1. Bi 1.The Biology and Biophysics of Viruses
9 units (4-0-5); third term. This course introduces non-biologists to recent advances in our understanding of how HIV and other viruses infect and cause damage to their hosts. Because understanding and treating HIV infection involves a basic knowledge of cell and molecular biology, virology, and immunology, the course will cover fundamental concepts in these areas from a quantitative, molecular, chemical and biophysical perspective. Instructors:
2. Bi 114, Immunology
12 units (4-0-8); second term. Prerequisites: Bi 8, Bi 9, Bi 122 or equivalent, and Bi/Ch 110 recommended. The course will cover the molecular and cellular mechanisms that mediate recognition and response in the mammalian immune system. Topics include cellular and humoral immunity, the structural basis of immune recognition, antigen presentation and processing, developmental regulation of gene rearrangement, biochemistry of lymphocyte activation, lymphokines and the regulation of cellular responses, T and B cell development, and mechanisms of tolerance. Instructors: Mazmanian, Rothenberg and Bjorkman.
3. Bi/BE/BMB 115. Viruses and Applications to Biological Systems
9 units (3-2-4); third term. Learn about viruses as fascinating biological machines, focusing on naturally-occurring and evolved variants, in silico viral vector engineering, and computational methods that include structure visualization and machine learning. This course will introduce the fundamentals in the chemistry and biology of viruses, emphasizing their engineerable properties for use in basic research and translational applications. Topics include: viruses by the numbers, mammalian and non-mammalian (plant, bacteria) viruses, enveloped vs. non-enveloped viruses, host-virus interactions, viral life cycles (replication vs. dormancy), immune responses to viruses, zoonosis, diverse mechanisms of entry and replication, the application of viruses as gene-delivery vehicles (with a focus on adeno-associated viruses or AAVs, lentiviruses, and rabies), and how to engineer viral properties for applications in basic research and gene therapy. The lectures will be complemented by short lab exercises in AAV preparation, bioinformatics and machine learning, and structure visualization. Instructors: Bjorkman, Gradinaru, Van Valen, Bjorkman. Given in alternate years; offered 2019–20.
4. Bch/Bi/Ch 170, Principles of Protein Structure
9 units (3-3-3); first term. Prerequisite: Bi/Ch 110. The forces determining the folding of proteins into their unique tertiary structures. Protein structures will be classified by organization of the structural elements and structural motifs, and their influence on function will be explored. Topics will include enzyme and antibody structure and function, virus structures, protein–nucleic acid interactions, methods of macromolecular structure determination, and protein structure analysis. A computer graphics system will be used for the display and analysis of macromolecular structure. Instructors: Clemons, Rees.