Biology Department photograph montage

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.   

 

Mark Chan: Assistant Professor of BiologyMy lab studies how organelle size is sensed and controlled by the cell by using the budding yeast vacuole as a model system. The vacuole is a highly dynamic organelle which shows a size scaling relationship with the cell, i.e. larger cells have larger vacuoles. I am interested in how the cell maintains the vacuole at the appropriate size, and how this control impacts function. Questions addressed in the lab include: Does the cell sense the size of the vacuole? Can a cell with too large or small of a vacuole tune various pathways (e.g. membrane trafficking and inheritance) to get the vacuole back to the right size? Can we engineer the structure of organelles to tailor cell function, fitness, pathogenicity, or biochemical yields? To answer these questions, we apply a number of techniques including live fluorescence microscopy; genetic, cell, and molecular biology; digital image analysis; and computational modeling.

 

Andrew Chang: Marine Ecologist, Smithsonian Environmental Research Center, Smithsonian Institution, and RTCOur lab has been based at the Romberg Tiburon Center for the past seventeen years. We study the population biology and community ecology of marine invertebrates along the Pacific coast, focusing on biological invasions of bays and estuaries by non-native species. In a broad sense, we investigate geographic patterns of diversity and invasions, and how they change over time. We have studied the effects of freshwater flow on community assembly, invasion patterns, and native oyster population dynamics. We examine the factors controlling the abundance, diversity and function of species and communities using a combination of field surveys and manipulative field and lab experiments. 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 and communities. Recent and upcoming REU projects will include filtration impacts of sessile invertebrates on water column productivity and the role of the environmental physiology of selected invertebrates in their success as invasive species.

 

Joseph Chen: Associate 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, in particular their effects on species that form Harmful Algal Blooms (HABs). We are investigating how multiple environmental factors such as ocean acidity (pH), temperature, light, and nutrients affect the physiology of phytoplankton and bacteria. We use unialgal cultures and field studies ranging from polar to equatorial waters. We are currently studying a number of highly toxic phytoplankton species, and investigating how these affect cellular growth and promote the production of neurotoxins, especially domoic acid produced by the pennate diatom Pseudo-nitzschia.  These biotoxins have detrimental impacts on mammals, marine ecosystems and commercial fisheries 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 biotoxin analyses.

 

Sarah Cohen: 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.

 

Robyn Crook: Assistant Professor of Biology: The long-term goal of our lab is to define mechanisms of behavioral and neural plasticity in cephalopod molluscs. We focus on understanding the plasticity of nociceptive (damage-sensing) neurons and how it is mediated at the molecular level, and in turn, how this cellular plasticity mediates changes in neural circuits, behaviors and ultimately, the fitness of individual animals coping with injury or other noxious experiences. REU research projects will provide training in assays of learned and innate behavior, extra-cellular electrophysiology, and pharmacology of neural plasticity. Our lab emphasizes best practices in data analysis, statistical methods and communication of science. REU students will also learn husbandry techniques for maintaining cephalopods in captivity. These skills and techniques will provide a strong conceptual and practical framework in marine biology, animal behavior and cellular neuroscience.

 

Karen Crow-Sanchez: Associate 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. 

 

José R. de la Torre: Associate Professor of Biology: Our lab studies the physiology, ecology and evolutionary history of microorganisms living in terrestrial hydrothermal systems (hot springs). In particular, we aim to understand the role that a group of recently discovered microorganisms, the ammonia-oxidizing archaea (AOA), play in Carbon and Nitrogen geochemical cycles. We have isolated over 25 strains of thermophilic AOA from hot springs around the world, which has allowed us to probe the genomic, physiological and ecological diversity of these organisms. REU students will participate in fieldwork (collection and characterization of environmental samples), and will learn molecular and biochemical approaches (nucleic acid extraction, PCR, cloning, sequencing, in situ hybridization) for studying these organisms. Students will also be able to learn and apply bioinformatic and genomic approaches to examine the evolutionary history and genomic diversity of these thermophilic AOA.

 

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 miRNAs 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.

 

Megumi Fuse: Associate Professor of Biology: Our lab investigates mechanisms of cell signaling during tissue damage and repair (including regeneration) in the model organism Manduca sexta. We are examining the mechanisms whereby regenerating imaginal discs signal the endocrine system to delay development (compensatory mechanism to synchronize development between damaged and intact tissues). We are particularly interested in the possible roles of insulin-like peptides and inflammatory signals that may target developmental hormones PTTH and ecdysteroids. We are also determining the mechanisms by which hypersentivity is induced in M. sexta after general insults such as bird predation (e.g. mechanical damage), environmental changes (e.g. thermal damage), and parasitization by the parasitoid wasp Cotesia congregata.  The roles of peptides, amines and second messengers are under investigation. This research has biomedical and agricultural significance, and provides insights into the evolutionary path of nociceptive signaling mechanisms within and between species. REU students will study these problems using bioassays, cellular,  molecular and electophysiological approaches.

 

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. 

 

Tomoko Komada: Associate Professor of Chemical Oceanography:  Our long-term research goal is to better understand the cycling of carbon in marine and coastal environments.  We are particularly interested in understanding the processes that transform non-living organic matter in the coastal ocean and the land-ocean margin, and evaluating their significance in the oceanic and global carbon cycles.  As a means of gaining insight into the dynamics of organic matter in the environment, a significant part of our research focuses on determining the abundances of natural isotopes of carbon (13C and 14C) in key carbon pools.  We are currently working on an NSF-funded project whose goal is to elucidate the nature and reactivity of dissolved organic carbon that accumulates in sediment pore waters.  Natural 13C and 14C isotopes are used in this project to trace the degradation pathways of organic matter.  Students will gain hands-on experience in carbon- and isotope-clean techniques, instrumental analyses (elemental analyzer, high-temperature combustion TOC/TDN analyzer, UV/VIS), and vacuum-line techniques.  Students will also gain a basic understanding of the significance of marine sediments in the oceanic and global carbon cycles over geologic time.

 

Pleuni Pennings: Assistant Professor of BiologyOur lab, named the CoDE Lab, works on understanding the evolution of pathogens. This is an important topic because when pathogens like viruses and bacteria evolve they often become drug resistant or they are no longer recognized by our immune system. We mostly work on the evolution of drug resistance in HIV. As an REU student you will have the opportunity to study the effect of the viral population size and pre-existing drug-resistance mutations on the rate of drug resistance. You will learn to write computer code to analyze sequence data (in the language R) and to do computer simulations (in the languages C++ and python). 

 

Blake Riggs: Associate 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.

 

 Rori Rohlfs: Assistant Professor of Biology. Our lab is broadly interested in how genetic variation contributes to diversity in populations and how that diversity is leveraged in adaptation.  Current research in the lab focuses on three topics.  First, we study the evolution of gene expression.  We created a statistical model for expression evolution which we applied to discover genes with evidence of expression level adaptation or plasticity (expression response to environmental factors) in primates.  Second, we quantify the accuracy of forensic genetic identification methods.  We have estimated the power and false positive rate of familial searching methods and investigated the empirical accuracy of population genetic models.  Third, in an emerging branch of lab research, we study the effect of classroom interventions meant to mitigate stereotype threat.  REU students will choose from a variety of projects, applying computational tools for evolutionary or forensic population genetic analyses, using R to analyze preliminary results of such analyses, or using R to analyze classroom intervention data. 

 

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.

 

Kevin Simonin: Assistant Professor of Biology. Research in the Simonin lab embraces the idea that understanding plant interactions with the environment will allow us to better understand ecosystem function and ecosystem response to climate change.  Increasing our understanding of plant physiological controls over carbon, water and nutrient transport between soils, plants and the atmosphere are of critical importance for understanding how natural and human reconfigured ecosystems respond to a changing climate.  A general theme in my research is the use of biophysical models to describe the coordination between plant water loss and carbon gain in order to assess the impact of atmospheric CO2 concentrations, temperature, water and nutrient availability, on plant productivity and ecosystem hydrology. REU students will participate in fieldworks or greenhouse studies and will learn to use infra red gas analyzers for measuring leaf level carbon gain and water use.  Students will also gain experience using stable isotope approaches for assessing variation in plant water use strategies and carbon gain.   

 

Jonathon Stillman: Professor of Biology, RTC: Our lab studies how organisms have adapted to different environments and how they may respond to future changes in their environments. Using cDNA microarrays we have discovered a number of genes that have dramatically different expression profiles in crabs that were acclimated to different thermal conditions in the laboratory. These genes (e.g., hsp40, sensor histidine kinase, extensin), can be used as molecular temperature data loggers as their expression is tied to the crabs’ immediate thermal history. In this project we will use the expression of these genes to examine shifts in organismal responses to finer gradients of habitat temperature. We will use laboratory and field-based sampling of crabs acclimated /acclimatized to slightly different temperatures and profile the expression of these genes using qPCR. If time permits, we will perform similar experiments in congeneric porcelain crab species that are adapted to different thermal microhabitats (e.g., intertidal zone vs. subtidal). The successful REU applicant will work in the field collecting specimens and temperature data, will perform laboratory acclimation, and will sample and process tissues for RNA-qPCR analyses.

 

Andrea Swei: Assistant Professor of Biology: Vector-borne disease systems are inherently complex and community-driven due to the numerous species and trophic levels involved in their maintenance and transmission. Research in the Swei Lab employ interdisciplinary approaches to understand the factors that determine the distribution and prevalence of Lyme disease and other tick-borne diseases. Work on Lyme disease includes ecological studies that examine the role of disturbance, habitat fragmentation, and biodiversity on Lyme disease ecology. REU students will have the opportunity to characterize the tick microbiome, that community of microbes residing in a tick, and how it interacts with the transmission of pathogens. In addition, projects are also focused on studying the ecology and epidemiology of emerging tick-borne pathogens. 

 

Vance Vredenburg: Associate Professor of Biology: Our lab is focused on understanding the causes and impacts of emerging infectious disease on threatened amphibians. The disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis, is specific to amphibians and is associated with more species extinctions than any other disease in recorded history. The lab investigates the dynamics of the disease on individuals and populations from a suite of different species using molecular as well as population and field ecology techniques. Recent work has shown that while most infected individuals die within 3 weeks of infection, some are able to survive. To determine how this occurs, REU students will take part in lab and field data collection and analysis. Students will learn to utilize a real-time PCR assay to detect the presence and infection load on individual amphibian hosts. This project will give students an introduction to lab techniques, experience with animal handling and population estimates, and an understanding of some of the conservation challenges scientists are facing.

 

Andy Zink: Associate 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 will have opportunities to study the importance of bacteria and offspring cannibalism in the maternal care behaviors of maritime earwigs.