- About Us
UCSC offers numerous courses relevant to stem cell research. The UCSC Training Program in Systems Biology of Stem Cells has three required courses and a number of suggested electives.
Introduction to Stem Cell Biology and Ethics (BIOL 206; next offered Fall 2011, then every other year). Fundamental issues, experimental approaches, and emerging areas in stem cell research accompanied by an exploration of some of the attendant ethical issues. Includes lectures, seminars from experts, and discussion of primary literature.
Current Protocols in Stem Cell Biology (BIOL 206L; offered every spring). Hands-on experience in embryonic stem cell culture methods: students grow, passage, freeze, and differentiate mouse embryonic stem cells. Demonstrations include blastocyst harvesting, embryonic stem cell injection, and human embryonic stem cells. Students read stem cell literature with the idea of testing out new protocols.
Advanced Molecular Biology (BIOL 200B). Structure, function, and synthesis of DNA, RNA, and proteins. The roles of macromolecules in the regulation of information in the cell.
Advanced Cell Biology (BIOL 200C). In-depth coverage of topics in subcellular organization, structure, and function. Emphasizes current research problems and includes a section on stem cell biology. Recommended for students with primarily computational backgrounds.
Advanced Molecular Neuroscience (BIOL 226). Covers the basis of neural behavior at the cellular, molecular, and system levels.
Applied RNA Bioinformatics (BME 237). Covers approaches for the analysis of RNA sequences: introduction to RNA structure and genomics, RNA structure prediction, RNA homology searches, RNA genomics, regulatory or processed structures in RNAs, antisense RNAs, application of RNA-seq data, RNA-seq for gene discovery and RNA function prediction. Methods will be applied to problems and data sets from students’ current research. No programming background required.
Cellular Signaling Mechanisms (BIOL 208). How eukaryotic cells use intricate signaling pathways to control such diverse events as cell–cell communication, cell division, changes in cell morphology, and differentiation into diverse cell types.
Chromatin (BIOL 204). The organization of chromatin and how chromatin modifications and remodeling regulate gene expression. Chromatin-level regulation is critical for the differentiation of stem cells and the nuclear reprogramming that occurs when a differentiated nucleus is transferred into a stem cell.
Computational Genomics (BME 230). The application of statistical methods to biological sequences in the context of genome analysis and comparative genomics. Gene structure and regulation, gene finding, RNA secondary structure prediction, and prediction of gene function. Covers standard tools, fundamental algorithms, and advanced statistical methods such as hidden Markov models, graphical models, and support vector machines.
Computational Systems Biology (BME 211). Methods and applications of high-throughput biology, with examples of how high-throughput technologies can be applied to understanding stem cell biology. Topics include genome-wide approaches to studying biological systems such as DNA microarrays, protein and genetic interaction mapping, genome-wide knock-out strategies, and systematic perturbation analysis. How to use probabilistic graphical models to formally integrate and interpret multiple functional genomics data sets.
Critical Analysis of Scientific Literature (BIOL 200A). Provides students with the tools needed to become active, critical, contributing scientists, including dissecting, discussing, analyzing, presenting, and critiquing the work of others and understanding biases in their own work.
Epigenetics (BIOL 205). In-depth coverage of the field of epigenetics, with a focus on how alterations in chromatin structure and DNA methylation establish and maintain heritable states of gene expression. Molecular mechanisms underlying the regulation of stem cell pluripotency and differentiation.
Eukaryotic Molecular Biology (BIOL 115). Eukaryotic gene and genome organization; DNA, RNA, and protein synthesis; regulation of gene expression; chromosome structure and organization; and the application of recombinant DNA technology to the study of these topics. Recommended for students with primarily computational backgrounds.
Immunology (BIOL 111). Immune systems, their manifestations, and their mechanisms of action. Explores hematopoietic stem cells of the bone marrow, which give rise both to cells of the hematopoietic lineages and to non-hematopoietic cells. Topics include stem cell properties, influences on differentiation, and medical applications of genetically modified stem cells.
Programming for Biologists and Biochemists (BME 160/BIOL 160). Provides non-computational scientists with a basic set of skills using the Perl programming language for processing and analyzing results of high-throughput studies, useful in functional genomics approaches to a systematic understanding of stem cell biology.
RNA Processing (BIOL 201). Biological aspects of RNA function and processing in eukaryotes, including the role of microRNAs in regulating stem cell self-renewal and differentiation. Topics include RNA structure, localization, and modification, structure and function of ribozymes, spliceosomes and non-coding RNA, regulation of splicing, processing and function of microRNAs, and the role of RNA processing and regulation in gene expression pathways.
Stem Cell Biology (BME 178/ BIOL 178). Basic concepts, experimental approaches, and therapeutic potential. Students gain experience in reading the primary scientific literature.
Stochastic Modeling in Biology (AMS 205). Application of differential equations and probability and stochastic processes to problems in cell, organismal, and population biology. Topics include life history theory, ecology, and population biology.