REU Research Mentors
SFSU BREED REU
Mentors and Possible REU Research Projects
Students in our REU program will have the opportunity to work with the following REU mentors. A list of these mentors and possible research projects are described below.
Laura Burrus: Professor of Biology: The long-term goal of our lab is to define the mechanisms that regulate the distribution and activity of Wnt signaling proteins in tissues. One of the best-described vertebrate Wnt gradients is in the chick neural tube, where dorsally expressed Wnt1 and Wnt3a form a dorsal to ventral gradient that controls proliferation and specification of cells. Work in C. elegans and Drosophila has identified Porcupine and Wntless as important regulators of Wnt distribution. To determine whether the roles of these proteins are conserved in vertebrates, REU students will knock down Porcupine and Wntless expression in the chick neural tube and measure the effect on the Wnt gradient. They will also design and perform studies in cell culture to elucidate the roles of these proteins in vertebrates. REU students will learn techniques of molecular biology, shRNA design, in ovo electroporation, cryosectioning, immunohistochemistry, in situ hybridizations, confocal microscopy, reporter assays and cell culture. These experiments will provide students with a strong conceptual framework in developmental and evolutionary biology.
Edward J. Carpenter: Professor of Biology, Romberg Tiburon Center for Environmental Studies (RTC). Our lab is examining how a widespread and abundant marine phytoplankton species responds to ocean acidification. Seawater is decreasing in pH as a result of increased CO2 concentrations from fossil fuel burning. The species we are studying, a coccolithophore, Emiliania huxleyi, produces calcium carbonate plates on its exterior, and as pH decreases, the calcium carbonate will dissolve. Together with the Stillman and Komoda labs at RTC, we will culture E. huxleyi at present day pH and that which is predicted for the end of the century, and we will examine gene expression, after many generations, as a means of determining if and how this organism adapts to decreased ocean pH. The student will learn cell culturing and counting techniques, microscopy, dissolved organic carbon and dissolved nutrient measurements and quantification of gene expression.
Joseph Chen: Assistant Professor of Biology: My lab investigates the roles of conserved proteins in the development of Sinorhizobium meliloti, a bacterium that forms symbiosis with legume plants. We examine bacterial strains with specific mutations to determine if there are measurable physiological defects, such as reduced motility or increased sensitivity to environmental stress, and if such defects disrupt the bacterium’s interaction with the host plant. The long-term goal is to unveil the multifaceted mechanisms that allow S. meliloti to invade plant roots and induce formation of nodules, where they reside and fix nitrogen in exchange for carbon compounds from the plant. Understanding such mechanisms provides insight into how microbes establish successful infections. REU students will learn about molecular cloning and bacterial genetics as well as gain experiences in culturing bacteria and plants, performing enzymatic assays, and conducting phenotypic tests.
Diana Chu: Associate Professor of Biology: Our lab investigates the role of evolutionarily conserved factors in male fertility using the model organism C. elegans. We have identified highly conserved phosphatase proteins that function in both sperm meiosis and motility called GSP-3 and GSP-4. Deletion of the gsp-3 and gsp-4 genes in C. elegans causes male infertility with defects similar to those exhibited in mice deleted for the homologous gene, PP1g. The lab has found that gsp-3 and gsp-4 deletion mutants exhibit defects in sperm activation similar to the PP1g knock-out in mice. Thus, although C. elegans sperm are morphologically distinct from mammalian sperm, they use conserved proteins to regulate sperm motility. REU students will study this mechanism using cytology, biochemistry, and genetic analysis of wild-type and mutant sperm. These studies will provide an in depth analysis of how basic developmental processes utilize conserved molecular components even in morphologically divergent cells.
William Cochlan: Research Professor of Biology, Senior Research Scientist, RTC: Our lab is focused on elucidating the abiotic factors that regulate marine phytoplankton growth in the ocean. We are investigating how multiple interactions such as light and nutrients, affect the physiology of phytoplankton and bacteria. We use unialgal cultures and field studies ranging from polar to equatorial waters. We have been studying the toxic microalgae that form Harmful Algal Blooms (HABs), and the factors that sustain their growth and promote the production of neurotoxins, especially domoic acid which has a detrimental impact on mammals and marine ecosystems on the west coast of North America and, increasingly, world-wide. REU students will gain experience in experimental design in phytoplankton ecophysiology (both field and laboratory based), manual and automated nutrient analytical methodologies, phytoplankton culturing techniques, epifluorescence and phase-contrast microscopy, and toxin analyses.
Sarah Cohen: Associate Professor of Biology, Director Core Genetics Facility, RTC, Co-PI: Our lab is interested in how ecological, behavioral, and environmental features shape evolution and genetic systems in diverse organisms. We work in marine and estuarine settings. Our results address questions about coastal and marine conservation and the role of anthropogenic effects on natural populations. Our lab is particularly interested in the ecology and evolution of recognition systems and has been investigating this in colonial invertebrates and estuarine fishes. REU students will learn skills in field and wet lab experimental design related to ecological variation, intra and interspecific genomic analysis using sequencing and microsatellite markers, and behavioral analysis using microscopy and image processing. Projects will be based on characterizing and understanding the relationship between environmental variation and developmental modes and patterns.
Edward F. Connor: Professor of Biology: My research focuses on understanding the processes that affect the structure of ecological communities and the population dynamics of their constituent species. My experimental field and laboratory research employs insect communities and insect-host plant systems as test systems to answer basic questions about the population dynamics of plant-eating insects and the structure of insect communities. Our lab is interested in trying to determine the role of bacterial symbiosis in the induction of plant tumors (galls) by insects. We hypothesize that bacteria supply tumor-inducing insects with phytohormones essential to tumorigenesis. REU students will have the opportunity to learn genetic and microbial approaches to detect genes in phytohormone pathways and symbiotic bacteria. REU students will also learn hierarchical models of the abundance of the component species in meta-communities to estimate correlations among species and make inferences about community structure.
Karen Crow-Sanchez: Assistant Professor of Biology: In “FishLab” we are interested in the evolution of novelty and diversity. Fishes are the most diverse vertebrate group, and as such, exhibit an amazing variety of body plan features and specialized modifications. We are particularly interested in a family of genes, called Hox genes, that specify body plan features. These genes were duplicated in a subgroup of fishes called teleosts, and it has been widely speculated that their success, in terms of diversity and novelty, is associated with genome duplication. For example, the duplicated HoxA13 genes are associated with development of a novel feature, found only in zebrafish and their relatives, called the yolk sac extension. We are also interested in the evolution of alternative reproductive strategies in fishes such as bidirectional sex change in gobies, and multiple embryos per egg capsule in skates. REU students will have opportunities to sample fishes, including some sharks and/or skate embryos, and should be comfortable in, and around, water. In addition, the REU student project will include some aspects of molecular biology including PCR, sequencing, and gene expression studies.
Wilfred Denetclaw: Associate Professor of Biology: Our lab investigates the development of the skeletal muscles in somites of chicken embryos. Somites are transient embryonic structures that are produced in a series along the anterior-posterior axis of the embryo and are differentially signaled by morphogens that antagonize or promote muscle development along the axis. Our lab has shown that nitric oxide (NO), a ubiquitous, short-lived messenger gas molecule, is dynamically elevated in the ectoderm and signals the dermomyotome. Inhibitors of NO production block myotome formation in somites. We propose to test the NO signaling relationship between the ectoderm and somite for myotome formation in close and distant vertebrate species like quail and frog embryos, respectively. We will determine whether NO signaling regulates early muscle development among vertebrates. REU students will learn confocal microscopy, microinjection, calcium and NO imaging, microsurgery, and in situ hybridization to assess protein or gene expression levels. This work will introduce REU students to embryology, myogenesis, and NO molecular signaling in development.
Carmen Domingo: Professor and Associate Chair of Biology, P.I: We are interested in understanding the process by which embryological cells give rise to specific cell types using the vertebrate model, Xenopus laevis. Recently our lab has been studying the role of microRNAs, small, non-coding sequences of RNA that regulate genes post-transcriptionally by binding specific messenger RNAs (mRNA) and blocking their translation. miRNAs have been shown to play a major role in the transcriptional regulation of cells during embryogenesis and in diseases. We are interested in understanding the role of these molecules during cell differentiation. REU students will examine whether knock down of specific miRNAs affect cell differentiation in Xenopus. REU students will learn microinjection, microdissection, fluorescence microscopy, and live time-lapse imaging. This project will give REU students an introduction to developmental processes in the context of understanding the role of microRNAs in development.
Toby Garfield: Professor of Geosciences and Director of RTC: Our research focus is on the ocean circulation over the continental shelf and slope. This is the region where the presence of the continental land mass imposes boundary conditions on the ocean flow and the resulting circulation is often complex. For the last five years our research group has concentrated on installing an array of land-based instruments capable of measuring the surface currents in San Francisco Bay and the Gulf of the Farallones (http://www.norcalcurrents.org). The instruments are radio-wave transmitters and receivers that determine the ocean surface currents by determining the Doppler shift of broadcast signals that are reflected back to the antennas by ocean surface waves. In addition, our lab is developing long-term data sets of in situ environmental ocean data. Students would be involved with standard operations and maintenance of the instruments as well as defined data analysis projects.
Wim Kimmerer: Research Professor of Biology, RTC: We have conducted studies in the San Francisco estuary on effects of freshwater and tidal flow on habitat, abundance, and movement of plankton and fish; the influence of introduced species; and population dynamics, reproduction, growth, and mortality of foodweb organisms. We use field and laboratory methods, modern statistical methods, and simulation modeling to examine how factors such as food supply, water movement, predators, and species introductions affect the distribution and abundance of planktonic species and their suitability as food for fish. Our lab is particularly interested in how the interactions among individual organisms results in observable outcomes at the ecosystem level, and interpreting changes in the foodweb that result from introductions to this heavily invaded estuary. REU students will gain skills in conducting fieldwork, designing and conducting experiments, culturing various organisms, and analysis and presentation of results.
Leticia Márquez-Magaña: Health Equity Institute Professor of Biology. Our lab studies cancer disparities. One of the areas of investigation is focused on gaining a better understanding of breast cancers in minority women as a function of human evolution. Pioneering transdisciplinary work that couples human evolutionary and health science research finds that certain health outcomes are more related to genetic ancestry than to other prognostic factors. We are interested in determining if triple-negative breast cancers are linked to African ancestry given their preponderance in African American and Latina women. Therefore, REU students interested in this line of investigation will engage in activities to determine the ancestral lineage of women with triple-negative breast cancers who have donated relevant biospecimens. This work may lead to the development of molecular diagnostic tools for triple-negative breast cancers that are currently not available due to the limited knowledge about these type of deadly cancers.
Robert Ramirez: Professor of Biology. Our research is focused on cellular responses to osmotic stress in yeast. When stressed by high salinity, yeast make glycerophosphocholine (GPC). GPC is generated by the deacylation of the membrane lipid phosphatidylcholine (PC). Deacylation (i.e., hydrolysis of the fatty acid "tails") is catalyzed by the enzyme Nte1 (neuropathy targeted esterase 1). Nte1 is an evolutionarily conserved enzyme that is also found in all eukaryotes (both invertebrate and vertabrate). In mammals for example, NTE catalyzes the production of GPC that is found in renal cells that are challenged by osmotic stress during urine production. In addition, studies in mammals and fruit flies have shown that NTE plays a role in embryogenesis and neural function. We are currently investigating the means by which Nte1 activity is regulated posttranslationally in yeast. REU students would participate in a project in which we use site-directed mutagenesis to make "custom" mutations. We will then examine the effects of these mutations on the cell viability and physiology.
Blake Riggs: Assistant Professor of Biology. Our lab examines the dramatic reorganization of cellular components that occurs during cell division. Entry into mitosis sees a rearrangement of cellular articheture, most notably condensation of the genetic material (chromosomes) and reorganization of the microtubule and actin cytoskeleton. Less understood is the reorganization of the intracellular membrane organelles including regulation of these changes by cell cycle regulatory factors. We are investigating the relationship between the reorganization of the endoplasmic reticulum (ER) and the mitotic cyclin dependent kinases (Cdks) that occur during mitosis. Mitotic cyclin:Cdk kinase complexes are master regulators of nuclear and cytoskeletal dynamics during cell division however their involvement in mitotic ER reorganization is unknown. The goal of this project is to define the regulation of ER reorganization during mitosis by cyclin:Cdk. This process will be studied in the model organism the fly, Drosophila melanogaster. REU students will learn basic flywork and genetic analysis, as well as realtime fluorescence analysis. This project will give REU students an introduction to basic cell biology and the processes of mitosis and cell division, which are well conserved across animal phyla.
Scott Roy: Assistant Professor of Biology. Our lab uses comparative genomics and transcriptomics to study the evolution of gene and genome structure. In particular, we are interested in the evolution and function of splicing in eukaryotic nuclear genes, wherein protein-coding sequences are divided into multiple pieces (called exons) which are separated by non-expressed regions (called introns): before RNAs are translated into proteins, introns must be removed and the exons ligated together by a complex cellular machine called the spliceosome. This mysterious intron-exon organization shows a wide range of variation across different species, from 200,000 introns averaging 2000 nts in humans to a single known intron in the parasite Trypanosoma. Moreover, intron-exon structures are used for a variety of functions in different species, from gene regulation to production of multiple products from the same gene by alternative splicing. To study why there are introns in genomes, and how introns are created, we are studying intron loss and gain in several novel model species. To understand how complex splicing networks evolve, we are studying the splicing networks regulated by various splicing factors in different species. To understand the diversity of splicing, we are studying a variety of intriguing variations on intron-exon structures. REU students in our lab will learn basic bioinformatics and sequence analysis to understand how splicing networks evolved.
Gregory Ruiz: Marine Ecologist, Smithsonian Environmental Research Center, Smithsonian Institution, and RTC: Our lab is interested in the population biology and community ecology of coastal marine organisms. Our research program has focused on biological invasions of bays and estuaries by non-native species, especially marine invertebrates. We examine the patterns of invasion (in space and time) and their effects on resident populations and communities. Our laboratory conducts field-based sampling and manipulative experiments, testing hypotheses about mechanisms that underlie the diversity, abundance, and function of marine communities. Our approach includes analyses of life-history, larval recruitment, physiological performance, genetic and morphological variation, as well as interspecific interactions (e.g., predation, parasitism). Our lab consists of approximately 30 staff, postdocs, and students, including a component based at Romberg Tiburon Center for the past nine years. REU students working with us will design and implement field-based research that will apply a variety of methods to understand the structure and dynamics of marine invertebrate populations.
Anne Todgham: Assistant Professor of Biology: Our lab is interested in understanding the molecular, biochemical and physiological mechanisms that underlie an animal’s capacity to cope with environmental change. In particular, we investigate how an animal's physiology and environment interact to structure organismal stress tolerance by studying the diversity of physiological specializations (or strategies) used by marine animals (limpets, urchins and intertidal fishes) distributed along the California coast as well as the coasts of New Zealand and Antarctica to tolerate fluctuations in environmental conditions. Presently our research focuses on determining whether contemporary marine animals have the physiological flexibility necessary to buffer the unprecedented rates of global climate change, specifically ocean warming and ocean acidification. REU students in my lab will study a range of life history stages, from larvae to adults, to better understand which developmental stages might be most vulnerable to future ocean conditions. REU students have the potential to learn a wide range of field collection and laboratory techniques, including molecular, biochemical, physiological, and organismal approaches in ecological and environmental physiology.
Andy Zink: Assistant Professor of Biology: Our lab investigates the evolution of social behavior with a specific focus on the evolution of parental care and communal breeding. Many animals decrease the costs of parental care by raising their offspring with other parents in a communal group. However, individual parents within these groups often experience large asymmetries in the number of offspring that they produce and the amount of care that they provide. Our work attempts to understand how these asymmetries can be maintained within social groups and how group members act to resolve these conflicts over reproduction and parental care. We are currently working on communally nesting salamanders in the genus Batrachoseps, using field and laboratory studies, in order to explore the relationships between social behavior and fungal pathogens. REU students would learn techniques of sampling field and museum salamander specimens, extracting salamander and fungal DNA, running quantitative PCR for fungal loads, and maintaining fungal or bacterial cultures.
