Department of Biology



SUMMER RESEARCH IN BIOLOGY 2020 – PROJECT DESCRIPTIONS APPLICATIONS DUE Tuesday, January 14, 2020To apply, fill out the application:: The application is only 1 page. Please do not submit test applications.This list includes projects both on and off campus: Please read carefully! Funded summer research is for current Stanford undergraduates only.Projects located at Stanford Main Campus:Prof. Martha Cyert - How do Calcium Signals Regulate Cellular Processes?Prof. Jose? Dinneny – How Roots Find WaterProf. Jose? Dinneny – Synthetic Biology in PlantsProf. Rodolfo Dirzo - The Effect of Human Disturbances on Species Interactions and Consequences for Avian DiseaseProf. Scott Dixon - Investigating the Regulation of FerroptosisProf. Jessica Feldman - Cells on the Move: In Vivo Models of Cell Migration to Better Understand Development and CancerProf. Jessica Feldman - How do cells know which end is up? Mechanisms Controlling Epithelial Cell PolarityProf. Jessica Feldman - Mechanisms Regulating Microtubule Organization During DevelopmentProf. Hunter Fraser - High-Throughput CRISPR ScreensProf. Judith Frydman - A Proteostasis Physical for the Aging CellProf. Judith Frydman - Chaperone Modulation of Huntingtin AggregationProf. Judith Frydman - Sorting Out the JUNQ: The Role of Mitochondria in Spatial Protein Quality ControlProf. Tadashi Fukami - Microbiome and Parasite Interactions in Honeybees Prof. Or Gozani - Protein Methylation Signaling in Epigenetic RegulationProf. Liz Hadly - Signals of the Anthropocene in Historic Lake Core SedimentsProf. Liz Hadly - Consequences of the Largest Ecosystem Engineer, the African Elephant, Hybridizing Across a Climatic-Transition Zone in Garamba National Park, D.R. CongoProf. Liz Hadly - Conservation Genetic Applications of Maternally Inherited Markers for the Illegal Wildlife Trade of Big CatsProf. H Craig Heller - Circadian Rhythms in Learning and MemoryProf. H Craig Heller - Investigating and Mitigating the Learning Disability Caused by Down SyndromeProf. H Craig Heller - Thermal Physiology and Physical PerformanceProf. Liqun Luo - How does prenatal neuronal activity shape the circuit maturation and behavior?Prof. Liqun Luo - Molecular Signaling of Neuronal Wiring SpecificityProf. Erin Mordecai - Effects of Climate, Geographic Region, and Phylogenic History on Interactions Between Vector-Borne Pathogens, Vectors, and HostsProf. Erin Mordecai - Modeling spatial and temporal occurrences of vector-borne diseasesProf. Ashby Morrison - Cancer-Related Genomic InstabilityProf. Ashby Morrison - Epigenetic-Regulated Metabolic StabilityProf. Mary Beth Mudgett - Plant Defense PrimingProf. Mary Beth Mudgett - Pre-invasion Defenses in PlantsProf. Lauren O’Connell - Pick Your Poison - How Prey Choice Shapes Toxicity in South American Poison FrogsProf. Lauren O’Connell - Toads in Space: Amphibian Spatial CognitionProf. Kabir Peay - Climate Change and Plant-Fungal SymbiosisProf. Noah Rosenberg - Mathematical Properties of Population-Genetic StatisticsProf. Jan Skotheim - Determining Why Cell Growth Triggers Cell DivisionProf. Molly Schumer - The Genetic Basis of Thermal Tolerance in Hybridizing FishProf. Molly Schumer - Hybrid Incompatibilities: A Dangerous MixProf. Alice Ting - Improved Technologies for Genome and Proteome EditingProf. Alice Ting - Optogenetic Tools for Labeling and Manipulating Functional Brain CircuitsProjects located at Hopkins Marine Station, Pacific Grove, CA: Prof. Barbara Block - Biomechanic and Physiology of Bluefin Tuna?Prof. Barbara Block - Photo ID of White Sharks and Mantas?Prof. Giulio De Leo - Discovering Parasite Species of Sea Otters and Sea BirdsProf. Giulio De Leo - Mapping Environmental and Socioeconomic Determinant of Neglected Tropical Diseases in Low Income CountriesProf. Jeremy Goldbogen - Investigating the Extent of Microplastic Pollution in the Monterey Bay EcosystemProf. Jeremy Goldbogen - Comparative Kinematics of Bubble-Net Feeding Humpback Whales in Three Different LocationsProf. Chris Lowe - The Role of Stem Cells in Developing Two Body PlansProf. Fiorenza Micheli - Evaluating the Role of Mobile Predators in Fostering Coral Reef/Open Ocean ConnectivityProf. Fiorenza Micheli - Reconstructing Biodiversity Change in Monterey BayProf. Fiorenza Micheli - Trophic Cascades, Mesopredator Release and Reef ResilienceProjects located away from Stanford and/or abroad: Prof. Deborah M. Gordon - Collective Behavior in Harvester Ants (Southwestern Research Station, Portal, Arizona)Prof. Steve Palumbi - Genetics and Field Work on Heat Resistant Corals in Palau (Hopkins and the Palau International Coral Reef Center)Prof. Peter Vitousek - Understanding Traditional Rain-Fed Agriculture in Hawaii (Puanui ahupuaa, Hawaii)Projects located at Stanford Main Campus:How do calcium signals regulate cellular processes?Stanford Main CampusProfessor Martha CyertLab Website: commitment: 10 weeks / 1 position availableChanges in the cellular concentration of Ca2+ serve as an intracellular signal that is decoded by Ca2+ regulated enzymes to control fundamental processes such as gene expression, protein trafficking, motility, cell death and neuronal transmission. We study calcineurin, which, when activated by Ca2+, removes phosphate groups from its substrate proteins to regulate their function, localization and/or degradation. Calcineurin is expressed in all human tissues, and is required for activating the immune response for this reason the calcineurin inhibitors, cyclosporin A and tacrolimus, are used clinically as immunosuppressants. However, chronic use of these drugs causes many unwanted effects by inhibiting calcineurin in tissues outside the immune system. Identifying all of the human proteins that calcineurin regulates will provide important information about how these negative consequences occur and will create new knowledge about Ca2+-regulated processes in all cells. We used structural information about how calcineurin binds to its substrates to predict >300 new substrates for this phosphatase including many transcription factors, kinases and cytoskeletal proteins (). We are seeking an undergraduate researcher to investigate possible changes in the activity and phosphorylation status of some of these new proteins by calcineurin. Approaches used will include some or all of the following: cloning, expression in mammalian cells, immunoblotting, analysis of phosphorylation in vivo and in vitro, proximity labeling and imaging of live and/or fixed cells.How Roots Find WaterStanford Main CampusProfessor Jose? DinnenyLab Website: commitment: 10 weeks / 1 position availableRoots have important functions in anchorage, and uptake of nutrients and water. Root systems represent complex branched networks that are generated through a simple set of developmental decisions that determine their architecture. Lateral root branches, which are multicellular organs that initiate their development from the internal tissue layers of the parent root, represent an important mechanism to increase the surface area of the root system and the expanse of soil that is ultimately explored, thus improving nutrient and water uptake. The number of lateral roots that are initiated, how they are positioned, and their subsequent growth after emergence from the parent root are all highly responsive to environmental cues and the physiological status of the plant. In the Dinneny lab, a novel mechanism was discovered by which lateral root branching is regulated by spatial differences in moisture availability around the root. This mechanism was termed hydropattering.Synthetic Biology in PlantsStanford Main CampusProfessor Jose? DinnenyLab Website: commitment: 10 weeks / 1 position availableThe shape of a plant’s root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. We are developing tools that enable the precise spatial, temporal, and magnitudinal control over gene expression in plants. Using these tools, we are building synthetic genetic circuits that reprogram plant root growth in a predictable manner. By engineering plant roots, we hope to learn more about how plants survive in water limited conditions.The Effect of Human Disturbances on Species Interactions and Consequences for Avian DiseaseStanford Main CampusProfessor Rodolfo DirzoLab Website: commitment: 10 weeks / 1 position availableDirzo Lab (Biology) would welcome a Stanford undergraduate to participate in an avian disease ecology project (May to mid-July 2020). The project examines the role of human impact on ecological interactions and its significance for human health risks. Specifically, we investigate the prevalence of tick-borne pathogens in birds as influenced by changing densities of large and small mammals due to human disturbance. The work will involve capturing wild passerines using mist nets (9 preserves around the Bay Area). Students will learn how to install mist nets as well as extract, handle, and band wild birds. There will also be potential for post-fieldwork if there is interest. In general, students will be expected to work 3-4 days/week (6-8 hours/day), with some variation depending on site. This involves one day for installation of mist nets, two days for capture and bird processing, and possibly one day for data entry and analysis, if time permits. Most days we will be working during peak bird activity hours so students need to be ready around sunrise. Previous experience with mist nets or handling wild birds would be an advantage, but this is not necessary, as students will be trained accordingly. For sites situated close to Stanford campus we will travel to our net locations each morning by carpooling, although it would be helpful if students had their own means of transport. For some sites, we will be camping near our nets for two nights while we band. Camping gear (tent, sleeping pad/bag) will be necessary. Students who do not own this equipment can reach out so that arrangements can be made. The project allows one to get up close and personal with many of the bird species found around the Bay Area, some of which are found nowhere else outside California. This will be a great opportunity to learn the basics of sampling avian communities and the fundamentals of bird biology, while exploring beautiful natural spaces in Stanford’s backyard.Investigating the Regulation of FerroptosisStanford Main CampusProfessor Scott DixonLab Website: commitment: 10 weeks / 2 positions available Ferroptosis is a new form of cell death that can be selectively activated in certain cancer cells. The goal of the project is to employ genome-wide CRSIPR-Cas9-mediated genetic screening to identify novel regulators of this process. The function of novel genes regulating ferroptosis will then be characterized using biochemical and cellular approaches.Cells on the Move: In Vivo Models of Cell Migration to Better Understand Development and CancerStanford Main CampusProfessor Jessica FeldmanLab website: commitment: 10 weeks / 1 position available Cells migrate across relatively long distances, and this migration plays a critical role in many aspects of biology including wound healing, embryonic development, immune responses, and cancer metastasis. Previous studies investigating cell migration have been performed in two-dimensional cell culture models, however, the mechanisms cells use to migrate through complicated three-dimensional environments in intact organisms are not fully understood. A position is open for the summer to use state of the art genetic techniques, including CRISPR, and live three-dimensional imaging of fluorescent proteins to track and manipulate migrating cells inside of the model organism C. elegans.How do cells know which end is up? Mechanisms Controlling Epithelial Cell PolarityStanford Main CampusProfessor Jessica FeldmanLab website: commitment: 10 weeks / 1 position available Polarization along an apico-basolateral axis is a hallmark of epithelial cells, essential for their selective barrier and transporter functions, as well as their ability to provide mechanical resiliency to organs. Loss of polarity along this axis perturbs development and is associated with a wide number of diseases including the vast majority of human cancers. A position is open for the summer to use the model organism C. elegans to identify molecular mechanisms that regulate epithelia polarization during development. This project will involve live confocal imaging, CRISPR-based genetic manipulation, and large particle flow cytometer based genetic screens.Mechanisms Regulating Microtubule Organization During DevelopmentStanford Main CampusProfessor Jessica FeldmanLab website: commitment: 10 weeks / 1 position available Cells, like whole organisms, have an incredible diversity of form that allows them to perform distinct functions. Often underlying this diversity is the specific patterning of the cytoskeleton, networks of intracellular polymers that allow for transport within the cell as well as cell shape, division, and movement. The cytoskeleton undergoes dramatic reorganization as cells divide and differentiate, which is critically important for development and for proper cell function. We are interested in understanding the mechanisms that regulate these patterning events during normal development so that we can better understand how these processes go awry in disease states such as cancer. A position is open for the summer to help identify mechanisms that regulate microtubule organization in differentiated cells using the model organism C. elegans. This project will harness the awesome power of C. elegans genetics in combination with live cell imaging. The undergraduate research fellow will learn microscopy, basic C. elegans biology and anatomy, and molecular biology and genetic techniques including CRISPR.High-Throughput CRISPR ScreensStanford Main CampusProfessor Hunter Fraser Lab website: commitment: 10 weeks / 2 positions available We have recently invented the first method able to perform high-throughput precision genome editing (Sharon et al, Cell 2018). Our CRISPR-based method can test the effects of thousands of mutations in a single experiment. We are scaling up our efforts and looking for students who are excited to join us! We prefer students who have taken BIO 45 or have previous lab experience, and who are interested in staying in the lab for an honors thesis.A Proteostasis Physical for the Aging CellStanford Main Campus Professor Judith FrydmanLab website: commitment: 10 weeks / 1 position availableThe proper folding and function of the proteome, termed proteostasis, is critical for cell viability and organismal health while protein misfolding contributes to many neurodegenerative pathologies such as Alzheimer’s, Huntington’s and Parkinson’s disease. Aging is the greatest risk factor that correlates with onset of many of these neurodegenerative diseases, however modeling neuronal aging in a cell culture dish is challenging. Derivation of neurons from patient samples by reprogramming into pluripotent stem cells results in rejuvenation and removes aging associated molecular marks and phenotypes; on the other hand, direct transdifferentiation of patient cells into neurons preserves aging associated phenotypes but this process is costly, challenging, and low throughput. We propose to develop a proteostasis physical to examine patient fibroblasts for aging associated changes in proteostasis phenotypes by employing a panel of targeted protein quality control inhibitors coupled with high content imaging to asses protein aggregation and monitor cellular viability. This strategy will enable dissection of subtle aging and disease associated changes in proteostasis directly in-patient samples thereby addressing whether there are inherent proteostasis deficiencies that arise with aging and enable us to optimally target particular samples for further study by transdifferentiation.Chaperone Modulation of Huntingtin AggregationStanford Main Campus Professor Judith FrydmanLab website: commitment: 10 weeks / 1 position availableChaperonins are a class of large multi-subunit proteins that mediate protein folding within the cell and prevent aggregation of misfolded proteins. The hetero-oligomeric chaperonin TRiC modulates polyglutamine-expanded Huntingtin exon1 aggregation and toxicity in a murine neuronal cell model. Furthermore, it was discovered that TRiC interacts with Huntingtin exon1 and prevents its aggregation in vitro regardless of the length of the polyglutamine region, despite the fact that aggregation of Huntingtin protein is mediated by the polyglutamine region. Based on these results, it is hypothesized that either of the amino acid segments located at the N-terminus or the C- terminus of the polyglutamine-expanded Huntingtin exon1 fragment mediate binding to TRiC. The goal of this project is to investigate the biochemical interaction between TRiC and Htt exon1 by isolating TRiC recognition sequences using deletion constructs and single amino acid replacements of Htt exon1.Sorting Out the JUNQ: The Role of Mitochondria in Spatial Protein Quality ControlStanford Main Campus Professor Judith FrydmanLab website: commitment: 10 weeks / 1 position availableWe are working to determine the role that mitochondria play in sequestering misfolded proteins into protein quality control compartments, transport of compartments, and ultimate clearance of the compartments by proteasomes or autophagy. The project will entail cloning and/or mutagenesis to generate any plasmids needed, learning to grow yeast cultures and express proteins under inducible expression systems, confocal microscopy to image the interaction between mitochondria and protein quality control compartments in different mutant yeast strains, and biochemical techniques such as Western blots to monitor protein clearance. We will also work to read and interpret scientific literature and the student will get the chance to hone their communication skills by presenting at lab meeting. Microbiome and Parasite Interactions in HoneybeesStanford Main Campus Professor Tadashi FukamiLab website: commitment: 10 weeks / 2 positions availableHost-associated microorganisms can affect animal health. For example, some gut bacteria prime host immunity and compete against pathogens. However, microbes live in an ecological community consisting of multiple species, and it remains unclear how multiple species of host-associated microbes interact with one another and with pathogens, which may have consequences for animal health. For example, Nosema ceranae is a highly virulent, obligate intracellular parasite that infects Western honeybees, Apis mellifera, but how this parasite is affected by multiple bacterial species in the honeybee gut is not well understood. We are seeking two undergraduate students who will work with graduate students to conduct experiments to inoculate sterile honeybees with various combinations of species of gut bacteria before or after parasite exposure. This is a good opportunity for students interested in gaining research experience in microbial ecology, community ecology, and molecular ecology. Students will also have a chance to interact with other members of the lab on a daily basis and learn about other ongoing projects in ecology. For more info, see: Methylation Signaling in Epigenetic RegulationStanford Main CampusProfessor Or Gozani, commitment: 10 weeks / 1 position available Methyltransferase enzymes are central regulators in epigenetics and cell signaling, and they are disrupted in cancer with extraordinary frequency. The Sage and Gozani labs use mouse and cell culture models to uncover how methyltransferases contributes to cancer progression. This project will explore how targeted gene knock-downs affect tumor cell growth, with the goal of discovering novel molecular mechanisms that could guide development of targeted therapeutics.Signals of the Anthropocene in Historic lake Core SedimentsStanford Main Campus & Jasper RidgeProfessor Liz Hadly, commitment: 10 weeks / 1 position available Anthropogenic activities changed our planet over the course of the last 10,000 years, but the scale of human impacts increased dramatically around the mid-20th century. Signals of these impacts and the resulting biological changes are captured in the geologic record, particularly in the sediments of lakes. We are studying environmental change in the Bay Area using lake cores from Jasper Ridge Biological Preserve which record environmental change over at least the last 1000 years. Projects could include anything from sedimentary/geologic analyses, assembly and analysis of historical documents for reconstructing past biota and environmental events, analysis of climate data and impacts of past climate on vegetation, analyzing invasive species data, etc.Consequences of the Largest Ecosystem Engineer, the African Elephant, Hybridizing Across a Climatic-Transition Zone in Garamba National Park, D.R. CongoStanford Main CampusProfessor Liz Hadly, commitment: 10 weeks / 1 position available Human-induced hybridization of wildlife is becoming more common, and understanding how this is reshaping the ecological networks of an ecosystem is critical. The goal is to assess the impact of hybridizing forest and savanna elephants on diet, habitat use and individual health (microbiome & parasite diversity) in Garamba National Park, DRC. Students joining the project will be trained on DNA metabarcoding techniques from DNA extractions, PCR, Next generation sequencing preparation and analysis. They will be focusing on elephants, but also other species from the region.Conservation Genetic Applications of Maternally Inherited Markers for the Illegal Wildlife Trade of Dig CatsStanford Main CampusProfessor Liz Hadly, commitment: 10 weeks / 1 position availableProject will use the amplification of several mitochondrial markers and test their use of identifying illegally traded big cat samples with these genetic applications. Students will evaluate low-quality sample amplification of hair, scat, and saliva. Possible opportunity of utilizing aDNA methods on bone and pelt samples.Circadian Rhythms in Learning and MemoryStanford Main CampusDr. Norman F. Ruby, Heller lab, commitment: 10 weeks / 2 positions available Humans and animals have internal clocks that oscillate on a 24-hour rhythm. When this rhythm is disrupted by aging, shift-work, or disease, it leads to cognitive deficits. The breakdown of rhythms accelerates the onset of Alzheimer's disease. We are using an animal model that allows us to investigate the neural circuits that underlie this kind of memory impairment. To that end, we are using a combination of surgical techniques to obtain in vivo measures of neurotransmitter changes that are associated with performance on a range of memory tests. We are looking for students who will stay on and pursue a senior honors thesis with this work.Investigating and Mitigating the Learning Disability Caused by Down SyndromeStanford Main CampusProfessor H Craig Heller, commitment: 10 weeks / 2 positions available Down syndrome (DS) is a common neurogenetic cause of learning disability with an incidence of about 1 in 700 births. DS is caused by partial or total triploidy of human chromosome 21. We use a mouse model of DS that has triploidy of most of the mouse genes syntenic with human chromosome 21. We have demonstrated a pharmacological treatment that normalizes learning and memory in this mouse model of DS, and we are now striving to understand the underlying mechanisms of this drug effect. We are also investigating the effects of normalizing the copy number of individual genes that are triplicated in our mouse model of DS. Students will be involved in mouse learning and memory experiments, experiments to activate or inactivate certain regions of the brain involved in learning and memory, and experiments to analyze effects of neural and genetic manipulations of other features of DS.Thermal Physiology and Physical PerformanceStanford Main CampusProfessor H Craig Heller, commitment: 10 weeks / 2 positions available We have discovered a previously unrecognized adaptation for heat loss in mammals including humans. This adaptation consists of unique blood vessels in the non-hairy skin. We have developed technology to exploit these adaptations for rapidly moving heat into or out of the body. Using this technology, we have been able to greatly extend the work duration in hot environments of individuals wearing personal protective equipment. We have also shown that heat extraction can greatly extend physical effort and therefore have a significant effect on physical conditioning. Also, our equipment has many hospital applications such as regulating patients temperatures while under anesthesia. Students will be involved in designing and testing new versions of the technology and applying them in research in human physical performance.How does prenatal neuronal activity shape the circuit maturation and behavior?Stanford Main CampusProfessor Liqun LuoLab Website: commitment: 10 weeks / 1 position available Neuronal activity during development has been shown to play an important role in assembling specific circuits in the brain, but the extent to which neuronal activity contribute to neural circuit wiring and function across the brain is unclear. Our lab has developed a technique to genetically label active neurons in the mouse, and we implemented this to reveal the scope of prenatal neuronal activity and study its potential function. The undergraduate student will help explore and manipulate this prenatal activity in select brain regions, with the goal of discovering new ways in which activity shapes the maturation of the brain and behavior. All levels of experience welcome, only enthusiasm for neuroscience is required!Molecular Signaling of Neuronal Wiring SpecificityStanford Main CampusProfessor Liqun LuoLab Website: commitment: 10 weeks / 1 position available During development of the human brain, trillions of synaptic connections are established among billions of neurons. How is this feat achieved? We are using state-of-art proteomic and genetic methods to explore fundamental principles and molecular mechanisms that regulate these wiring processes in the olfactory system of the fruit fly, Drosophila. The undergraduate student will learn to plan and perform molecular, biochemical and genetic experiments to study how a membrane protein, Teneurin, transduces signals to its molecular partners. Given that Teneurin is highly conserved from flies to humans, and mutations in human Teneurin homologs are associated with various brain disorders, the mechanisms we uncover may contribute to the understanding of wiring of the mammalian brain and pathogenic processes of human brain disorders.Effects of Climate, Geographic Region, and Phylogenic History on Interactions Between Vector-Borne Pathogens, Vectors, and HostsStanford Main CampusProfessor Erin MordecaiLab Website: Time commitment: 10 weeks / 1 position availableVector-borne pathogens are transmitted between vertebrate hosts by arthropod vectors (e.g., insects, ticks, mites, etc.). These pathogens span the full continuum from specialists that infect only a small number of hosts and vectors (e.g. Lymphatic Filariasis) to extreme generalists that can infect upwards of 20 host and mosquito species (e.g. Ross River virus). Pathogens from across this continuum can infect humans, leading to a substantial human health burden. An interested student would complete a two-part project: 1) A literature review to extract the degree of generality (number of suitable vector and host species) and global distribution of all known vector borne diseases; 2) Use these data in phylogenetic regression analysis, and/or ordination techniques to explain the variation in degree of generality and human infection risk among these vector borne-diseases. The student should be interested in mathematical and statistical modeling in ecology and the literature review and data extraction process.Modeling Spatial and Temporal Occurrences of Vector-Borne DiseasesStanford Main CampusProfessor Erin MordecaiLab Website: Time commitment: 10 weeks / 1 position availableTransmission of vector-borne diseases results from ecological interactions between vectors, hosts, and their environment. Understanding these interactions allows for better control and prediction of these diseases. This project will use existing data in combination with statistical and mechanistic models to understand the distribution of human cases of vector-borne diseases and the environmental conditions allowing for their transmission. Students should have a background in data-analysis, mathematical modeling, and/or programming, or be interested in building these skills.Cancer-Related Genomic InstabilityStanford Main CampusProfessor Ashby Morrison, commitment: 10 weeks / 1 position availableStudents will be involved in innovative research that utilizes genomic techniques, such as CRISPR-Cas9 genome editing and Illumina sequencing. The focus of the research is to investigate how genome stability mechanisms become disrupted during evolution of a cancer cell.Epigenetic-Regulated Metabolic StabilityStanford Main CampusProfessor Ashby Morrison, commitment: 10 weeks / 1 position availableStudents will be investigating the relationship between nutrient environment and histone modifications that regulate gene expression. Molecular biology and biochemical techniques will be utilized in a metabolically-synchronized yeast model system.Plant Defense PrimingStanford Main CampusProfessor Mary Beth Mudgett, commitment: 10 weeks / 1 positions available Systemic acquired resistance (SAR) is a global immune response induced at the site of infection that leads to long-lasting and broad-spectrum disease resistance at distal, uninfected tissues. Despite the importance of this priming mechanism, the identify to the mobile defense signal that moves systemically throughout plants to establish SAR has remained elusive for years. Using untargeted metabolite profiling, we recently discovered that the initiation of SAR in Arabidopsis thaliana requires the plant metabolite N-hydroxypipecolic acid (NHP). NHP establishment of SAR is characterized by the induction of transcriptional and metabolic programs in systemic tissue. Moreover, leaves treated with NHP display enhanced resistance to pathogens, indicating that the level of NHP in tissues plays a critical role in establishing the magnitude and timing of the disease resistance response. How plants regulate the biosynthesis of NHP to establish SAR signaling is largely unknown and a central question for plant defense priming. This summer students will have the opportunity to participate in research aimed to: (1) determine where and when NHP signaling initiates and terminates defense priming in plants; (2) determine the spectrum of pathogen resistance governed by NHP signaling; and/or (3) engineer the biosynthesis of NHP in crop plants.Pre-Invasion Defenses in PlantsStanford Main CampusProfessor Mary Beth Mudgett, commitment: 10 weeks / 1 positions available Protein complexes that regulate pre-invasion immunity in plants. Tomato atypical receptor kinase1 (TARK1) is a pseudokinase and a positive regulator of tomato innate immune responses. To elucidate TARK1’s role in tomato immunity, we performed a proteomic screen to identify TARK1 interacting proteins. We discovered that TARK1 interacts with proteins that are related to stomatal movement and disease resistance signaling in tomato leaves. Stomatal pores close in response to bacterial invasion to prevent infection of leaf tissue. Stomatal immunity is thus a critical pre-invasion defense response that limits pathogen entry into plant tissues. The mechanisms controlling stomatal reopening is poorly understood. Physiological studies indicate that TARK1 plays a key role in the regulation of stomatal opening during pathogen triggered immunity. This summer students will be able to participate in biochemical and physiological experiments to understand the underlying mechanisms by which TARK1 and its interacting proteins coordinates stomatal reopening in tomato leaves upon pathogen challenge.Pick Your Poison - How Prey Choice Shapes Toxicity in South American Poison FrogsStanford Main CampusProfessor Lauren O’Connell, Time commitment: 10 weeks / 1 position available Poison frogs (Family Dendrobatidae) are native to Central and South America and carry small molecule alkaloids in their skin for defense against predation. Poison frogs acquire these chemical defenses solely from their arthropod diets. Previous studies on diet and toxicity across the Dendrobatidae clade suggests that the independent origins of chemical defenses in the family are associated with a dietary specialization on ants and mites. However, the role poison frog prey electivity plays in chemical defense acquisition remains unclear. To examine poison frog dietary repertoire, I went to wild poison frog habitats in Ecuador to collect leaf litter arthropods, which represent their prey menu, and frog stomach contents to sample their prey consumption. I collected these samples across multiple populations of the toxic Little Devil Frog, and then within overlapping populations of the non-toxic Chimbo rocket frog and the toxic Phantasmal poison frog. Since the overlapping species have access to the same prey menu, it will be interesting to compare dietary habits of a toxic and non-toxic species living in the same place. Through my collections, I have obtained thousands of arthropod specimens, all of which will need both morphological and molecular identification. Therefore, I will need assistance in photographing and genetically barcoding our arthropod specimens through Cytochrome-oxidase-1 sequencing. I believe this project is an effective way to introduce early scientists to molecular research. This is because they have the opportunity to start off with something macroscopic (whole arthropods) in the experimental workflow.Toads in Space: Amphibian Spatial CognitionStanford Main CampusProfessor Lauren O’Connell, Time commitment: 10 weeks / 1 position availableAll animals inhabit and move through space to complete a variety of tasks, from foraging for food to long range seasonal migrations. Several classes of vertebrates have been characterized with respect to brain function during spatial tasks. However, amphibians, many of which show complex spatial/navigation abilities, remain virtually uncharacterized. This blind spot is part of a larger knowledge gap regarding amphibian brain functions, and one that must be filled for a thorough understanding of vertebrate neural evolution.For this project, students will be using cane toads (Rhinella marina) to study navigational mechanisms on the behavioral and neural levels. Students will design and build mazes to target different navigation paradigms, test animal ability to complete different classes of spatial tasks, and characterize brain activity associated with different tasks through immunohistochemistry. Large amounts of experimental time will be devoted to implementing mazes and observing/recording animal behavior within the maze, with the goal of finding a neural signature of navigation tied to these behaviors. Students will learn how to design and carry out behavioral experiments and how to study brain activity underlying relevant behaviors.Climate Change and Plant-Fungal SymbiosisStanford Main CampusProfessor Kabir Peay, commitment: 10 weeks / 2 positions available Students will be involved in research on symbiotic relationships between plants and fungi, and how relationship with diverse communities of fungi can buffer plants against anthropogenic changes to the environment. Research will occur both in the field and lab (primarily coastal California). Students will gain experience in designing experiments, the use of molecular data (DNA sequencing) and bioinformatics to characterize microbial communities, and statistical techniques to analyze changes in diversity and function of microbial organisms.Mathematical Properties of Population-Genetic StatisticsStanford Main CampusProfessor Noah Rosenberg, commitment: 10 weeks / 2 positions availableMathematical features of the statistics used in population genetics affect the biological interpretations of population-genetic data. Students will complete mathematical proofs, stochastic simulations, and/or bioinformatics analysis pertaining to statistical methods used in population genetics.Determining Why Cell Growth Triggers Cell Division Stanford Main CampusProfessor Jan M. Skotheim, commitment: 10 weeks / 2 positions available To maintain a consistent cell size, cells need to grow before dividing. Yet, the molecular mechanisms underlying how cell growth triggers division remain largely unknown. Students will work on this question in either budding yeast or mammalian cells.The Genetic Basis of Thermal Tolerance in Hybridizing FishStanford Main CampusProfessor Molly Schumer, commitment: 10 weeks / 1 position availableOne puzzle in genetics and evolutionary biology is how organisms adapt to new environments. An important environmental adaptation that has occurred over and over in evolution is adaptation to new thermal environments. This project will ask about the genetic causes of differences in temperature tolerance in two species of swordtail fish, X. birchmanni and X. malinche, and in their naturally occurring hybrids. We will use a combination of genetic mapping, cell culture, and RNAseq based approaches to identify genes that are important in differences in thermal tolerance in both species and in their hybrids. Successful applicants will bring an enthusiasm for science, excellent organizational skills, and optionally a background in molecular biology or evolutionary biology.Hybrid Incompatibilities: A Dangerous MixStanford Main CampusProfessor Molly Schumer, commitment: 10 weeks / 1 position availableOne recent surprise in evolutionary biology and genetics has been the discovery that many species can produce offspring, or hybridize, with their close relatives. This even includes our own species, where some human populations mixed with our relatives the Neanderthals and Denisovans thousands of years ago. Although hybridization seems to be common, hybrids can also have problems caused by combining genes from two species into one organism; these are known as hybrid incompatibilities Our lab uses swordtail fish as a model system to try to identify which and what types of genes are involved in hybrid incompatibilities. For example, a recent project in the lab has focused on characterizing the causes of a melanoma that forms only in hybrids. This project will use genetic, molecular, and bioinformatics approaches to identify hybrid incompatibilities and understand the problems they cause in hybrids.Improved Technologies for Genome and Proteome EditingStanford Main CampusProfessor Alice Ting, commitment: 10 weeks / 2 position availableCRISPR technology has revolutionized the study of the nuclear genome. We are interested in developing next-generation tools for extending CRISPR-based approaches to other genomes, to RNA, and to proteomes. Join our team to work on technologies that could be transformative for cell biology and medicine!Optogenetic Tools for Labeling and Manipulating Functional Brain CircuitsStanford Main CampusProfessor Alice Ting, commitment: 10 weeks / 2 position availableFLARE (Fast Light and Activity-Regulated Expression) is a light and calcium-gated transcription factor useful for gaining genetic access to activated neural ensembles (Wang et al. Nature Biotech 2017). We are now using protein engineering and directed evolution approaches to develop next-generation FLARE and related optogenetic tools, with the overall goal of identifying and dissecting functional brain circuits with ever-greater spatial and temporal precision.Projects located at Hopkins Marine Station, Pacific Grove, CA: Biomechanic and Physiology of Bluefin Tuna?Hopkins Marine Station, Pacific Grove, CAProfessor Barbara Block,? commitment: 10 weeks / 1 position available?Join our lab team that holds in captivity some large bluefin tuna. Projects will include biomechanics of locomotion, physiology of digestion. Research will entail whole animal biology, engineering, biomechanics and physiology.Photo ID of White Sharks and MantasHopkins Marine Station, Pacific Grove, CAProfessor Barbara Block,? commitment: 10 weeks / 1 position available?We are using photo ID techniques to identify large pelagic predators. In this project we will be building a catalogue of manta and white shark identification files that will enable the team to conduct a census and population survey.Discovering Parasite Species of Sea Otters and Sea BirdsHopkins Marine Station, Pacific Grove, CAProfessor Giulio De Leo, commitment: 10 weeks / 1 position available People thought the CA sea otter population had been hunted to extinction at the turn of the 20th century. A couple decades later, one family of otters was found in Big Sur, and since that time, conservation biologists and many volunteers have brought the population up to 3200 individuals. Unfortunately, the population now is heavily affected by attacks by great white sharks and disease. 50 years ago, conservation biologists began to investigate sources of mortality in the otters and found a parasite of birds, known as a thorny headed worm, in 1% of otters. Graduate student Richard Grewelle, in the De Leo lab, investigates otters and birds along CA coast for this parasite and finds it now in up to 60% of otters. This drastic increase in 50 years must have an explanation, and it is unclear which species of the parasite are finding their way into otters and birds. Genetics provides a path to discover which species are now the source of up to 25% of sea otter deaths in CA. Prof. Giulio De Leo and student Richard Grewelle are seeking an undergraduate researcher to aid in the investigation that will include hands on experience in parasitology, laboratory genetics, and bioinformatics. Previous experience with laboratory genetics or bioinformatics is preferred.Mapping Environmental and Socioeconomic Determinant of Neglected Tropical Diseases in Low Income CountriesHopkins Marine Station, Pacific Grove, CAProfessor Giulio De Leo, commitment: 10 weeks / 1 position available Within the Stanford Program for Disease Ecology, Health and the Environment () and our research line on the ecological levers of health () and the environmental drivers of diseases in South America, Africa and Asia, we will offer a range of internships, especially focused on investigating environmental, ecological and socioeconomic drivers of Neglected Tropical Diseases (NTDs). NTDs, such as amebiasis, Chagas disease, hookworm, leishmaniasis, and schistosomiasis affect more than 1.4 billion people worldwide. Their impacts tend to be greatest among the global rural poor. Controlling NTDs is particularly challenging because of a lack of vaccines that can provide life-long immunity, and the existence of important environmental reservoirs where pathogens persist even as populations are successfully treated for their infections. After mass drug administrations (MDA) of the population at risk, treated people are commonly re-exposed to the parasite or pathogen in the environment, resulting in an endless cycle of treatment and reinfection. Half a billion-dollar worth control effort is directed each year mainly toward MDA, with minimal theoretical understanding of the environmental drivers of disease, the dynamics of elimination, nor of the conditions for optimal, cost-effective intervention. Within this internship we are specifically interested in mapping environmental, ecological and socio-economic drivers of schistosomiasis in Senegal, Ivory Coast, Brazil and Madagascar, a debilitating disease of poverty caused by a parasite of the blood vessels that requires specific genus of freshwater snails to compete its life cycle. Depending upon the specific skill set of the candidate student, this internship will focus on the use of Geographical Information Systems (GIS) to map the determinants of schistosomiasis in one of the countries we work in, develop habitat suitability/species distribution models, use of ordinary differential equations to analyze the dynamics of disease under present climate and future climate changeWe are also working on additional projects at the intersection between conservation and health in Borneo and Uganda, so if you have specific GIS, statistical, modelling, public-health related skills and are interested in any of these topics, please do not hesitate to contact us!Investigating the Extent of Microplastic Pollution in the Monterey Bay EcosystemHopkins Marine Station, Pacific Grove, CAProfessor Jeremey GoldbogenLab Website: commitment: 10 weeks / 1 position available Microplastics are an emerging and pervasive threat to marine ecosystems globally; however, they are understudied in the Monterey Bay ecosystem. The selected student researcher will assist a postdoctoral researcher and graduate student in the Goldbogen Lab with field collections, laboratory preparation, and chemical digestion of baleen whale, anchovy, and water samples. Synthetic particles in the digested samples will then be quantified using microscopy and possibly spectroscopy. There will also be an opportunity to participate in laboratory flow tank experiments that focus on whether baleen can filter plastic debris of different parative Kinematics of Bubble-Net Feeding Humpback Whales in Three Different LocationsHopkins Marine Station, Pacific Grove, CAProfessor Jeremey GoldbogenLab Website: commitment: 10 weeks / 1 position available The goal of this study will be to compare the bubble-net feeding kinematics of humpback whales in three different locations: Southeastern Alaska, Stellwagen Bank, and the Antarctic Peninsula. We will use data from inertial sensing bio-logging tags that quantify energetically relevant movement parameters that relate to prey-capture success of highly maneuverable forage fish.The Role of Stem Cells in Developing Two Body PlansHopkins Marine Station, Pacific Grove, CAProfessor Chris Lowe, commitment: 10 weeks / 1 position available The Lowe Lab at the Hopkins Marine Station seeks a motivated summer researcher interested in the intersection of cell biology, evolution, development, and marine biology. Specifically, a candidate will help investigate how fundamental cell biological processes shape the formation of two body plans. Currently, we understand very little about how the often-dramatic process of metamorphosis transforms the larval body plan into the adult body plan, which can be radically different in organization and cellular composition. We study Schizocardium californicum, an indirect developing deuterostome hemichordate worm, which provides a novel perspective for understanding processes of transdifferentiation, proliferation, and cell death that remodel and reshape the larval body plan. We will use a combined genomics and cell biology to answer the following: given that two life phases of Schizocardium californicum are drastically different, how does development build the larval versus adult body plan?We have recently completed a study in which we identified transcripts specific to proliferating cells, using an irradiation depletion sequencing approach. A motivated candidate will participate in analyzing this data, performing in-situ hybridization to look at the expression of these stem cell candidate genes as well as work to develop methods to knock down these genes. Familiarity with basic molecular biology and cell biology and an interest in evolutionary questions are desire, the only requirement is a strong work ethic and enthusiasm.Evaluating the Role of Mobile Predators in Fostering Coral Reef/Open Ocean ConnectivityHopkins Marine Station, Pacific Grove, CAProfessor Fiorenza Micheli, commitment: 10 weeks / 1 position available This project evaluates the role of large mobile predators such as tunas, sharks, and billfishes in fostering energetic and function linkages between the coral reef and open ocean habitats of Palau, an island nation in the Central Pacific. This study is part of an initiative to establish baseline understanding of interdependencies between Palau’s marine habitats ahead of the establishment of the Palau National Marine Sanctuary which will ban fishing in 80% of Palau’s exclusive Economic Zone. This study uses a variety of techniques including stable isotope analysis of animal tissues to examine the relative contribution of different prey bases to predator diets, analysis of electronic tagging data, and video and diver surveys. This position will involve both lab and computer analyses conducted at Hopkins Marine Station.Reconstructing Biodiversity Change in Monterey BayHopkins Marine Station, Pacific Grove, CAProfessor Fiorenza Micheli, commitment: 10 weeks / 1 position available This project investigates long-term change in marine biodiversity in the Monterey Bay region using a variety of field and lab approaches. The position involves re-surveying intertidal field plots established nearly 100 years ago and monitored since then, using shell growth rings to reconstruct demographic change of mollusks, and analyzing historical documents. This position will involve field, lab and computer work at the Hopkins Marine Station.Trophic Cascades, Mesopredator Release and Reef ResilienceHopkins Marine Station, Pacific Grove, CAProfessor Fiorenza Micheli, commitment: 10 weeks / 1 position available This project evaluates trophic cascades, mesopredator release and coral reef resilience in the Chagos Archipelago, Indian Ocean through a variety of techniques: benthic composition and diversity, stable isotope analysis and herbivore foraging. This position will involve both lab work and computer work at the Hopkins Marine Station.Projects located away from Stanford and/or broad: Collective Behavior in Harvester AntsSouthwestern Research Station, Portal, ArizonaProfessor Deborah M. GordonLab website: commitment: 3 weeks / 3 positions availableOur lab examines how systems work without central control. We will investigate collective behavior in harvester ants, asking how a colony, operating without any central control, regulates its foraging behavior. We will continue a long-term study of the ecology and demography of this population of colonies, and the evolution of colony behavior. Colonies live for 20-30 years, and the location and age of all colonies are known, so that we can study how colony behavior changes as the colony grows older and larger. We will stay at the Southwest Research Station in the Chiricahua Mountains, and go out each day to the field site, about a 20-min drive from the station. Students will participate in observations and experiments, and may get to learn how to mark individual ants with colored paint. This project will be most enjoyable for people who like to be outside and like to watch ants. Genetics and Field Work on Heat Resistant Corals in PalauHopkins Marine Station & PalauProfessor Stephen Palumbi, commitment: 10 weeks / 3 positions available Reef building corals are sensitive to small changes in water temperature, but some colonies survive much higher exposure to heat than others. This project involves the mapping and testing of coral colonies in Palau, Micronesia for heat sensitivity. Students will work in a collaborative working group with faculty, postdocs and graduate students, engaging in field sampling, lab testing, sample preparation and various aspects of work in a remote field setting. The Palau portion will likely last 3-4 weeks. Before and after the field portion, student researchers will work at the Hopkins Marine Station in Monterey on coral genetics, and other laboratory methods.?Understanding Traditional Rain-Fed Agriculture in HawaiiPuanui ahupuaa, Island of HawaiiProfessor Peter Vitousek, commitment: 10 weeks / 2 positions available We will work with community members in the restoration of a traditional intensive agricultural system, and (in consultation with me) develop independent research projects along environmental gradients (rainfall, soil age, or disturbance history) in the region. The independent projects may be agricultural or not, depending on the interns’ interests. ................
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