Biology Department photograph montage

REU Research Mentors


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.


Jason T. CantleyAssistant Professor of Biology. The Cantley Lab studies plant evolution through the holistic combination of molecular genetic/genomic techniques, phylogenetic systematics, population genetics, morphometrics, bioinformatics, and common greenhouse experiments. Broadly, a major theme of the lab  is biogeography and the evolutionary factors that promote the generation of novel biodiversity (i.e. new species formation). Current projects involve the whorled wattles (Acacia sect. Lycopodiifoliae) and spiny bush tomatoes (Solanumsect. Leptostemonum) from the Australian Monsoon Tropics, pilo (Coprosma spp.) from the Hawaiian Islands, and population genetics of the endangered Suisun thistle (Cirsium hydrophilumssp. hydrophilum) and its relatives from the California Floristic Province. REU students will gain experience working with live plants in a greenhouse setting, wet lab techniques to isolate then prepare DNA for genomic sequencing, bioinformatic skills for genomic data analyses, and gain skills on how to collect and analyze morphometric data for the process of describing new species.


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 Estuary & Ocean Science Center for the past eighteen 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 (1) filtration impacts of sessile invertebrates on water column productivity, (2) the environmental physiology of selected invertebrates in their success as invasive species, and (3) the role of major environmental events (marine heat waves akd "The Blob", and wet years and droughts) in controlling the assembly of communities.


Diana Chu: Professor of Biology: Life depends on transmitting genetic information encoded on DNA reliably from cell to cell and generation to generation.

Our diverse team of researchers investigates molecular mechanisms that package and transmit DNA during sperm formation that are needed for fertility and development. Because these processes are critical for fertility, they are highly conserved across species. We therefore use the tiny roundworm C. elegans  as a model organism to study sperm formation. One key process to making sperm or eggs is to replicate and divide up DNA in a process called meiosis. Our work shows that meiosis duing sperm formation is very different than oocyte formation. In particular chromosomes are segregated using distinct molecular players, like GSP-3 and GSP-4, which are sperm-specific proteins that are critical to sperm meiotic chromosome segregation. When these proteins are missing, sperm fail to complete meiosis. We are applying proteomic, biophysical, and cell biological methods to both how sperm chromosomes move during meiosis and how GSP-3 and GSP-4 function specifically in sperm chromosome segregation.

Our work has been published in Nature and PLos Genetics and is funded by the National Science Foundation and National Institutes of Health.


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 co-PI, Estuary and Ocean Science (EOS) Center. 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. 


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.  


Carmen Domingo: Professor of Biology and Interim Dean of COSE, P.I with Julio Ramirez, Domingo Lab Manager, Biology: 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.


Colleen Ingram, Director GTAC, Adjunct in Biology Department. My research spans evolutionary genetics of vertebrates from population genetics and phylogenetics and phylogenetics to genome evolution, particularyly the evolution of repetitive DNA and its impact on gene expression, behavior, and chromosomal evolution. Current projects includes the evolution and dynamics of social behavior in the naked mole-rat, Heterocephalus glaberBy combining demographic records and an accompanying tissue collection from wild colonies during an 18-year mark-recapture study, we are directly estimating the local metapopulation dynamics of H. glaber colonies, testing several hypotheses on the number and source of founders, patterns of mating over time, and the ecological and genetic correlations of colony growth and reproduction from an long-term mark-recapture study. All of these processes will allow us to test factors driving eusociality in this species. REU students will examine the impact of mating pair turnover events on colony genetics structure and relatedness over time. REU students will get the opportunity to learn basic molecular techniques (DNA extraction, gel electrophoresis, PCR, gragment analysis) as well as analysis used in population genetics.


Michelle Jungbluth, Adjunct Assistant Professor of Biology, Estuary and Ocean Science Center. In association with the Kimmerer Laboratory, my research is focused on aquatic food web ecology, population dynamics of zooplankton, and the application of molecular tools to study fine-scale interactions between planktonic organisms and their predators in aquatic ecosystems. Current research focuses on the prey important to larval and juvenile fishes in the San Francisco Estuary, particularly of the threatened and anadromous longfin smelt, Spirinchus thaleichthyes. Like many fishes in the Estuary, longfin smelt depend upon shallow low-salinity habitats in the Estuary for spawning and rearing their young, which in turn depend upon zooplankton food resources to recruit to adulthood. REU students will have opportunities for participating in field work on research vessels in the San Francisco Estuary, will gain experience in microscopic zooplankton identification, and apply molecular biological approaches including DNA extraction, PCR, DNA sequencing “barcodes” for species identification, and inter- and intraspecific phylogenetic analysis of sequenced taxa.


Jessica Audrey Lee, Adjunct Assistant Professor of Biology. I study microbial diversity and evolution. Specifically, I am interested in how individual bacterial cells sharing the same environment and the same genome can sometimes nonetheless behave differently from one another -- a phenomenon called phenotypic heterogeneity, or non-genetic diversity. In some cases, phenotypic heterogeneity may simply be due to noise, but in others, it can be a strategy that helps a mocrobial species survive in a variable environment. REU students working with me on this project would gain experience in a variety of methods for culturing microorganisms and monitoring their growth (in liquid culture, on plates, and in both aerobic and anaerobic conditions), genetic maniplation (introducing novel genes into our bacterial strains), and advanced techniques in monitoring the activity of microbial populations (for instance, fluorescence microscopy and flow cytometry). In addition, I also study the diversity of microbes in the natural environment, and carry out projects involving field sampling, next-generation sequencing, and bioinformatics to understand the ecology of environmental microbes.


Alejandro Velez Melendez: Assistant Professor of Biology, Research in our lab focuses on understanding the mechanisms, function and evolution of animal communication systems. Specifically, we seek to answer the following questions using frogs and songbirds as model systems: (1) How plastic are animal vocalizations and how do they evolve? (2) How are these vocalizations used to make behavioral adaptive decisions? (3) What are the physiological mechanisms that underlie auditory perception, and (4) How plastic are thses auditory mechanisms and how do they evolve? We integrate behavioral, ecological, physiological, and anatomical studies under a comparative framework to answer these questions. REU students will participate in projects in the field (recording animal vocalizations, conducting behavioral experiments, and collecting individuals) and in the laboratory (behavioral and neurophysiological assays of auditory processing). REU students will also gain experience in sound analysis, data analysis, and science communication.


Karina NielsenProfessor of Biology and Executive Director of the Estuary and Ocean Science (EOS) Center in collaboration with Chela Zabin, Adjunct Associate Professor of Biology and Smithsonian Environmental Research Center, Project title: Ecological restoration and nature-based climate adaptation in an urban estuary: are reckweeds part of the solution? Karina and Chela are both marine community ecologists based at the EOS Center. This summer we are colloborating on a research project that will help inform ecological restoration and climate adaptation planning(e.g, adapting to sea level rise) in urban estuaries. Intertidal macroalgae such as rockweeds, including Fucus distichus a local rockweed found in San Francisco Bay (SFB), are ecologically important, habitat-forming species. In SFB, F. distichus is already identified as habitat forming species that should be conserved, but it is not clear if or how it should be used in naturebased adaptation planning. Highly tolerant of heat and desiccation, F. distichus may promote the abundance and diversity of intertidal invertebratesby providing shade and moisture retention, especially in the mid to upper intertidal zone. This ecological function may become even more important as the climate warms. Based on observations at numberous sites in SFB, we hypothesize that the presence of F. distichus increases native invertebrate species diversity, and more specifically allows the native oyster, Ostrea lurida, to survive at highter tital elevations than it does when the rockweed is absent . This summer REU students will be able together work with us and our graduate students to 1) evaluate the potential for rockweeds to enhance the diversity of native invertebrates, 2) facilitate the survivorship and growth of native oysters and 3) assess ecological similarities and differences between rockweed habitats on human-built (rip-rap, seawalls) and natural (outcrops and cobble) rocky shores. Students will learn about the ecological restoration and climate adaptation planning and policies.


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.