PER Project Descriptions
DIRECTIONS: Read the list of mentors and brief research descriptions in the table below. To see a more detailed description of a mentor's project click on their name or scroll past the table. Each of the detailed project descriptions are named after the associated mentor, for example, "FRANKLIN". To complete the PER application, you will need to identify up 3-4 mentors that have project(s) that interest you. If a mentor has more than one project please indicate which specific project(s) interest you. For example: Franklin 1 & 3, Banneker 2, Jemison 1, Molina 1 & 2. It is also suggested that you look up the labs of each of the mentors to gain more information about their research.
Please identify up to four mentors that have project(s) that interest you. If a mentor has more than one project please indicate which specific project(s) interest you. For example: Franklin 1 & 3, Banneker 2, Jemison 1, Molina 1 & 2
**DO NOT CONTACT THESE MENTORS DIRECTLY ABOUT THE PROGRAM**
Brief Research Description
|Irina Conboy||Irina Conboy||Bioengineering||Stem cell engineering, Boosting Regneration of Aging Tissues|
|Chun Yang||David Schaffer||Bioengineering||Tissue engineering, Neurobiology|
|Jacquelyn M Blake-Hedges and Mitchell Thompson||Jay Keasling||Bioengineering||Biochemistry|
|Robert Full||Robert Full||Integrative Biology||Animal Locomotion|
|Eileen Lacey||Eileen Lacey||Integrative Biology||Behavioral Ecology and Evolutionary Biology|
|Michaela Huffman||Leslea Hlusko||Integrative Biology||Dentistry, Quantitative Genetics, Anthropology, Biology|
|Kimberly La Pierre||Ellen Simms||Integrative Biology||Mutualism Ecology|
|Cathy Rushworth||Noah Whiteman||Integrative Biology||Evolutionary Genetics|
|Kirsten Verster||Noah Whiteman||Integrative Biology||Animal behavior, Genomics|
|Austin Peck||George Brooks & Daniela Kaufer||Integrative Biology||Neurobiology and Metabolism|
|Paul Fine||Paul Fine||Integrative Biology||Botany, Ecology and Population genetics|
|Jay Goodman||Elcin Unal||Molecular and Cell Biology||Yeast Biology, Organismal Aging|
|Polina Kosillo||Helen Bateup||Molecular and Cell Biology||Neurobiology|
|Jared Bard||Andreas Martin||Molecular and Cell Biology||Biochemistry|
|David Weisblat||David Weisblat||Molecular and Cell Biology||Evolution, Embryo Development, Bioinformatics|
|Christopher Emerling||Michael Nachman||Museum of Vertebrate Zoology||Evolutionary Genomics|
|Erica Rosenblum||Erica Rosenblum||Envionmental Science, Policy and Management||Ecology, Evolution, Genetics, Genomics, Global Change Biology|
|Xingeng Wang||Kent Daane||Envionmental Science, Policy and Management||Entomology|
|Sarick Matzen||Céline Pallud||Envionmental Science, Policy and Management||Soil remediation|
|Eoin Brodie||Eoin Brodie||Envionmental Science, Policy and Management||Microbial Biology|
|Patrick O'Grady||Patrick O'Grady||Envionmental Science, Policy and Management||Biodiversity and Evolutionary Biology|
|Ian Wang||Ian Wang||Envionmental Science, Policy and Management||Ecology & Evolution|
|Stephanie Carlson||Stephanie Carlson||Envionmental Science, Policy and Management||Fish Ecology and Conservation|
|Elke Eichelmann||Dennis Baldocchi||Envionmental Science, Policy and Management||Environmental Sciences|
|Alex McInturff||Justin Brashares||Envionmental Science, Policy and Management||Wildlife Ecology and Conservation|
|Marta Vuckovic||Joseph Napoli||Nutritional Sciences & Toxicology||Metabolic Biology|
|Vineetha Zacharia||Matthew Traxler||Plant and Microbial Biology||Microbiology|
|Cat Adams||Tom Bruns||Plant and Microbial Biology||Microbial Biology|
|Benjamin Blackman||Benjamin Blackman||Plant and Microbial Biology||Plant Evolutionary Biology|
|Clarice de Azevedo Souza||Shauna Somerville||Plant and Microbial Biology||Plant Biology|
|Michi Taga||Michi Taga||Plant and Microbial Biology||Microbiology and Chemical Biology|
Detailed Research Descriptions
CONBOY-1: Understanding and reversing molecular changes in stem cell environments that have been caused by tissue aging and pathology.
CONBOY-2: Novel CRISPR approaches to treat genetic diseases; Orthogonal labeling of mammalian proteomes in vivo; Reversing tissue senescence.
YANG: We will engineer and harness synthetic multivalent ligands to understand the functional role of receptor clustering in neural stem cell function and differentiation, work that will advance our fundamental knowledge of cellular signaling mechanisms, particularly on the effect of Eph receptor clustering in neurogenesis. It will also enhance our capacity to control stem cell differentiation for regenerative medicine applications, thus contributing to public health by providing powerful therapeutics for the treatment of degenerative diseases, such as Alzheimer’s and Parkinson’s.
BLAKE-HEDGES/THOMPSON: Sigma factors are essential for the initiation of transcription in all known bacteria. These small proteins enable RNA polymerase (RNAP) to recognize a specific promoter and initiate transcription by “melting” the DNA at the transcriptional start site and allowing RNAP access to the coding strand. Recent work has shown that subfamilies of sigma factors recognize promoters with surprising specificity, making them attractive candidates as reliable parts for the building of synthetic genetic circuits. Further research has shown that some sigma factors also contain putative autoregulatory domains which would allow the sigma factor’s RNAP recruitment ability to be turned on and off in the presence of a specific environmental signal.
We are very interested in understanding the biochemistry behind the role these sigma factor autoregulatory domains play, as well as discovering the environmental signals they may recognize. These discoveries are hampered by the fact that these proteins are often found in bacteria that lack sophisticated systems for genetic manipulation. To overcome this difficulty, we are a looking for a motivated student to help us develop an in vitro method to rapidly identify the promoters that these sigma factors bind.
The student involved in the project would work at the Joint BioEnergyInstitute (www.jbei.org) located in Emeryville which can be reached by a free shuttle from campus.
FULL: Animals differ in leg number, posture, and motion. Why? Students will capture and measure the structure of animal legs using a new photographic technique termed photogrammetry, now even available on cell phones. Students will capture the motion of animals running on tracks and treadmills using high-speed video cameras. Data will be used to inspire the next generation of search-and-rescue robots.
LACEY-1: Maternal effects in captive tuco-tucos An increasing body of evidence indicates that in mammals, the early maternal environment can have profound effects on an individual’s eventual behavior, stress physiology, and neuroendocrinology. As part of an ongoing project to explore the effects of the early maternal environment on individual colonial tuco-tucos, the student researcher will characterize the behavioral phenotypes of juveniles at specified time points. This will involve videotaping juveniles during open arena trials and then coding the behaviors captured in videotapes.The project will be supervised by Professor Eileen Lacey and Doctoral Student Shannon O’Brien.
LACEY-2: Genetic determination of sex in pocket gophers Some species of mammals are highly sexually dimorphic, making it easy to visually distinguish between males and females, even among neonates. For other mammals, however, determining the sex of individuals is more challenging and requires PCR-based analyses of X and Y chromosome markers. Pocket gophers are common rodents in the western US, including on the Berkeley campus. As part of an ongoing study of sex ratio variation in a population of pocket gophers from southern CA, the student researcher will extract DNA from tissues samples and then use PCR analyses to determine the sex of individuals in the study population. Analyses will be conducted in the Museum of Vertebrate Zoology’s Evolutionary Genetics Laboratory. The project will be supervised by Professor Eileen Lacey and Doctoral Student Dana Lin.
LACEY-3: Comparative morphology of social and solitary tuco-tucos The structure of the mammalian skull provides considerable information about the environmental conditions experienced by a species. Among subterranean rodents like tuco-tucos, multiple aspects of the skull reflect the challenges that these animals face when using their teeth to dig new burrows. As part of efforts to test the hypothesis that hard (i.e., difficult to excavate) soil conditions favor group living in subterranean rodents, the student researcher will photograph the skulls of tuco-tuco specimens housed in the Museum of Vertebrate Zoology. Using morphometric equipment housed in the MVZ, the student will then compare multiple elements of skull structure in a solitary and a social species of tuco-tuco from Argentina. The project will be supervised by Professor Eileen Lacey and Research Associate Risa Takanaka.
HUFFMAN: Are you interested in conducting research on human teeth? Professor Leslea Hlusko in the Department of Integrative Biology is conducting a multidisciplinary research program to collect data on skeletal human remains at the University of California’s Phoebe A. Hearst Museum of Anthropology. Our research combines information and approaches from dentistry, quantitative genetics, anthropology, and biology to understand the oral health of Native Californians over the past 5,000 years. We are assessing how differences in oral health may or may not relate to cultural practices, environment, and/or the size and shape of teeth.
We are looking for undergraduate research assistants to dedicate 4+ hours per week to the project. Students will be involved in protocol development, data collection, literature reviews, analyses, and/or manuscript preparation depending on your interests and experience. No prior research experience is required, just a keen interest in learning how to conduct research.
LA PIERRE-1: Microbes drive vital processes in all ecosystems, yet are often overlooked. Invading plants can fundamentally alter plant-microbial feedback loops that stabilize native ecosystems; so microbial community dynamics must be considered when choosing management methods. Invasive legumes exhibit particularly strong plant-microbial feedbacks. Legumes benefit from symbiotic relationships with nitrogen-fixing bacteria called rhizobia, which colonize nodules in legume roots. Drs. Kim La Pierre and Ellen Simms are working on a project that addresses three important ecological questions: (1) how does invasion by three leguminous plant species (French broom, Spanish broom, and Scotch broom) affect soil rhizobial community structure in Marin County parks and open space; (2) how do three common management techniques (hand–pulling, prescribed burning, and herbicide) affect the soil rhizobial community; and (3) does the state of the soil rhizobial community influence the success of native and/or invasive legumes in these landscapes?
LA PIERRE-2:Ecological theory predicts that niche and relative fitness differences among plant species underlie variation in the biodiversity-productivity relationship. However, the mechanisms underlying this variation among plant species are rarely experimentally quantified, leaving causal connections between plant variation and the biodiversity-productivity relationship elusive. Plants in the legume family are infected by beneficial soil bacteria called rhizobia, which fix atmospheric nitrogen (N) in exchange for carbon (C) from their plant hosts. As most plants obtain N from the soil, access to atmospheric N via this mutualism can differentiate legumes from non-legumes, thus influencing the productivity-diversity relationship. Increased atmospheric carbon dioxide (CO2) and soil N will likely influence the effect legume species have on the productivity-diversity relationship by altering the legume-rhizobia mutualism. We are experimentally examining the biotic processes that differentiate three legume species from each other and from non-legumes to understand how these differences cause variation in patterns of primary productivity.
RUSHWORTH-1: What traits underlie the spread of invasive species? Drosophila suzukii is a new invasive fruit fly that lays its eggs in ripe or ripening fruits, costing nearly $400 million each year to California farmers. The structure it uses to lay its eggs (the ovipositor) can pierce the skin of many different types of fruits. These fruits vary in skin thickness; thick-skinned fruits such as cherry offer a harsher environment than thin-skinned fruits such as raspberry. Using a combination of microscopy and host choice tests, we will identify ("phenotype") the ovipositor traits that have enabled its successful invasion, and that enable it to survive in both harsh and permissive fruit environments. We will measure multiple ovipositor traits in fly colonies from cherry and raspberry orchards and identify traits that differ between colonies. Choice tests will subject female flies to cherry and raspberry fruits to see which they prefer.
RUSHWORTH-2: What genes underlie phenotypic variation in an invasive species? A major question in evolutionary biology is what maintains variation in organisms. Drosophila suzukii is a new invasive fruit fly that lays its eggs in ripe or ripening fruits, costing nearly $400 million each year to California farmers. The structure it uses to lay eggs (the ovipositor) has a toothed edge, which the fly uses to pierce the skin of many types of fruits. Another drosophilid species with a similar ovipositor displays substantial variation in tooth number; previous research has shown that four regions of the genome underlie this variation. We will use nextgen sequencing to identify regions of the genome underlying variation in ovipositor traits in D. suzukii, and assess allele frequencies in natural populations from two different fruit environments (cherry and raspberry). Work will involve phenotyping ovipositors, DNA extraction and library building, and potentially some basic bioinformatics.
RUSHWORTH-3: How do hybridization and reproductive shifts change plant chemical defenses? One of the main ways in which plants defend themselves is producing defensive chemicals such as capsaicin, which makes hot peppers spicy. Previous work has shown that hybridization and reproductive mode (inbreeding vs. outcrossing or asexual reproduction) can alter the defensive chemistry of many different plants, which might make them more or less appealing to insects. In the wildflower Boechera, hybridization co-occurs with asexual reproduction. We will use asexual lineages collected from the field as well as recently-made hybrids to ask: what happens to defensive chemistry in hybrid Boechera? And how does this compare to the defensive chemistry of asexual hybrids? Work will include basic molecular biology (DNA/RNA extraction, library building, potentially basic bioinformatics) and greenhouse experiments, so you must be comfortable working in dirty and wet conditions. This is a long-term project, lasting one year or longer.
VERSTER:Lining genotype to phenotype in a leafmining fly. I am using the species Scaptomyza flava, which develops inside leaves, to investigate genes associated with behavior. Two different populations of this fly species have different leafming behaviors, possibly in response to attack to parasitoid wasps. This semester I will be doing one of the following: 1) phenotyping mined leaves, 2) conducting selection experiments using wasps and flies, 3) using genetic techniques to identify loci associated with this behavioral variation.
PECK-1:Neurological insults, such as Traumatic Brain Injury (TBI), have varied primary and secondary effects on neural health. Utilizing rodent and tissue culture models, we investigate the impact of opening the Blood Brain Barrier (BBB) on mitochondrial function of astrocytes. Rat and mouse models allow us to study the effects of primary and secondary BBB disruption after either severe or repeated mild TBI in vivo. Tissue culture studies will allow us to directly study the metabolic response of astrocytes upon exposure to serum albumin, which has been shown to cause excitatory synaptogensis and increased risk of epileptogenesis.
PECK-2: Wearable technology has allowed the 'quantified self movement' to provide meaningful physiological information to the users. Sweat is emerging as one of the next possible targets for obtaining useful information regarding the wearer's physiological state - especially for athletes and patients with certain diseases. In collaboration with a lab in EECS we will be validating a sensor platform that measures sweat analytes in real time for potential applications in tracking hydration status during exercise. This project involves running exercise test protocols using cycle ergometry on human subjects.
FINE: Our project integrates the fields of botany, ecology and population genetics to study the evolution of a lineage of extremely common trees in the Neotropics (Protium heptaphyllum, Burseraceae). We are conducting an innovative approach to understanding how this widespread tree species has thrived over a wide range of environmental and climatic conditions, and how habitat heterogeneity might promote the divergence of tropical plant lineages. Our results will generate new insights into the origin and maintenance of tree species diversity in the Neotropics. Students will learn multidisciplinary tasks including using bioinformatics to measure morphological and ecological traits, working with methods for DNA extraction in the lab and learning statistical and computational skills.
GOODMAN: Characterizing proteins associated with aged-induced aggregation:
In budding yeast, replicative aging arises as mother cells lose their propensity to make new daughter cells. In parallel, mother cells that have produced multiple daughter cells overtime obtain protein aggregate deposits in the cytosol. Evidence has shown that these aggregates are never inherited in daughter cells as aged mother cells continue to bud. However, the composition and biological function of these aggregates remains poorly understood. Classifying the individual components of these aggregates would help us determine how they contribute to replicative aging. With the guidance of a graduate student, we would like to have an undergraduate student who is interested in identifying proteins that are part of these aged-induced aggregates through in vivo proximity labeling and quantitative proteomics, while learning basic techniques in molecular genetics and protein biochemistry.
KOSILLO: Research in the Bateup lab seeks to understand how deregulation of mTOR signaling impacts brain development and function, especially in the context of neurodevelopmental disorders. The specific research project we are seeking an undergraduate assistant for aims to determine how deletion of the autism risk gene and mTOR regulator Tsc1 from mice affects the anatomical and functional characteristics of dopamine neurons. The work involved will be directly supervised by a post-doctoral research fellow. The skill set for this project will include sectioning of fixed mouse brain tissue using a freezing microtome, immunohistochemical processing of mouse brain sections, mounting and preparation of processed brain tissue for microscopy, and imaging and quantification of the morphological properties of single dopamine neurons and their axon terminals.
BARD: Investigate the mechanisms by which the large macromolecular machine, the proteasome, unfolds and degrades substrate proteins. We use in vitro biochemical techniques to purify and reconstitute the proteasome, and then perform assays to assess various aspects of its motor function. We incorporate unnatural amino acids into specific locations in the proteasome, which can then be labeled with a fluorophore. This allows us to then perform both bulk and single molecule FRET based assays to monitor the conformational state of the proteasome as it degrades it's substrates. For the proposed project, the student will extend these techniques to monitor ATP binding to the motor.
Weisblat: Work in the Weisblab lab is broadly focused on the biology of glossiphoniid leeches, (genus Helobdella) for purposes of understanding evolutionary processes operating across diverse kinds of animals. Leeches are of particular interest becuase they represent a large, but relatively understudied super-phylum of animals, the super-phylum Lophotrochozoa. We are mainly interested in investigating embryonic development at the cell and molecular level; this work involves tools of genomics, bioinformatics, molecular biology and experimental embryology. Other projects include the development of behavioral assays that can be used to compare wild-type animals with those in which specific nervous system mutations have been induced by "genome editing", and comparing the developmental and behavioral differences between closely related species. The specific project in which students might be involved will be determined by their interests, experience and time availability.
EMERLING: As mammals have adapted to various dietary niches (e.g., carnivory, herbivory, ant-eating, frugivory), we expect that their complements of digestive enzymes have evolved in association with such dietary specializations. This might happen in various ways: 1) the duplication of genes encoding enzymes to allow for greater digestive efficiency (e.g., more enzymes for protein breakdown in carnivores), 2) the loss of genes that no longer provide benefits for a particular diet, and 3) adaptive changes in the available enzyme complement as reflected in protein sequence evolution. Despite being an aspect of biological evolution that in many ways is expected, scientists have hardly explored this area of research. As such, this research has the potential to yield important insights into how mammals have adapted to variegated diets over time, and is almost certainly guaranteed to lead to one or more scientific publications.
ROSENBLUM-1: The overarching goal of this project is to investigate whether differences in genomic divergence are correlated with environmental parameters across the geographic range of a spatially-expanding mammal species, the nine-banded armadillo (Dasypus novemcinctus). D. novemcinctus evolved in South America but has been expanding its range northward for millions of years. Today, the most-recently colonized populations occur in the northeastern U.S., which may represent the species' thermal limit. Using genetic data generated from next-generation sequencing (NGS), the first aim of this project involves inferring the timing and sequence of the species' expansion in the Americas. We are seeking an enthusiastic undergraduate student to assist with this aim. The student will have the opportunity to learn basic molecular biology techniques as well as an introduction to computational and statistical methods in the fields of phylogenetics and phylogeography while helping to answer questions related to the aim. Students who are interested in evolutionary biology, particularly in how invasive species cope with novel environmental conditions, are encouraged to apply. This project will be mentored by a postdoctoral researcher, Lucy Tran.
ROSENBLUM-2: The Rosenblum Lab studies the processes that generate and impact biological diversity. One of our core projects focuses on understanding how quickly organisms can adapt to changing environments. In the Chihuahuan Desert of New Mexico, a number of species have rapidly evolved striking variation in coloration associated with the geologically recent formations of White Sands. Blanched color morphs of lizards, mice, and invertebrates are found on the white gypsum dunes and brown color morphs in the surrounding desert. We use this system to address important questions about rapid adaptation and speciation. Undergraduate researchers on this project are involved in laboratory work using molecular genetics to understand the genes involved in adaptation to White Sands and stable isotope analysis to understand desert food webs.
ROSENBLUM-3:The Rosenblum Lab studies the processes that generate and impact biological diversity. One of our core projects focuses on emerging infectious diseases that affect wildlife. Specifically we study the deadly chytrid fungus Batrachochytrium dendrobatidis (Bd) and its amphibian hosts. Amphibians around the world have been experiencing massive population losses and extinctions due to Bd, with hundreds of species infected. We use this system to study how new pathogens emerge and how hosts respond to novel diseases. Undergraduate researcher on this project are involved in laboratory work using molecular genetics to understand the history of Bd and its frog hosts.
XWANG: Invasive insect pests have been major threats to sustainable agricultural production in the USA and globally. Grower interest, economics of pest management, and increasing enforcement of environmental and food quality standards in the USA have generated great interests in developing sustainable pest management strategies such as biological control. We investigate biological controls of invasive insect pests in California. Exotic natural enemies of the invasive pests are imported from the pests’ native ranges and evaluated at the UCB Insectary and Quarantine Facilities for their relative efficiency against the targeted pests and their potential risks to attack non-target species. Specifically, we investigate the basic biology of natural enemies (mainly parasitoids) including host specificity, temperature effects on development, survival and reproduction, searching efficiency, longevity and life-time fecundity, and potential interactions with other introduced and resident natural enemies. Most effective but safest agents will be selected and approved for field release.
MATZEN:This project is part of a larger phytoremediation project researching use a fern, Pteris vittata, to remediate soils contaminated with arsenic. The fern takes up arsenic from the soil and concentrates it in its fronds, which we then harvest to remove the arsenic from the soil while leaving the soil undisturbed. In this project, the student will investigate how arsenic concentrations in fern fronds change over time and with location in the frond. The student will track growth of fern fronds, harvest frond at timepoints over a period of 16 weeks, measure biomass and (with the help of the graduate student) arsenic concentration in the fronds.
BRODIE: Microbial mining of phosphorus in tropical soils: The response of tropical forests to climate change and elevated atmospheric CO2 concentrations is still uncertain and processes controlling tropical forest carbon cycling are not yet well established. Nutrients, particularly phosphorus, are key controls on the trajectory of tropical forests under a changing climate. Furthermore, recent studies show that in tropical forests, phosphorus, rather than co-limitation of nitrogen and phosphorus, is the main nutrient constraint for microbial decomposers. In tropical forests, immobilization of phosphorus in the microbial biomass, late in the decomposition process, can effectively prevent the loss of essential nutrients through leaching or occlusion in the mineral soil. In this project the goal is to develop mechanistic understanding of tropical forest litter decomposition through elucidation of the above- and below-ground plant and microbial traits related to phosphorus mobilization, allocation and uptake.
O'GRADY-1: Insects are among the most diverse lineages of life, with over 1 million named species and many millions more awaiting discovery and description. While we have developed powerful new tools in molecular biology and genomics over the past two decades, the number of experts capable of describing this biodiversity is rapidly dwindling, due to retirements and shifting research and training priorities. Unfortunately, the world is currently facing a biodiversity crisis, the largest mass extinction since the disappearance of the dinosaurs, ~65 million years ago. This crisis, coupled with the lack of expertise, means that many species will slip into extinction before we are able to discover and name them, much less understand much about their basic biology or the impact that their unique biochemistry may have on human society.
Within the western United States, there are several cranefly lineages that make excellent focal groups for student taxonomic and phylogenetic work. These are relatively easy to collect, are manageable in diversity (20-50 species), and require additional taxonomic and phylogenetic work. Our goals are to involve undergraduates in (1) coordinating taxonomic revisions, (2) creating morphological data sets, and (3) generating genomic datasets using next generation DNA sequencing methods in these cranefly lineages. This work will involve both field collections throughout California and the western US and laboratory research in Berkeley.
O'GRADY-2: The Evolution of Salt Tolerance in Diptera
Salinity is a source of stress for animals, shaping distributions and influencing community structures of saltwater ecosystems. The inability to respond to high salt conditions may compound negative consequences of climate change, such as drought in arid and hyper-arid climate conditions, for some flies. Evolving salt tolerance may allow flies to escape predation, to reduce competition and to avoid water loss. A comprehensive phylogeny of Diptera (flies) has recently been proposed, allowing for studies of adaptations across this diverse group. At least 20 families (e.g., Ephydridae, Canacidae, Culicidae, Dolichopodidae, Limoniidae) of flies have independently adapted to salt and brackish water. Canacidae (beach flies) is a small cosmopolitan family of 308 species (27 genera) that are found in intertidal ecosystems where their larvae feed on algae. Notably, one lineage of Hawaiian species has lost the ability to tolerate saline habitats and now occupy high elevation freshwater streams.
This research will take a genomic approach to examine the evolutionary transitions involved in salt tolerance at two main taxonomic levels: (a) across several fly families that have independently evolved salt tolerance and (b) within the family Canacidae, where salt tolerance has been lost at least once in the Hawaiian Islands. The Hawaiian Archipelago is often referred to as an “evolutionary laboratory” because of its extreme isolation, novel community and species assemblages, and multiple chronologically ordered islands. Biogeographic dates exist for each island and can be used to calibrate phylogenies to place the evolution of salt tolerance in a temporal context and test hypotheses about the evolution of its required genes.
IWANG: Many organisms now exist in a habitat matrix composed of both natural and human-modified environments. This project seeks to understand the implications of these urban-wildland habitat matrices for population structure and genetic diversity. We will use genetic data and GIS tools to investigate spatial patterns of genetic variation and their relationship to different environments in amphibian and reptiles species from the greater Bay Area. These studies will have significant implications for our understanding of how human-modified environments impact upon natural populations and how these species persist under these conditions. Students involved in this project will perform DNA extraction and quantification, PCR, microsatellite genotyping, and basic population genetic analysis.
CARLSON: For the past few years, we have been studying the evolution and ecology of a partially migratory fish species common in coastal watersheds in California: Oncorhynchus mykiss. Within populations of O. mykiss, some individuals spend their entire lives in freshwater (“rainbow trout”) and others migrate between freshwater and the ocean (“steelhead trout”). A graduate student in the lab is leading research to understand the landscape factors that promote divergence of the two forms, and the consequences of divergence for stream ecology and species conservation.
One potential project is to explore the behavioral ecology of migratory and resident juveniles that co-occur in streams and to test whether their behavior (e.g., dominance, boldness) differs in predictable ways. We are in the process of recording videos of trout under different density regimes. From these videos, we can extract information on the time spent engaged in various activities (feeding vs. resting, etc.). This is a new element of the project with much potential for an undergraduate to get involved and carve out an independent piece.
We are seeking a student with enthusiasm for stream and fish ecology to join our team! We will work with the intern to develop an independent project related to the larger project described above. Depending on the particular research project, the intern may spend time ageing fish, exploring potential prey (stream invertebrates), or examining fish behavior. Students will also learn basic data entry and analysis skills, and become familiar with pertinent scientific literature in this field.
We've had several BSP interns in the lab in the past and have enjoyed working closely with BSP students. Many of our past BSP students presented the results of their work at national scientific meetings (e.g., Ecological Society of America, SACNAS), and some have gone on to graduate school in the sciences. We strive to provide a meaningful experience for students and to help expose students to the process of science.
If this project is of interest to you, please contact us!
CARLSON-2: For several years, the Carlson Lab has been studying the impacts of reduced streamflow during the summer dry season on aquatic biodiversity, including fishes, frogs, turtles, and bugs. Much of California experiences a Mediterranean climate, with long dry summers. Under Mediterranean seasonality, many small streams are “intermittent”, meaning they dry for a portion of the year. Despite the seasonal drying, remnant pools within intermittent streams can support aquatic biodiversity, including populations of imperiled salmon and trout.
The Carlson Lab has been conducting research to highlight the conservation value of California’s intermittent streams, including through a study of aquatic biodiversity in the Pine Gulch Watershed, in west Marin County. This has involved surveys of aquatic biodiversity including in stream reaches with year-round flow (“perennial” reaches) and intermittent tributaries with seasonal flow. With two years of data in hand, there is considerable opportunity for an undergraduate to assist with ongoing research and to carve out an independent research project.
We are seeking a BSP intern with enthusiasm for stream ecology and fish ecology to join our team! We will work closely with the intern to develop an independent research project. Depending on the particularly project, we expect the intern will learn basic skills in data entry (Excel), mapping (GIS), and statistics (R), and to become familiar with relevant scientific literature. There is also a chance for the intern to learn invertebrate identification and to assist with field sampling efforts in the fall.
We've had several BSP interns in the lab in the past and have enjoyed working closely with BSP students. Many of our past BSP students presented the results of their work at national scientific meetings (e.g., Ecological Society of America, SACNAS), and some have gone on to graduate school in the sciences. We strive to provide a meaningful experience for students and to help expose students to the process of science.
Please contact us if this project is of interest to you!
EICHELMANN:"The Biometeorology lab at UC Berkeley investigates biosphere – atmosphere trace gas fluxes (e.g. CO2 and CH4 fluxes) and tries to understand how these fluxes are influenced by biophysical drivers such as environmental conditions, plant functional properties, and disturbances in land use.
Among others, we have several continuous flux monitoring stations in restored wetland sites in the San Joaquin/Sacramento river delta where we have been measuring greenhouse gas fluxes and environmental variables for multiple years.
We are looking for a student helping us investigate the effect of increasing salinity on these restored wetlands. Our sites are located across a salinity gradient and we have been observing trends in salinity at some of these sites over the last years. The student would be responsible for interpreting the available data and looking for relationships of salinity with other variables such as observed greenhouse gas fluxes and productivity of the wetland."
MCINTURFF-1: The Brashares lab is conducting a multi-year study at the Hopland Research and Extension Center (HREC) in Mendocino County to understand how a mammalian community of deer and their predators (mountain lions, bears, and coyotes) responds to anthropogenic landscape features and activities. To study behavior and distribution of wildlife in response to human influences, our lab deploys motion-activated “camera traps” that take photos and videos of wildlife at HREC. Camera trap data are widely used to monitor and estimate diversity, abundance, movement and behavior of wildlife populations. Working with camera traps is an exciting window into the lives of wild animals and an opportunity to learn a cutting edge tool in wildlife research. The BSP student will work with the mentors to design an independent study using camera traps, and will travel to HREC to deploy and monitor camera traps, review photographs and videos, and summarize and analyze data.
MCINTURFF-2:The Brashares lab is conducting a multi-year study at the Hopland Research and Extension Center (HREC) in Mendocino County, and one of our objectives is to test and compare robust methods for estimating deer populations. Although deer populations are declining statewide, we lack inexpensive, non-invasive methods for monitoring deer densities. In collaboration with the California Department of Fish and Wildlife, our research group is exploring the possibility of using genetic mark-recapture methods to estimate deer populations, and we are looking for a BSP student to assist with piloting this effort at HREC. The BSP student will have the opportunity to conduct fieldwork, using deer trail transects to collect fecal samples. The student will also gain experience in the laboratory, extracting deer DNA from fecal samples and genotyping samples to identify individual deer, and using statistical mark-recapture methods to estimate population size.
VUCKOVIC-1: Our research focuses on regulation of vitamin A metabolism in adipose tissue, and specifically in brown adipose tissue (BAT). Brown adipose tissue exists in hibernating animals, rodents and humans. Its function is to burn energy and to produce heat, specifically during cold exposure. Its pharmacological and neurological activation holds enormous potential for treating obesity and metabolic disorders. Retinoic acid active form of vitamin A and its activity regulates critical processes in cellular function, such as differentiation and gene expression. In Napoli lab, we focus our research on enzymes that generate retinoic acid in adipose tissue, and their role in activation of BAT function.
VUCKOVIC-2:Our research focuses on regulation of vitamin A metabolism in the brain, and specifically in aging brain. Retinoic acid is the active form of vitamin A and its activity regulates critical processes in cellular function, such as differentiation and gene expression. In Napoli lab, we focus our research on enzymes that generate retinoic acid in the brain, specifically retinol dehydrogenase 10 (Rdh10), and its role in regulating biosynthesis of retinoic acid in aging adult brain and preserving brain function in aging process.
ZACHARIA: The primary goal of this project is to determine what factors influence the soil-dwelling bacterium Streptomyces coelicolor into making various antibiotics and differentiate into unique cell types. Using exciting techniques such as microscopy, we will visualize the onset of the production of two colorful antibiotics S. coelicolor makes including actinorhodin, which has a deep blue hue and prodigiosin, which is bright red, to see where these natural products localize within a colony. To do this, we will use green and red fluorescent proteins that are under the control of promoters that are involved in antibiotic biosynthesis to help us visualize where inside a S. coelicolor colony the antibiotic producing cells are located. Additionally, we will test how different environmental gradients, including oxygen, pH, and nutrients, affect antibiotic production by monitoring fluorescence in S. coelicolor. This project aims to establish a fundamental understanding of cell-decision making in S. coelicolor.
ADAMS-1:The poisonous death cap mushroom, Amanita phalloides, is an invasive species. Once found only in Europe, this obligate symbiont of trees has been spread all over the world, including California. However, the traits that facilitated its invasion success remain unexplored, as does the mushroom’s possible impacts on native California diversity.
My research examines how the toxins in Amanita phalloides contribute to the invasion success of this fungus. I am working to answer a number of questions, such as: In its introduced range in California, have the toxins decreased or increased in abundance compared to native European samples? Who do the toxins protect the fungus against? Does Phalloides negatively impact native soil microbes?
Primary tasks include DNA and RNA extraction, PCR and gel electrophoresis, toxin extraction, and data analysis.
ADAMS-2:Cat has received support from the Joint Genome Institute to sequence the genome of a new, undescribed fungal pathogen. This Phomopsis-like species was isolated from infected seeds of the wild Bolivian chili pepper, Capsicum chacoense. The fungus is highly resistant to capsaicin, the main component of chili spice. Sequencing its genome would elucidate the enzymes and proteins that convey spice tolerance, and will pinpoint a new novel enzyme that allows the fungus to cleave capsaicin.
The project entails making media with energy inhibitors such as capsaicin, culturing fungi, DNA and RNA extraction, PCR, and data analysis.
BLACKMAN-1:Many plant functions occur with regular daily rhythms so that these functions occur at times of day most favorable for enhancing growth and reproduction. We are studying how internal circadian rhythms and cycling factors in the environment like light and temperature regulate the daily timing of floral developmental events, as well as how these processes evolve, using sunflower and its relatives as a model system. A potential project would be for a student to film and observe how the daily timing of pollen release and stigma opening vary among focal species in season in the UC Botanic Garden. This data would then be analyzed to ask whether variation in these traits reflects broader evolutionary relationships to geography, pollinator, or other factors.
BLACKMAN-2:Plants often use day length as a primary cue to sense the timing of the growth season and decide whether to initiate flowering. While in most systems, plants accelerate flowering in response to either long days or short days, we have found that both long days and short days interact to regulate when sunflowers initiate flowering. A potential project would be for the student to grow plants under several day length conditions, collect tissue at key developmental time points, extract RNA, and conduct sequencing to examine what gene expression pathways are responding to particular day lengths. In doing so, we anticipate learning how sunflowers have evolved to cope with seasonal fluctuations in the environment at a mechanistic level.
DE AZEVEDO SOUZA:Plants recognize pathogens in the environment by perceiving conserved microbial molecules (Pattern Associated Molecular Patterns; PAMPs). Pathogens penetrate the plant cell wall mostly by chemical hydrolysis to gain access to the plant’s cytoplasm, and this penetration process generates plant-derived Damage-Associated Molecular Patterns (DAMPs). Plant cells can, in turn, recognize these self-derived molecules as signals of an invasion attempt, and a defense process is initiated to prevent pathogen spread. We are interested in investigating the immune response mounted by the plant after concurrent recognition of multiple eliciting molecules, in particular of those representing plant cell wall damage (DAMPs) co-occurring with pathogen derived molecules (PAMPs), which could be a way by which plants differentiate pathogenic from non-pathogenic microbes in the environment. Research will involve one or more of the following laboratory techniques: plant care, measurements of calcium influx, protein phosphorylation and gene expression.
TAGA: Microbial communities populate nearly every environmental niche and influence earth’s biogeochemical cycles and human health. In an effort to understand the molecular interactions that shape microbial communities, the Taga lab investigates how microbes interact through the sharing of metabolites. We focus on a class of shared metabolites called corrinoids, which include vitamin B12 and related cofactors. Corrinoids are synthesized by only a subset of the microbes that need them, and therefore can serve as a model for nutritional interactions. A variety of structurally different corrinoids are found in many communities, but the functional relevance of this diversity is poorly understood. We are looking for a highly motivated student with an interest in microbes and metabolites who will investigate the functions of structurally different corrinoids in bacteria by genetic, biochemical, chemical, and/or bioinformatic approaches, with the overall goal of understanding how metabolites are utilized and shared in microbial communities.