UC Santa Cruz is a host institution for the San Jose State University Consortium for Stem Cell Internships in Laboratory-based Learning Program (SCILL), along with Stanford University, the Parkinson's Institute, and Escape Therapeutics. The program provides coursework towards a Master’s degree at San Jose State University in the Department of Biological Sciences (Master of Arts or Master of Biotechnology) and a 12-month, full-time internship in stem cell research in one of the four host institutions.
The SCILL Program is supported by a Bridges to Stem Cell Research Grant from The California Institute of Regenerative Medicine (CIRM).
Interns in the Bridges to Stem Cell Research program devote most of the internship year to laboratory research at the host institution, where they also take advantage of seminars and courses offered there (at UCSC, this includes programs offered by the CBSE Research Mentoring Institute). Internships at UC Santa Cruz focus on basic research in the systems biology of stem cells.
Each intern develops an individual research plan as part of a professional development plan. Plans are developed in concert with a mentorship team that includes an internship coordinator from SJSU, a research mentor from the host institution, and a faculty mentor from SJSU.
Camilla Forsberg laboratory: The Forsberg lab aims to understand the molecular mechanisms that determine the migration and location of hematopoietic stem cells (HSC). The HSCs are the long-term active ingredient in bone marrow transplantation therapy for a wide variety of disorders. To function properly upon intravenous infusion into the blood stream, HSC must travel to the bone marrow and engraft in specific sites. The long-term goal is to improve the efficiency and safety of hematopoietic transplantation therapies to treat blood disorders, cancer, and autoimmune disease.
Interns will investigate the role of known and novel molecules in HSC migration and location. Experimental approaches typically include in vitro and in vivo migration and adhesion assays, analysis and purification of bone marrow cells by multicolor flow cytometer, and transplantation assays.
David Haussler laboratory: The Haussler lab studies the origin and function of non-protein coding regions of the human genome during development. The lab focuses on analyzing the function of selected genomic elements in the development of the nervous system by using mouse and human embryonic stem cells (ESCs) to generate neurons in a petri dish. These assays recapitulate to a large extent the gene expression patterns and cell fate changes observed in the developing embryo. Experimental approaches include genome-wide analysis of RNA expression and epigenetic genome modifications at various stages during neuronal differentiation to identify candidate regulatory elements and gene targets for their regulation. To dissect the role of specific genomic regions, the lab uses reporter assays and gain- and loss-of-function analysis.
To date, all of the lab's human ESC neural differentiation assays have been done using H9, which was one of the original hESC lines derived by the Thompson lab at the University of Wisconsin. It has been reported in the literature that hESC lines differ in their differentiation capacity. For example, some lines produce predominantly forebrain type neurons, whereas others produce predominantly midbrain neurons using the same differentiation protocol. The lab now has a collection of older and more recently derived hESC lines that are male and female to use for comparative analysis.
Interns joining the Haussler group will help expand the analysis to additional human ESC lines. Interns will culture hESCs, perform neural differentiation assays, and characterize the cell types generated by isolating RNA for gene expression analysis and by examining cell-type-specific protein expression using immunofluorescence and fluorescence activated cell sorter (FACS) analysis. Where possible, FACS will be used to enrich for desired cell types for use in downstream functional analysis. These experiments will expand knowledge of the molecular events underlying neuronal differentiation and provide a basis for deriving specific neuronal cell populations for use in cell based therapies or as targets for pharmacological modulation. Interns will gain valuable hands-on experience in many of the techniques used to study and manipulate human embryonic stem cells.
Bill Sullivan laboratory: Maintaining division fidelity in stem cell populations is critical, because they serve as the founding populations for most the cells in the adult organism. To address mechanisms of stem cell division fidelity, the Sullivan lab has developed a system to efficiently generate double-strand DNA breaks in drosophila neuroblast stem cells. These breaks create acentric chromosome fragments (chromosomes without kinetochores/centromeres). By following acentric behavior in living neuroblasts as they progress through mitosis, the lab discovered that rather than remaining on the metaphase plate as expected, these acentric fragments efficiently segregate to the poles. The mechanism by which the acentrics segregate is equally unexpected and extraordinary: DNA-based tethers pull the fragments poleward so that they are included in daughter cells. Thus these tethers act much like tow ropes, ensuring that both daughter cells of the stem cell division contain a complete genome. Because stem cells are particularly critical to normal development and the health of adult organisms, they have a number of special properties that make them resistant to environmental insults. The Sullivan lab suspects that these DNA-based tethers are one such property unique to stem cells, making them highly resistant to the most devastating form of DNA damage: double strand breaks. They propose to test this idea by examining tether formation in other drosophila somatic and germline stem cells and in non-stem cell populations. In addition, they plan to determine whether tethers form in mammalian embryonic and adult stem cells. The results of these studies could explain why stem cells are particularly resistant to radiation and suggest alternative therapies for treating stem-cell-based cancers.
Interns will gain conceptual and practical experience in using model organisms to address outstanding issues in stem cell biology. They will be trained in a range of molecular and genetic techniques and in wide-field and confocal fluorescence microscopy. Interns will also participate and present their findings in weekly lab meetings and at journal clubs.
Amy Ralston laboratory: To develop effective stem cell-based therapies, it is essential to understand how stem cells are established and maintained in the body. The mouse embryo provides a powerful system for studying the origins and regulation of stem cells. Several types of stem cells can be derived from the early embryo, and these produce different tissue types upon differentiation. For example, pluripotent embryonic stem (ES) cells and multipotent trophoblast stem (TS) cells can both be derived from the mouse embryo at the blastocyst stage, and these form different tissue types during development. Identification of genes regulating embryonic versus trophoblast stem cell fates is a key goal of the Ralston Lab. Another approach to examining stem cell establishment is by reprogramming mature cells to induced pluripotent stem (iPS) cells. Understanding similarities and differences between ES cells and iPS cells is a fundamental yet underexplored issue in the field.
Interns will use bioinformatic, functional genomic, imaging, and gene expression analysis techniques to examine the role of new candidate genes in stem cell fate decisions. Candidate genes will be introduced into mouse ES, TS, and/or iPS cells and formation of mature tissue types assessed using a variety of techniques, including quantitative PCR, immunofluorescence staining, fluorescence microscopy, flow cytometry, and other assays established in the lab. Interns will receive exposure to the state-of-the-art UCSC Shared Stem Cell Facility and will be encouraged to participate in stem cell research seminars and journal clubs.
Joshua Stuart laboratory: In collaboration with the Forsberg and Haussler labs, the Stuart lab is constructing a compendium of gene expression data sets covering a diverse set of human and mouse stem cells. The database and web resource will incorporate several meta-analysis methods to help investigators identify significant sets of genes that are up-regulated in stem cells compared to differentiated cells across multiple experiments. The project has two parts: 1) application of machine-learning algorithms in the Stuart lab to identify candidate marker genes and 2) follow-up experimental validation of computational hypotheses in the Forsberg lab. The computational prediction component will take place during the first half of the internship. The student will apply or implement supervised algorithms for identifying gene modules, sub-networks of interacting genes, and curated structured genetic pathways that are consistently up- (or down-) regulated in stem cells compared to differentiated cells. To test whether these genes provide robust signatures of stem cells, the student will perform high-throughput cell sorting experiments using antibodies against several of the newly identified markers. The project will increase the repertoire of sorting markers to isolate pure cell populations and shed light on stem cell mechanisms.
Interns will participate in a team of graduate students and postdocs. They will learn how to use machine-learning methods in WEKA, including Support Vector Machines, Random Forest, and WINNOW. They will learn how to develop new code for displaying genome-wide data sets using Web 2.0 technologies with the UCSC Stem Cell Genome Browser. Interns will also work with an experimental stem cell lab to use UCSC's state-of-the-art cell sorting facility and learn basic cell culture techniques and various molecular biology skills to manipulate and prepare DNA, RNA, and antibodies.
Interns must have Bachelor's-level proficiency in computer programming and understanding of molecular biology. Experience with relational databases (e.g., MySQL) and web programming (e.g., Javascript and AJAX) is highly recommended, as is experience applying statistical hypothesis testing. Interns must be familiar with bioinformatics tools such as sequence alignment, calling local and remote BLAST servers and parsing hits, and mapping identifiers and aliases from proteins to genes to transcripts.