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.  

 

Ivan A. Anastassov: Assistant Professor of Biology The overall goal of our laboratory is to define the basic principles that guide the formation of vertebrate sensory circuits at the organismal, cellular, and molecular level. We study the visual system and use the retina of the cartilaginous fish skate as a model system. The skate retina is unique in the animal kingdom in having only one type of light-sensitive cell, which is called a rod photoreceptor and is classically thought to be responsible for mediating vision in dim light conditions. However, skate retinas appear capable of carrying visual functions that are normally mediated by light sensitive cells called cones, which are used for bright light vision and appear to be completely absent in the skate. We investigate the morphological and physiological mechanisms that allow the skate retina to adapt to widely varying light conditions and aim to understand what factors guide the assembly of this unique sensory circuit. Currently, the laboratory uses a variety of molecular, electrophysiological and imaging techniques like immunofluorescence, in situ hybridization, genetic material extraction, fluorescent dye injections, intracellular/extracellular recordings, patch-clamp electrophysiology, 3D-EM reconstruction, and cell morphology analysis to answer questions about the role of neuronal cell diversity in the development of the all-rod retina of the skate. REU students will have the opportunity to get familiar with data analysis, science communication and the wet lab techniques most relevant to their selected project.

 

Jason T. Cantley:Assistant Professor of Biology. Assistant Professor of Biology. The Cantley Lab studies plant evolution through a combination of molecular genetic/genomic techniques, phylogenetic systematics, population genetics, morphometrics, bioinformatics, and common greenhouse experiments. Broadly, a major theme of the lab is evolution and the factors that promote the generation of novel biodiversity (i.e. new species formation) and adaptation to different environments. This summer, REU students will be investigating various adaptations of Hawaiian 'aweoweo (Chenopodium oahuense) to harsh environmental conditions (ex. salt spray, limited water). Chenopodium oahuense exhibits striking leaf heteroblasty in some locations. For instance, populations on the sea cliffs of Moloka'i Island have juvenile leaves that are thin with have large surface areas, but adult leaves are much smaller and can become succulent, particularly when in the presence of oceanic salt spray. Our hypothesis is that the perceived adaptation of smaller succulent adult leaves could be a response for production of more physiologically efficient leaves as the dry Hawaiian summer season approaches and the plants transition from juveniles to adults. To detail significance of heteroblasty and test our above hypothesis, this summer project will involve managing plants in a greenhouse, taking physiological and morphological measurements, and analyzing data using a an R based analytical package. Additionally, the REU student will work with Dr. Cantley and a Masters student to learn plant DNA extraction and other relevant wet laboratory techniques. There will also be opportunities to for herbarium museum curation and digitization.

 

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 ChangMarine Ecologist, Smithsonian Environmental Research Center, Smithsonian Institution, and EOS Center. Our lab has been based at the Estuary & Ocean Science Center since 2000. 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 aka "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. 

 

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: Professor of Biology: In FishLab, we use molecular approaches to understand the evolutionary forces that generate biological diversity, novelty, reproductive strategies and reproductive isolation in fishes. Much of our work focuses on Hox genes-a family of genes that specify body plan features. We are interested in understanding the role of the posterior HoxA and HoxD genes in the evolution and development of appendages and adornments that contribute to morphological diversity in fishes. We have found that Hox genes structure a variety of fin modifications, such as claspers in cartilagenous fishes, cephalic lobes in manta rays and their relatives, barbels in paddlefish, and the cloaca/vent in jawed vertebrates. We are currently looking at the role of Hox genes in the development of derived features in the Catalina goby, surfperches and the evolution of male pregnancy in Syngnathids. We are also interested in the role duplicated Hox genes in paddlefish and teleosts, and the putative relationship between genome duplication and the evolution of complexity and diversity in vertebrates. While previous work has focused on questions varying in scale from paternity to genomics, including reproductive isolation, mechanisms of speciation, estimating phylogenetic relationships, and alternative life history strategies such as parental care, variation in courtship rituals, and sexual selection, the underlying theme is to understand the evolutionary processes that contribute to the evolution of novelty and diversity in fishes.

 

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.  

 

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 focuses 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 understanding mechanisms behind survival and mortality in zooplankton in the San Francisco Estuary and on building a genetic database of zooplankton to contribute to DNA metabarcoding studies of food web interactions. REU students will have opportunities to participate in fieldwork on research vessels in the San Francisco Estuary. REU students will gain experience in and learn a variety of techniques used to study foodweb ecology, starting with basic zooplankton identification. Students may choose a project that focuses on measuring recruitment rates and estimating mortality rates in field-collected zooplankton, or a project that focuses on applying molecular biological approaches (including DNA extraction, PCR, DNA sequencing) to understand genetic diversity of zooplankton taxa in the San Francisco Estuary.

 

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.

 

Evan Lau: Associate Professor, Menlo CollegeI am a microbiologist by training. My research interests include studying the ecology and evolution of microbes in natural environments. My current projects involve environments such as seastar tissues (these seastars are affected by wasting disease off the west coast, stretching from Alaska to California), soil and mudflats of San Francisco Bay (these microbes are affected by warming and sea level rise) and mouse trachea and lungs during Pseudomonas infection. My colleagues and I are using multiplex sequencing, together with computational phylogenetic and ecological analyses to study how microbiomes are affected by the environment, such as water chemistry or influence host disease. REU students will collect seastars off the Callifornia coast and soil and mudflat samples of south San Francisco Bay and extract DNA from them. They will also design and perform PCR to amplify the ribosomal and metabolic genes of the microbes and use multiplex sequencing, together with computational phylogenetic and ecological analyses to study the ecology of these microbes in nature. REU students will learn molecular techniques such as gel electroporation and band excision, DNA extraction and purification, light microscopy, polymerase chain reaction (PCR) and computational analyses. These experiments will provide students with a strong conceptual framework in ecological and evolutionary biology.

 

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). 

 

 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.   

 

Nicole Salazar VelmeshevAssistant Professor of Biology, We train undergrads and master’s students in cell and molecular biology techniques to understand the role of chemokine receptors in the tumor microenvironment. We study chemokine receptors in the context of breast cancer, brain cancer, and prostate cancer. These cancers result from a genetic process of cell population diversity and evolution, and its interaction with environmental stressors, that appear to follow the rules of Darwinian evolution. A primary goal of our REU project is for the student to understand the relationship of a relevant current environmental problem and cancer. Summer 2020 REU student projects are based on characterizing and understanding the effects of environmental microplastics on receptor levels in cancer cells during exposure, cell migration and proliferation. REU students will work with master’s students to learn skills in cell and molecular biology and science communication.