gene and chromosome organization; Introduction to Human Genetics; Mutations and DNA repair; Cancer Genetics; Genomic methodologies; Biochemical genetics; Murine Genetics; Epigenetics; Neurodegenerative diseases; Mitochondrial disorders; Pharmacogenetics; Introduction to human population genetics; Applications of modern human genetics; Introduction to web-based informatics tools for molecular genetics. One of the required courses in the Quantitative Human Statistical Genetics graduate program.

Credit 3 units.

Typical periods offered: Fall

BBS 5288 Special Topics in Molecular Genetics

A special topics course with lectures and discussion on the molecular basis of cancer including cell cycle regulation, tumor suppressor genes, tumor invasion, angiogenesis, immune evasion, resistance to apoptosis, signaling, imaging, gene expression, chromosomal translocations, and viral oncology.

Credit 2 units.

Typical periods offered: Spring

BBS 5303 Protein NMR Journal Club

This journal club covers the recent literature on protein NMR with a focus on using NMR to study protein function, NMR dynamics, and novel methods that expand the range of systems accessible to solution NMR studies. Students, postdocs and faculty discuss a recent paper and present background information on the relevant technical aspects of NMR. Students receive 1 credit for participation and presenting one paper.

Credit 1 unit.

Typical periods offered: Fall

BBS 5311 Dynamics in Mesoscopic Molecular Systems

This course will provide a background in the theory of the dynamics of mesoscopic systems and introduction to methods for measuring the dynamics of these systems. It will include measurement methods, some of which are in common use and others that have only recently been introduced. This course would be useful for biophysics students and others that are interested in molecular processes and mechanisms in small systems such as cells.

Credit 3 units.

Typical periods offered: Spring

BBS 5312 Macromolecular Interactions

This course will cover equilibria, kinetics and mechanisms of macromolecular interactions from a quantitative perspective. Thermodynamics, multiple binding equilibria (binding polynomials), linkage phenomena, cooperativity, allostery, macromolecular assembly, analysis of binding isotherms, enzyme catalysis and mechanism, steady-state and pre-steady-state kinetics, kinetic simulation, and isotope effects.

Credit 3 units.

Typical periods offered: Spring

BBS 5318 DNA Repair

This course is an advanced graduate course that explores all aspects of DNA damage and the cellular responses to DNA damage. It is designed for graduate students who have a working knowledge of chemistry, molecular biology and cellular biology, and for interested postdocs and researchers. Specific topics that will be covered are: The chemical basis of DNA damage, specific DNA repair mechanisms, cell cycle responses to damage, translesion DNA replication and mutagenesis, and human diseases related to defects in DNA damage response. The course consists of a lecture module, open to all, and a discussion module for registered students. In addition, several invited speakers in the field of DNA repair will give seminars and meet with registered students for discussion. Students will present and discuss research papers. Grades will be given based on student presentation and participation. Prerequisite; Permission of instructor.

Credit 2 units.

Typical periods offered: Spring

BBS 5319 Molecular Foundations of Medicine

This course will cover fundamental aspects of biochemistry and cell biology from a medical perspective. The course begins with a treatment of protein structure and the function of proteins in the cytoskeleton and cell motility. The principles of enzyme kinetics and regulation are then discussed and basic pathways for the synthesis and metabolism of carbohydrates and lipids are introduced. This leads in to a discussion of membrane structure and the function cellular organelles in biological processes including energy production, protein degradation and protein trafficking.

Credit 3 units.

Typical periods offered: Fall

BBS 5327 Optical Spectroscopy: Theory and Applications

Spectroscopic methods to be covered include fluorescence, both ensemble and single molecule, and absorption (circular dichroism); fluorescence correlation spectroscopy will also be discussed. The quantum chemistry /physics behind these methods will be reviewed.

Credit 2 units.

Typical periods offered: Fall

BBS 5328 Structural Biology Journal Club

Multi-laboratory research colloquia for DBBS graduate students focused on structural biology and complementary biophysical techniques. Course credit requires student presentation for credit.

Credit 1 unit.

Typical periods offered: Spring

BBS 5336 Computational Biophysics Journal Club

This course covers a combination of classic and recent publications on computational methods for studying biomolecules. Students participating for credit will be required to present at least once.

Credit 1 unit.

Typical periods offered: Spring

BBS 5357 Chemistry and Physics of Biomolecules

This course covers three major types of biomolecular structures: proteins, nucleic acids, and membranes. Basic structural chemistry is presented as well as the biophysical techniques used to probe each type of structure. Selected topics covered include protein folding, protein design, X-ray crystallography, NMR spectroscopy, nucleic acid bending and supercoiling, nucleic acid:protein interactions, RNA folding, membrane organization, fluidity, permeability and transport, and membrane channels. The weekly discussion section will cover problem sets and present current research papers. This is one of the required courses for the biochemistry and for the molecular biophysics graduate programs. Prior course work in biochemistry and physical chemistry is recommended but not required.

Credit 3 units.

Typical periods offered: Fall

BBS 5358 Biochemical and Biophysical Investigations of Infectious Diseases Journal Club

Biochemical and biophysical approaches continue to advance as powerful approaches to the understanding of human disease processes. This journal club covers recent papers in which these approaches address aspects of infectious diseases or inflammation. Students who enroll for credit will be expected to participate in weekly presentations and to present one to two papers along with accompanying background information.

Credit 1 unit.

Typical periods offered: Spring

BBS 5392 Molecular Microbiology & Pathogenesis

Course is devoted to studying microorganisms, particularly those that cause disease, with an emphasis on the molecular interactions between pathogens and hosts. First third of the course focuses on virology, second third on bacteriology and the last third on eukaryotic pathogens.

Credit 4 units.

Typical periods offered: Fall, Spring

BBS 5393 Molecular Virology Journal Club

Journal club covering a broad range of topics in virology with an emphasis on pathogenesis or molecular biology of medically important viruses. A minimum of one student presentation with faculty critique.

Credit 0.5 units.

Typical periods offered: Fall, Spring

BBS 5397 Current Literature in Microbiology

Presentations by students on a broad range of topics of current interest in microbiology. The course will emphasize presentations and discussion skills. Credit requires attendance and participation at all sessions and one presentation.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5412 Tropical and Molecular Parasitology

Graduate level seminar course focusing on current scientific literature in molecular parasitology. The journal club will meet biweekly during the Fall and Spring semesters. Students will attend both semesters in order to receive one credit. The seminar series will run jointly with a research conference in Tropical and Molecular Parasitology. Outside speakers will be invited for the seminar series to emphasize important developments in tropical medicine and molecular parasitology. In advance of the invited speakers, topics will focus on their previous research publications.

Credit 0.5 units.

Typical periods offered: Fall

BBS 5417 Hematology Division Journal Club: Current Topics in Cellular, Molecular, and Stem Cell Biology

This journal club covers a broad range of topics of current interest, including the fields of biochemistry, molecular biology, cell biology, developmental biology, and immunology. Speakers usually give a brief background to introduce the topic and then focus on one-two papers from the current literature. Presentations are given by graduate students, post-doctorates, and faculty. Each attendee presents two-three times per year. Participants are expected to attend all the sessions. This journal club was founded in 1966.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5425 Immunology of Infectious Diseases Journal Club

The goal of this Journal Club (JC) is to provide 2nd year students in MMMP program a platform to discuss new and emerging concepts on mechanisms by which host immune responses mediate protection against infectious diseases. This exercise will also enable the student who attend the fundamental Immunology course to apply their knowledge to understand the basis for immunology of infectious diseases. The format will include faculty who will select cutting-edge papers and head the discussion during the JC session.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5426 ID Gateway: Translational and Public Health Aspects of Basic Infectious Disease Research

This course provides an opportunity for students, postdoctoral fellows, infectious disease fellows and faculty to explore issues at the interface between patient care, public health and basic research in the area of microbial pathogenesis.

Credit 2 units.

Typical periods offered: Spring

BBS 5445 DNA Metabolism Journal Club

Presentation of current research papers in DNA replication, DNA repair, and DNA recombination, with an emphasis on basic biochemical and biophysical approaches.

Credit 1 unit.

Typical periods offered: Spring

BBS 5456 Advanced Crystallography

The advanced course in Protein Crystallography will address all aspects of modern protein crystallography including fundamentals of crystallography, the derivation of the structure factor and electron density equation, symmetry and space groups, direct methods, isomorphous replacement, molecular replacement, data collection, and crystal growing theory and techniques. Prerequisite, Physical Chemistry & Bio 5325 Protein Structure and Function. Two class hours per week.

Credit 2 units.

Typical periods offered: Spring

BBS 5469 Biochemistry, Biophysics, and Structural Biology Seminar

Student presentation of Biochemistry, Biophysics or Structural Biology topic. Second Year Students present from literature; senior students give formal research seminar. Attendance required of all BBSB Graduate Students.

Credit 0.5 units.

Typical periods offered: Fall, Spring

BBS 5480 Nucleic Acids & Protein Biosynthesis

Fundamental aspects of the structure, biosynthesis, and function of nucleic acids and the biosynthesis of proteins. Emphasis on mechanisms involved in the biosynthetic processes and the regulation thereof. Lecture course supplemented with student discussions of research papers.

Credit 3 units.

Typical periods offered: Fall

BBS 5483 Human Genetic Analysis

Basic Genetic concepts: meiosis, inheritance, Hardy-Weinberg Equilibrium, Linkage, segregation analysis; Linkage analysis: definition, crossing over, map functions, phase, LOD scores, penetrance, phenocopies, liability classes, multi-point analysis, non-parametric analysis (sibpairs and pedigrees), quantitative trait analysis, determination of power for mendelian and complex trait analysis; Linkage Disequilibrium analyses: allelic association (case control designs and family bases studies), QQ and Manhattan plots, whole genome association analysis; population stratification; Quantitative Trait Analysis: measured genotypes and variance components. Hands-on computer lab experience doing parametric linkage analysis with the program LINKAGE, model free linkage analyses with Genehunter and Merlin, power computations with SLINK, quantitative trait anaylses with SOLAR, LD computations with Haploview and WGAViewer, and family-based and case-control association anaylses with PLINK and SAS. The methods and exercises are coordinated with the lectures and students are expected to understand underlying assumptions and limitations and the basic calculations performed by these computer programs. Auditors will not have access to the computer lab sessions.

Credit 3 units.

Typical periods offered: Fall

BBS 5484 Genetics and Development of C. Elegans Journal Club

Students will present a research paper (or present their current thesis research) and the appropriate background material.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5487 Genetics and Genomics of Disease

The course will cover the use of genomic and genetic information in the diagnosis and treatment of disease, with an emphasis on current practice and existing gaps to be filled to achieve precision medicine. Areas of discussion include: bioinformatics methods; assessment of pathogenicity; use and curation of disease variant databases; discovery of incidental findings; genomics applications in Mendelian disease, complex traits, cancer, pharmacogenomics, and infectious disease; design of clinical trials with genetic data; ethical and policy issues.

Credit 2 units.

Typical periods offered: Fall, Spring

BBS 5488 Genomics

This course is designed for beginning graduate students who want to become familiar with the basic concepts and applications of genomics. The course covers a wide range of topics including how genomes are mapped and sequenced as well as the latest computational and experimental techniques for predicting genes, splice sites, and promoter elements. High throughput techniques for ascribing function to DNA, RNA, and protein sequences including microarrays, mass spectrometry, interspecies genome comparisons, and genome-wide knock-out collections will also be discussed. Finally, the use of genomic techniques and resources for studies of human disease will be discussed. A heavy emphasis will be put on students acquiring the basic skills needed to navigate databases that archive sequence data, expression data and other types of genome-wide data. Through problem sets, the students will learn to manipulate and analyze the large data sets that accompany genomic analyses by writing simple computer scripts. While students will become sophisticated users of computational tools and databases, programming and the theory behind it are not covered in this course.

Credit 4 units.

Typical periods offered: Spring

BBS 5489 Human Genetics Journal Club

In this biweekly journal club on Human Genetics we will present and discuss current cutting edge papers in human and mammalian molecular genetics. Students learn presentation skills, how to critique a paper and how to interact with a very active and critical audience. Any person interested in the current state of the art in Human Genetics may attend this course. It is a requirement that all students wishing to earn credit in this course must present a 1.5 hour journal club talk and must regularly attend and participate in the journal club throughout the year.

Credit 0.5 units.

Typical periods offered: Fall, Spring

BBS 5491 Advanced Genetics

Fundamental aspects of organismal genetics with emphasis on experimental studies that have contributed to the molecular analysis of complex biological problems. Examples are drawn primarily from yeast, nematodes, fruit flies, mouse, and humans. Students will conceive and write an original research proposal with a substantial genetics component; the learning goal is to build skills in developing hypotheses from the literature and designing experimental approaches to test those hypotheses.

Credit 3 units.

Typical periods offered: Spring

BBS 5496 Seminar in Computational Molecular Biology

Students present current research papers and the appropriate background material in the field of Computational Biology. Arts & Sciences students must take this course for credit; Engineering students must take this course Pass/No Pass.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5499 Cancer Informatics Journal Club

This journal club will explore current topics in cancer informatics. Current literature will be reviewed for advanced cancer genome analysis methods, statistics, algorithms, tools, databases, and other informatics resources.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5500 Medical Genetics

A significant portion of the first-year course in basic medical genetics devoted to human and clinical genetics, with emphasis on how genomic information will transform the practice of medicine. Topics covered include population genetics; molecular basis of mutations; human functional genomics; mouse models of human disease; pharmacogenomics; metabolic defects. Lectures, small group discussions, patient information session.

Credit 2 units.

Typical periods offered: Spring

BBS 5501 Biology of the Visual System

The purpose of the course is to provide a fascinating view of vertebrate eye development, anatomy, physiology and pathology. Topics to be covered include the molecules that control eye formation, ocular stem cells, the physiology of transparency, hereditary ocular diseases, phototransduction, the neurobiology of the retina and central visual pathways, age-related eye diseases, and many others. The course is open to all second year graduates students and above. Ophthalmology residents and postdocs with an interest in vision are strongly encouraged to attend.

Credit 3 units.

Typical periods offered: Fall

BBS 5505 Independent Study in Fundamentals of Molecular and Microbial Genetics

This literature-based course will introduce students to seminal and current studies in molecular and microbial genetics. Students will read and present a minimum of 12 landmark papers that helped shape our understanding of molecular and microbial genetics. Emphasis will be placed on students' ability to comprehend and explain these studies via chalk talks. All presentations will be given by students.

Credit 2 units.

Typical periods offered: Fall, Spring

BBS 5507 Genome Engineering Methods and Applications

This course will cover the basic principles of genome engineering with emphasis on Cas9/CRISPR technology. It will consist of discussion sessions in which students will present assigned manuscripts followed by a general discussion of the topic directed by the instructor. The course will cover the mechanisms of genome editing using host DNA repair systems, the function of Cas9, and how Cas9 can be harnessed to introduce defined mutations into almost any genome. The use of Cas9 to activate or repress genes, alter chromatin modifications, and the application of these Cas9 systems to conducting genome-scale screens in mammalian cells as well as its use in studying cell fate will be highlighted. Finally, we will study how Cas9 methodologies can be used to introduce disease-associated variants into pluripotent stem cells (e.g. iPSCs) that can be differentiated into disease-relevant cell for use in functional genomic studies.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5512 Diseases of Membrane Transport & Excitability

Classes will consider the molecular basis of the disease as well as animal models and current clinical studies. Addressing studies from the level of basic biophysical and molecular properties of the underlying ion channels/transporters, to the cellular deflects, to organ and animal outcomes and therapies., which will encourage and force students to develop their ability to integrate understanding at multiple levels. Students will be introduced to emerging ideas in clinical diagnosis, management and treatment, when appropriate, clinical specialists will allow student participants to directly observe and participate in the clinical experiences.

Credit 2 units.

Typical periods offered: Spring

BBS 5513 ITVS Project Building

The overall goal is to have intense guidance to construct a grant/fellowship application. Students should expect to have a near completed F30/F31 application by the end of this course Students will study previous F30/F31 applications and sit on a mock panel to review real world grants from their peers. They will use this experience to understand the reviewers perspective when writing fellowships and grants in the future. Students will draft all portions of a research proposal with feedback from their peers, the course instructor and faculty mentors.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5540 Neural Sciences

An integrated course dealing with the structure, function and development of the nervous system. The course will be offered in the Spring of the first year Medical School calendar.

Credit 5 units.

Typical periods offered: Spring

BBS 5543 Oral Presentation of Scientific Data

Practical course on how to prepare and present scientific data to an audience. Meets once a week for 90 minutes.

Credit 1 unit.

Typical periods offered: Spring

BBS 5571 Cellular Neurobiology

This course will present a fully integrated overview of nerve cell structure, function and development at the molecular and cellular level.  Broad topics to be covered include gene structure and regulation in the nervous system, basic neurophysiology, presynaptic and postsynaptic mechanisms of chemical neurotransmission, sensory transduction, neurogenesis and migration, axon guidance and synapse formation. Three 90 minute lectures plus one 75 minute paper discussion section per week. There will be four exams, as well as weekly quizzes.

Credit 6 units.

Typical periods offered: Fall

BBS 5572 Principles of Medicinal Chemistry

Overview of basic principles of medicinal chemistry covering drug targets and concepts of metabolism, efficacy and potency as relevant to drug design.

Credit 3 units.

Typical periods offered: Fall

BBS 5577 Synapses Journal Club

Synaptic function and malleability are fundamental to nervous system function and disease. This is an advanced seminar in the development, structure, and function of the synapse in health and disease. It is a natural extension of topics covered in Bio 5571. It may be primarily of interest to students in the Neurosciences Program, but also to students in MCB, Development, Biochemistry, Computational Biology, and Molecular Biophysics. Generally a topic for the semester helps focus the group; past topics have included Synapses and Disease, Neurotransmitter Transporters, Glutamate Receptors, Dendrites, GABA receptors. Participants (students, postdocs, and faculty) alternate responsibility for leading critical discussion of a current paper. Active participation offers the opportunity for students to hone their critical thinking and presentation skills. Students enrolling for credit will be expected to attend each week, to lead discussion once per semester and to provide written critiques (1-2 pages each) of two papers.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5617 Development Biology PhD Program Seminar

In response to student feedback for additional training in Developmental Biology obtained from surveys and group meetings, we propose a new seminar course in Developmental Biology. This once a week course will introduce student in the Developmental, Regenerative, and Stem Cell Biology PhD Program both to the classical embryological experiments that define key concepts in developmental biology, such as cellular fields, equivalence groups, cytoplasmic determinants, and the more modern experiments that uncovered the genetic and molecular basis of these processes. In general, the classes will be individual sessions on professional development, such as scientific presentation, how to navigate graduate school, etc.

Credit 1 unit.

Typical periods offered: Fall

BBS 5619 Advanced Cognitive, Computational, and Systems Neuroscience

This course will develop critical thinking and analysis skills with regard to topics in Cognitive, Computational and Systems Neuroscience. Course format will be a series of modules composed of intensive, faculty-led case studies on interdisciplinary topics at the intersection of psychology, computation and neuroscience. The goal will be to highlight the benefits of integrative, interdisciplinary approaches, by delving into a small set of topics from a variety of perspectives, rather than providing a survey-level introduction to a broader set of topic areas. Modules will involve a combination of lectures and student-led discussion groups, with students further expected to complete a multi-disciplinary integrative final review paper. Case-study topics will vary somewhat from year to year, but are likely to include some of the following: temporal coding as a mechanism for information processing, coordinate transformations in sensory-motor integration, mechanisms of cognitive control, motor control strategies including application to neural prosthetics, and memory systems in health and disease.

Credit 3 units.

Typical periods offered: Fall

BBS 5622 Cognitive, Computational, and Systems Neuroscience Project Building

The goal of this course is to help students in the CCSN Pathway develop the critical thinking skills necessary to develop and implement high quality, interdisciplinary research projects. Throughout the course of the semester, each student will develop a research plan in their chosen area of interest. The plan will be developed in consultation with at least two faculty members (from at least two different subdisciplines within the pathway) as well as the other students and faculty participating in the course. The culmination of this course will be for each student to produce an NIH-style grant proposal on the research project of their choosing. For most students, this will serve either as their thesis proposal or a solid precursor to the thesis proposal. The course will be designed to help facilitate the development of such a research plan through didactic work, class presentations, class discussion, and constructive feedback on written work. The course will begin with a review of written examples of outstanding research proposals, primarily in the form of grant submissions similar to those that the students are expected to develop (i.e., NRSA style proposals, R03 proposals). Review of these proposals will serve as a stimulus to promote discussion about the critical elements of good research proposals and designs in different areas. Each student will be expected to give three presentations throughout the semester that will provide opportunities to receive constructive feedback on the development and implementation of research aims. The first presentation (towards the beginning of the semester) will involve presentation of the student's general topic of interest and preliminary formulation of research questions. Feedback will emphasize ways to focus and develop the research hypotheses into well-formulated questions and experiments. The second presentation will involve a more detailed presentation of specific research questions (along the lines of NIH-style Specific Aims) and an initial outline of research methods. The final presentation will involve a fuller presentation of research questions and proposed methods. Feedback, didactic work, and group discussion throughout the semester will include guidance on critical components of the development of a research plan, including how to perform literature searches, formulate testable hypotheses, write critical literature summaries, and design experiments and analyses. The course will meet once a week, with faculty members from different tracks within the Pathway present at each meeting. This will allow students to receive feedback from several perspectives.

Credit 3 units.

Typical periods offered: Fall, Spring

BBS 5646 First-Year Fundamentals

This course will provide a two-part introduction to neuroscience research fundamentals. Namely, it will introduce elementary statistical analysis for neuroscience research as well as grant writing to support neuroscience-related research. Enrollment is limited to first-year neuroscience students.

Credit 0.5 units.

Typical periods offered: Spring

BBS 5648 Coding and Statistical Thinking in the Neurosciences

Students are introduced to scientific programming in Python. Students will learn common programming constructs and how to visualize and analyze data. Coding will be integrated into a statistics curriculum introducing summary statistics, probability distributions, simulation and hypothesis testing, and power analysis for experimental design.

Credit 3 units.

Typical periods offered: Fall, Spring

BBS 5651 Neural Systems

The course will consist of lectures and discussions of the sensory, motor and integrative systems of the brain and spinal cord, together with a weekly lab. The lectures will present aspects of most neural systems, and will be given by faculty members who have specific expertise on each topic. The discussions will include faculty led group discussions and papers presented and discussed by students. The labs will include human brain dissections, examination of histological slides, physiological recordings, behavioral methods, computational modeling, and functional neural imaging.

Credit 6 units.

Typical periods offered: Spring

BBS 5663 Neurobiology of Disease

This is an advanced graduate course on the pathology of nervous system disorders. This course is primarily intended to acquaint Neuroscience graduate students with a spectrum of neurological diseases, and to consider how advanced neuroscientific approaches may be applied to promoting recovery in the brain. Topics will be presented by Washington University faculty members and include: neurooncology, stroke, retinal disease, perinatal brain injury, neurodegenerative disorders, neuroinflammation, epilepsy, and psychiatric disorders. The class will meet for 2 hours each week. Each session will be led by a faculty guest with expertise in a specific neurological or psychiatric disease. In the first hour, the speaker will discuss clinical manifestations and pathophysiology. Where possible, the clinical presentation will be supplemented with a patient demonstration or videotape. After a 30 minute break for pizza and soda, the second hour will follow a journal club format. Two or three students will review current papers assigned by the speaker or course director. This course is offered in alternate years. Prerequisite: Introductory neuroscience course at the graduate or medical school level.

Credit 2 units.

Typical periods offered: Spring

BBS 5678 Clocksclub

Clocksclub focuses on recent advances in the study of biological timing including sleep and circadian rhythms. Participants discuss new publications and data on the molecules, cells and circuits underlying daily rhythms and their synchronization to the local environment. Students registered for this journal club will lead a discussion once during the semester.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5702 Current Approaches in Plant and Microbial Research

This course is designed to introduce graduate students and upper-division undergraduates to contemporary approaches and paradigms in plant and microbial biology. The course includes lectures, in-class discussions of primary literature and hands-on exploration of computational genomic and phylogenetic tools. Evaluations include short papers, quizzes, and oral presentations. Over the semester, each student works on conceptualizing and writing a short NIH-format research proposal. Particular emphasis is given to the articulation of specific aims and the design of experiments to test these aims, using the approaches taught in class. Students provide feedback to their classmates on their oral presentations and on their specific aims in a review panel.

Credit 4 units.

Typical periods offered: Spring

BBS 5703 Experimental Design and Analysis in Biological Research

In-depth exploration of landmark and current papers in genetics, molecular and cell biology, with an emphasis on prokaryotes and eukaryotic microbes. Class discussions will center on such key discoveries as the chemical nature of genetic material, the genetic code, oxygen producing light-spectrum, cell-cell signaling, transcriptional regulation, the random nature of mutation, and cell cycle regulation. Emphasis will be placed on what makes a good question or hypothesis, expedient ways to address scientific problems, and creative thinking. The last third of the course will consist of student-run seminars on selected topics to increase proficiency in the synthesis of new material and public presentation skills.

Credit 2 units.

Typical periods offered: Fall

BBS 5723 Seminar in Plant and Microbial Bioscience

This course emphasizing presentation skill and critical analysis counts towards the PMB Graduate Program's journal club course requirement. Students will be responsible for dividing and presenting 30 current research publications selected by the course masters. In addition to assembling brief PowerPoint presentations providing background and significance for their assigned articles, students are expected to provide classmates with a 1 page primer and short list of relevant references

Credit 2 units.

Typical periods offered: Fall, Spring

BBS 5801 Biochemistry & Molecular Biophysics Seminar Journal Club

This will be a journal club-based seminar course mirroring the topics covered by Biochemistry and Molecular Biophysics (BMB) seminar speakers during the concurrent semester. Students will present a paper published by one of the BMB seminar speakers one-week ahead of that speaker's seminar. This will allow students and faculty to become more familiar with the research programs of BMB invited speakers, likely stimulating discussion within the Q&A period after the seminar, as well as during informal meet-the-speaker lunch sessions. Students will be evaluated on their journal club presentation, attendance and class participation.

Credit 1 unit.

Typical periods offered: Spring

BBS 5840 Climate Change Reading Group

The Climate Change Reading Group is made up of multi-disciplinary faculty and students from multiple institutions in St Louis: WUSTL, UMSL, SLU, Missouri Botanical Garden, Danforth Center, and more. Many of us in different labs, departments, and institutions around STL are actively investigating aspects and effects of climate change; this reading group provides a venue for interacting with others in the community. Subject matter within the context of Climate Change will be chosen each week by a different presenter. Students can join this reading group for 1 credit if they agree to read all papers, actively participate in discussions, find and present one high quality scientific paper on climate change in the field of their choice and moderate the discussion of this paper. The students will be evaluated on their participation, their understanding of the issues, and their presentation.

Credit 1 unit.

Typical periods offered: Spring

BBS 5850 Seminar in Floristic Taxonomy

This weekly seminar provides an introduction to/overview of Plants, each semester progressively covering orders and families in a sequence derived from the Angiosperm Phylogeny Website (http://www.mobot.org/MOBOT/Research/APweb/welcome.html); in Spring 2015, the seminar will cover several crown orders of the monocots, including grasses and relatives. Weekly presentations include a summary of all relevant information (molecular, chemical, anatomical, embryological, morphological, ecological, geographical, historical/paleontological, etc.) about the plant group under consideration, review of the classification/phylogeny of the group, examination of fresh and/or preserved specimens, and discussion of relationships, human uses, and other relevant aspects of the biology of that group. Credit will be contingent on one (or two) seminar presentation(s) per student, regular attendance and active participation in group discussions.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5866 Communicating Science: Writing for Multiple Audiences

This course introduces strategies for writing effectively and communicating scientific research to a variety of audiences. Students will learn to reduce jargon, explain scientific concepts in common language, write clearly and concisely, and use sentence structure to maximum efficiency. Written assignments emphasize the significance and innovation in scientific research that appeal to broad audiences, including: the general public, students, policy makers, grant reviewers, and journal editors. This course meets biweekly and consists of lectures and small group sessions. You must enroll in both the lecture session (section 1) and a small group (section A, B, C, or D).

Credit 1 unit.

Typical periods offered: Spring

BBS 5867 Career Planning for Biological Scientists

This course will guide you through nationally recognized and evidence-based career exploration curricula. It is intended for DBBS Ph.D. students and bioscience postdocs who want to jump-start career planning and professional skills needed for a broad range of scientific careers. Topics include self-assessment, career exploration, and goal-setting for long-term success. You will work on a team to research the scientific career path of your choice. Each team will study the specific required knowledge, skills, and attributes of their career interest or employment sector. As part of this research project, you will complete a simulated job exercise and network with alumni or local leaders in your chosen field, gaining valuable real-world insights and creating essential professional connections.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5900 Research

Enrolled students will meet in-person with faculty for a minimum of 1 hour per week. Pass/No Pass Only.

Credit 12 units.

Typical periods offered: Fall, Spring, Summer

BBS 5902 Introduction to the Scholarship of Teaching and Learning

In this course, advanced graduate students and postdocs in STEM will 1) learn the fundamentals of the Scholarship of Teaching and Learning (SoTL)-which is the practice of developing, reflecting on, and evaluating teaching methods to improve student learning, 2) Develop a working knowledge of SoTL, which draws on research in education, STEM education, and cognitive science, 3) Understand how SoTL can lead to the dissemination of new knowledge to a broad audience of educators through publication and presentations., and 4) Develop the central elements of a SoTL project. These elements include articulating questions about classroom teaching that can be addressed in a SoTL research project; developing working hypotheses in response to the questions; designing an evaluative plan, including specific research methods, the type of data to be collected, and how the data will be analyzed in relation to the hypotheses; identifying and understanding necessary procedures to obtain IRB approval for the research.

Credit 1 unit.

Typical periods offered: Spring

BBS 5910 Nano Topics in Biology and Biomedical Sciences

This course will expose students to advanced topics, methods, and skills in biomedical sciences. The course will rapidly fill gaps in student knowledge in areas that are relevant to their research and or professional development. Each section of the course will be offered independently, sometimes in coordination with existing journal clubs and other seminars. Some sections will focus on technique; others will be theoretically or conceptually focused. Each section will be led by a faculty member drawn from DBBS in an area of their expertise. Objectives include deepening students knowledge and skill sets in critical thinking, experimental design, and technical prowess as related to the specific themes of each section.

Credit 0.5-1 units.

Typical periods offered: Fall, Spring

BBS 5911 Seminar in Biology & Biomedical Sciences

These seminars cover the recent literature in various areas not included in other courses, or in more depth than other courses. Credit to be arranged.

Credit 12 units.

Typical periods offered: Spring

BBS 5915 Teaching Practice in Biology & Biomedical Sciences

Students serve as teaching assistants for undergraduate and graduate level courses. Faculty-supervised activities include: lecture preparation and presentation; leading discussion and problem-solving sessions; laboratory instruction.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5922 Entering Mentoring

This course is a series of facilitated discussions aimed at developing and improving mentoring skills for those involved in supervising undergraduate research experiences. It is designed for postdocs and graduate students who are or will be 'bench mentors' for undergraduates doing Bio 500 and/or Summer Research. Participants will receive Entering Mentoring materials, including articles and worksheets to facilitate mentoring interactions with their mentee, plus several resource books relevant to mentoring. They will develop a mentoring philosophy statement, work on specific assignments designed to improve their relationship with their mentee and share their present and past experiences as mentors and mentees. Bench mentors will be eligible for a travel award to help defray expenses for attending a meeting with their mentee, if that student wins one of the HHMI SURF travel awards (4-5 awarded annually) or is otherwise being supported to present at a scientific meeting. Graduate students and postdocs do NOT need to be mentoring a student at the time of the course; it is open to all with an interest in mentoring now or in the future. Note: The sessions will be held either at the beginning of the day or the end of the day at the Danforth campus. Once registration closes, an email will be sent to those registered to poll for the best days & times.

Credit 1 unit.

Typical periods offered: Fall, Spring

BBS 5923 Foundations in Cancer Biology

This basic cancer biology class is designed to provide a didactic foundation into cancer biology principles. These will include tumor suppressors & oncogenes, DNA damage pathways, protein modifications, tumor progression, metastasis, tumor microenvironment and numerous other topics relevant to cancer biology.

Credit 3 units.

Typical periods offered: Fall

BBS 5928 Experimental Cancer Biology

This basic cancer biology class is meant to coincide with the Foundation course. Topics will be discussed in parallel with Foundation course topics but from the perspective of the laboratory experimentalist. Experimental details will provide the basis for understanding how to ask and answer important questions in the cancer biology laboratory.

Credit 3 units.

Typical periods offered: Fall

BBS 5940 Foundations in Cancer Biology and Experimental Cancer Biology

This advanced course will teach the clinical perspective of cancer biology using topics from oncology, radiation biology, radiology, pathology, immunology and surgery. Students will learn to write a grant proposal that includes a clinical trial element while also shadowing physicians in a real cancer clinical setting.

Credit 3 units.

Typical periods offered: Spring

BBS 5989 Advanced Topics in Neuroscience

This course will expose upper-level and postdoctoral students to advanced topics and methods in neuroscience. The course will rapidly fill gaps in student knowledge in areas that may be relevant to new directions in thesis work or interest areas. Each section of the course will be offered asynchronously, sometimes in coordination with existing journal clubs and other seminars. Each section will meet for two hours per week for three weeks. Sections may start with a didactic component or a review paper, but they will quickly delve into the discussion of primary papers curated by faculty and covering a focused topic. It is expected that papers will cover both historical and current contexts. Some sections will focus on technique; others will be conceptually focused. Each section will be led by a faculty member drawn from the Neuroscience program in an area of their expertise. Objectives include deepening critical thinking, statistical knowledge, experimental design, and technical prowess.

Credit 0.5-1 units.

Typical periods offered: Fall, Spring

BBS 5999 Independent Work

This course is designed for individual students wishing to explore indepth specialized areas of literature or technology with one or more faculty members. Credit will vary with the amount of work and discussion, but cannot be more than 3 credits.

Credit 3 units.

Typical periods offered: Fall, Spring

BBS 9000 Full-Time Graduate Research/Study

Full-Time Graduate Research/Study

Credit 0 units.

Typical periods offered: Fall, Spring, Summer

BBS 9001 Full-Time Graduate Study in Absentia

Full-Time Graduate Study in Absentia

Credit 0 units.

Typical periods offered: Fall, Spring, Summer

BBS 9002 Full-Time Graduate Study Extension

Full-Time Graduate Study Extension

Credit 0 units.

Typical periods offered: Fall, Spring, Summer