UCSD Biomedical Sciences (BMS) Graduate Core Course
The primary goal of this course is to enable incoming students to transition from passive "fact-based" learning to an active, collaborative, and skeptical thinking and learning style necessary for success in graduate school and beyond. Through a series of eleven week-long modules taught by School of Medicine scientists and physicians, students will learn to identify important open questions, design experimental strategies, and evaluate results critically.
In most modules, students will immerse themselves in a different aspect of basic science and explore the links between research and human disease; in others, students will explore a few important experimental approaches that they may not have been exposed to during undergraduate classwork. During the course, students will expand their knowledge of some key questions facing current medical researchers, and will develop a framework for conceptual thinking to guide their own research projects.
For enrolled students: The BIOM 200 Course Web Site is at ted.ucsd.edu
(Log in with your UCSD ACMS (email) username and password)
Fall 2016 Class schedule
Module 1 (September 21-28) - Bioinformatics Bootcamp
Special times! September 21 (8:30A-12:30P), 22 (9A-1P),23 (9A-11A), 26 (9A-1P), 27 (9A-1P), 28 (9A-1P)
Taking command of the command line: A biologist’s guide to RNA-Seq. The goal of this module is to provide an interactive one week workshop to familiarize students with the command line and basic computational tools that are now commonly used in research. We will work through an example of calculating differential expression of an RNA-Seq dataset as a way to introduce concepts such as installation and workflow of new programs, reading documentation, and interpreting results. By the end of this week, students will have the necessary skills to continue to explore computational methods relevant to their own research.
Module 2 (September 29-october 4) - human Genetics
Regular class schedule resumes, 9 AM to 11 AM (M/T/Th/F)
Scientific emphasis: This module will cover modern concepts and directions in human genetics research including: patterns of inheritance, use of single-nucleotide polymorphisms as gene markers, individualized genomes and cancer genome re-sequencing. The module will also cover basic concepts and methodologies regarding the composition, function and regulation of eukaryotic genomes.
Concept emphasis: Critical reading and presentation of publications.
Module 3 (OCTOBER 6-11) - Microbes, Immunity, and the microbiome
Scientific emphasis: In this module, we will study the molecular and cellular basis of viral and bacterial pathogenesis, and the role of the microbiome in health and disease. Topics that will be discussed include virulence factors, exploitation of the host cell, host immunological responses and microbial counter-responses, microbial evasion of the innate and adaptive immune system, and finding the Achilles heel of microorganisms for therapy and prevention of disease.
Concept emphasis: Groups will be assigned a set of papers, and based on these will present a "plenary lecture" synthesizing the body of work and summarizing its importance and impact.
Module 4 (October 13-18) - Kinases and phosphatases in Cancer
Scientific emphasis: This module focuses on the role of phosphorylation in cancer signaling, focussing on protein and lipid kinases and phosphatases and how to study their disruption in cancer using live cell imaging and bioinformatics tools.
Concept emphasis: Groups will be expected to formulate a research plan in a given topic area, and write a short grant proposal which will be presented to the class.
Module 5 (October 20-25) - Proteins: sequence to structure to function
Scientific emphasis: This module will explore the relationships between protein sequence, structure, and function through the lens of structural biology, with an introduction to structure determination by x-ray crystallography and electron microscopy.
Concept emphasis: The module will include hands-on work with software tools for protein sequence alignment, protein structure prediction, and molecular visualization.
Module 6 (October 27-november 1) - Stem Cell Biology
Scientific emphasis: This module is designed for students to learn the fundamentals of stem cell biology and to gain familiarity with current research in the field. Topics will include: stem cell concepts, methodologies for stem cell research, embryonic stem cells, adult stem cells, cloning and stem cell reprogramming, organogenesis and disease modeling in a dish.
Concept emphasis: Student groups will choose a contemporary problem in stem cell biology, and prepare both a 1-page research proposal and 30-minute group presentation.
Module 7 (November 3-8) - Neurobiology
Scientific emphasis: Students will be introduced to molecular and cellular neuroscience research involving the development, function and dysfunction of the nervous system. Emphasis will be placed on techniques and approaches for modern neuroscience research.
Concept emphasis: An overview of select neuroscience topics by the instructor(s) will be followed by group discussion of pre-assigned scientific papers.
Module 8 (NOVEMBER 9-15) - Immunology
Scientific emphasis: This module will introduce students to the cellular and molecular components of the immune system, and will highlight its functional organization in the context of maintaining organismal integrity in the midst of intrinsic and extrinsic microbial threats.
Concept emphasis: Students will read cutting-edge pre-assigned research papers and then present critical discussions of the data contained and conclusions drawn.
Module 9 (november 17-18) - Microscopy mini-bootcamp
Scientific emphasis: This module will explore the theory and practice of light microscopy, and introduce students to both microscopy instrumentation and image processing.
Concept emphasis: The module will include hands-on work with microscopes and image processing programs.
Module 10 (November 21-29) - Trafficking and Glycosylation
Scientific emphasis: The Secretory Pathway for proteins and lipids predominantly originates in the endoplasmic reticulum and passes through the Golgi apparatus. Major functions of the pathway include the initial glycosylation and quality control of proteins, the further post-translational modification of glycoproteins and glycolipids, and the sorting and delivery of these molecules to various cellular destinations. The secretory pathway is also intimately linked with autophagy, an important cellular "recycling" system. Human genetic diseases affecting these pathways will be discussed.
Concept emphasis: This module will focus on synthesizing concepts in the fields of trafficking and glycosylation, identifying critical questions and experimental strategies to approach them, on an individual basis.
Module 11 (December 1-6) - G-protein signaling
Scientific emphasis: G-protein coupled receptors (GPCRs) are the largest family of signaling receptors in the mammalian genome and respond to diverse stimuli. Studies of GPCRs have delineated major paradigms by which signals from the extracellular milieu are transduced into intracellular responses. GPCRs are the most common drug targets and used clinically for the treatment of numerous diseases, including cardiovascular, psychiatric, pulmonary and immune disorders. This module examines GPCR regulation of the cardiovascular system using lectures, problem based learning and a laboratory session to illustrate GPCR ligand binding, activation, signaling to intracellular effectors and regulation in normal physiology and cardiovascular disease.
Concept emphasis: Groups will be expected to pitch a new therapeutic approach/strategy to venture capital investors, competing for startup funding for their new biotech company.