REU Research Mentors & Projects

Dr. Andrew Chang: Marine Ecologist, Smithsonian Environmental Research Center, Smithsonian Institution; Estuary and Ocean Science (EOS) Center lab. 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.

Dr. Jaime Chaves: Assistant Professor of Biology, SFSU Main Campus Lab. My lab studies how biodiversity is generated and maintained. In particular, we focus on understanding the link between molecules and phenotype. By combining molecular genetics and field biology, we explore evolutionary questions at the levels of populations (speciation-in-action), species (phylogeography and systematics), and apply these data to conservation efforts (conservation genetics). To this end, we use molecular techniques on an array of organisms, but birds are our favorite group given their incredible diversity and life forms. Most work takes place in the Galápagos Islands studying the iconic group of Darwin’s Finches where we look at the role of urbanization affecting beak evolution, gut microbiome assemblies, and behavior. We also are curious about the origin and evolutionary history of other endemic bird species such as the Galapagos Rail, the Lava Heron, and Galapagos Yellow warbler. To this end, we work in the lab extracting DNA and creating phylogenies to explore their evolutionary history.

Dr. Diana Chu: Professor of Biology, SFSU Main Campus Lab. 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.

Dr. Sarah Cohen: Professor of Biology PI, EOS Center and main campus.&nbspOur 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 invertebrate ascidians and estuarine fishes. We also work with seagrass disease ecology, sea star population differentiation, invasive species, and anemone/symbiont interactions in the field. REU students may learn skills in field and wet lab experimental design related to ecological and behavioral variation, intra and interspecific genetic analysis using sequencing or microsatellite markers, or microscopy and image processing. Projects are generally oriented around characterizing and understanding the relationship between environmental variation and developmental modes and patterns that relate to population connectivity. A special emphasis this summer may include collaboration with the California Academy of Sciences in characterizing native ascidian species in coastal Central California in comparison to historic collections.

Dr. Robyn Crook: Associate Professor of Biology, SFSU Main Campus Lab.  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.

Dr. Jenna Ekwealor: Assistant Professor of Biology, SFSU Main Campus Lab. The Moss Eco-Evo-Physio (MEEP) Lab investigates moss adaptations to the desiccating and irradiation conditions of life on land. Our research focuses on the moss genus Syntrichia, whose species are key primary producers in biological soil crusts (biocrusts), complex communities of bryophytes, lichens, and other microorganisms living on the soil surface of drylands. In mosses with separate sexes (unisexual species), male and female sex organs are controlled by a non-recombining sex chromosome pair; a unique chromosome in each sex. However, at least ⅓ of mosses instead are bisexual, producing both male and female sex organs on the same individual and to-date, the sex chromosome status in these species is inconclusive. The overarching goal of this project is to understand the genomics of reproductive biology in bisexual Syntrichia species. Our focal species for this project, S. princeps, is a bisexual species that occurs commonly throughout California, including on the San Francisco peninsula. In the MEEP Lab, interns will have opportunities to contribute to several stages of biological research through this project, including: field work, microscopy, tissue culture, DNA extraction, PCR amplification and enzyme digest, gel electrophoresis, DNA sequencing, bioinformatics, and statistical data analysis.

Dr. Derrick Groom: Assistant Professor of Biology, SFSU Main Campus Lab. The Groom Lab is broadly interested in understanding the biology of birds, and how birds are being impacted by environmental change. We combine field techniques and physiological tools to uncover the relationship between morphology, physiology, and the environment in determining an animal’s locomotor capabilities and daily energy requirements. By flexibly changing their activity and metabolism in response to varying environmental demands, animals may be able to cope with increasingly challenging conditions. We also explore how different temperature regimes influence the intricate relationship between water balance and dietary food habits. To these ends, we examine hummingbirds, a group of birds capable of sustained hovering flight and possessing some of the most extreme metabolic rates among vertebrates. REU students in our lab will learn skills in animal physiology, bird handling techniques, data analysis, and experimental design. REU projects will be focused on exploring the interrelationship between environmental variation and metabolic performance.

Dr. Colleen Ingram: Director GTAC, Adjunct Assistant Professor in Biology, SFSU main campus. My research spans evolutionary genetics of vertebrates from population genetics and phylogenetics to genome evolution, particularly 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 glaber,  By 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 a long-term mark-recapture study. REU students will get the opportunity to learn basic molecular techniques (DNA extraction, gel electrophoresis, PCR, fragment analysis) as well as data analysis used in population genetics.
 

Dr. Jaime Jahncke / Meredith Elliott: Adjunct Professor of Biology, EOS and Point Blue. Our lab examines the marine food web to assess ocean health. We focus on marine predator diet studies and zooplankton studies. We investigate the diets of avian piscivores and California sea lions and an avian zooplanktivore by examining regurgitations, feces, or dropped prey; parts from fish (e.g., otoliths, scales), cephalopods (e.g., beaks), and zooplankton (e.g., telsons, carapaces) are identified and, in some cases, measured and weighed. We identify zooplankton found in samples collected in the Greater Farallones and Cordell Bank National Marine Sanctuaries; samples are analyzed for taxa of interest (euphausiids, decapods, mysids, fish). REU interns will build lab skills, understand foraging strategies of marine predators, and learn about common marine forage species in the Central California Current.

Dr. Michelle Jungbluth: Adjunct Assistant Professor of Biology, Estuary and Ocean Science (EOS) Center lab. 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 and larval fishes 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.

Dr. Candace Low: Researcher and Lecturer in Biology, SFSU Main campus.. The focus of my research is understanding how evolutionary mechanisms can drive on ecological dynamics. For the past 20 years, I have studied how the decisions that animals make, the fitness consequences of their decisions, and how trade-offs can impact the distribution of individuals across both space and time. In a nutshell, how do the rules for the evolution of behavioral strategies shape the dynamics of what we observe on ecological time and space? My work is integrative in both method and theory, combining field experimentation and observations, molecular ecology, systematics, mathematical modeling, and basic ethology – never forgetting the natural history of the study system. I am a naturalist-at-heart, and my areas of expertise are experimental design and statistics, plant-herbivore-enemy systems, and the economics of interactions (game theory and evolution). REU students will record behavioral data from videos of insect larvae in the field, create spatial coordinate maps of individuals on leaves, and help to test whether signaling between individuals is associated with their spatial positioning on a leaf. Alongside this, the relatedness of individuals will be overlaid onto the data to determine whether larvae might be communicating with their kin. REU students will gain experience in animal behavior, statistics, and hypothesis testing.

Dr. Pleuni Pennings: Associate Professor of Biology, SFSU Main campus.. Our 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 and transmission of drug resistance in bacteria. As an REU student you will have the opportunity to study drug-resistance in E coli or M. tuberculosis or another pathogen. You will learn to write computer code or use bioinformatics programs to analyze sequence data (in the language R). No prior coding or research experience needed

Dr. Jonathon Stillman Professor of Biology, SFSU Main Campus Lab.  The core focus of our lab is to understand the physiological mechanisms of how coastal marine organisms respond to environmental changes including temperature, pH and microplastics.  Our projects take place in the field and laboratory, and we use a wide range of methods, from molecular and biochemical analyses to organismal physiology, morphology and behavior.   Current research foci are on understanding the degree to which transgenerational plasticity influences how thermal stress experienced by parents shift the response to temperature in their offspring.  REU research projects will provide training in live animal work, microscopy, respirometry and possibly other approaches.  REU students will develop skills in the use of image analysis software and the use of software for scientific graphics and statistical analyses involved with large data sets.  These experiences will provide REU trainees with skills that can help to build their professional portfolio for whatever future path they choose to follow.

Dr. Andrea Swei: Associate Professor of Biology, SFSU Main Campus Lab. 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 collect and analyze field and molecular data to understand the transmission dynamics and risk of tick-borne diseases in the San Francisco Bay Are