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STARS 2017 - Research Project Descriptions

The following UC San Diego faculty members have offered to host STARS students in Summer 2017. Identify the department and three faculty mentors with whom you would like to work and describe the research interests for your selection in the online application.

If you have trouble identifying three faculty members, you can also search the department homepages and faculty information here: https://apply.grad.ucsd.edu/departments

Biological Sciences – Cell and Developmental Biology

Eric Schmelz

The Schmelz laboratory has a research focus on biochemical mechanisms that mediate crop plant defenses against insect and pathogen attack. Globally, a significant portion of human protein consumption is in the form of high protein vegetables such as beans. Select legumes in the Phaseoleae tribe including dry beans (Phaseolus vulgaris), black eye peas (Vigna unguiculata) and mung beans (Vigna radiata) naturally ward off herbivorous pests such as caterpillars through the perception of partially digested protein fragments present in the pests oral secretions. Specifically portions of chloroplastic ATP synthase γ-subunits, termed inceptin-related peptides (In), act as extremely potent elicitors of plant defense responses including rapid hormone changes and induced volatile emissions. In the wild, induce volatiles serve as the plant’s ‘cry for help’ by acting as reliable host location signals for predators, parasitoids, and other natural enemies seeking insect herbivores. Contrasting rapid plant recognition and response, further amino acid truncations of inceptin (termed In-A) by legume specializing caterpillars result in the production of antagonists of elicitation and comparatively stealthy pest attack. One prediction of an active evolutionary arms race is that a select subset of legumes may exhibit the added capacity to perceive and activate defenses following contact with In-A.  STARs student mapping and delineation of inceptin and In-A activity in diverse select members of the Phaseoleae tribe is part of a larger project aimed at discovery the inceptin receptor and predicted receptor variants. The long-term vision is to move the inceptin receptor, through either classical breeding or transgenic approaches, into crop plants currently lacking this specific mechanism of insect pest resistance. (Harley Riggleman - Probing how plants recognize insect attack by screening natural variation in elicitor induced defenses to identify genetic resources useful for receptor QTL mapping.)

Julian Schroeder

Julian Schroeder's research is directed at discovering the signal transduction mechanisms and the underlying signaling networks that mediate resistance to environmental stresses in plants, in particular drought, salinity stress and CO2 responses in plants. These environmental ("abiotic") stresses have substantial negative impacts on plant growth and crop yields. These environmental stresses are also relevant in reference to climate change and to maintaining crop growth and food production to meet human needs. Research in Julian Schroeder's laboratory is using multidisciplinary approaches including genetics, genomics, cell signaling, physiological, proteomics, molecular biological and bioinformatics towards uncovering the signal transduction network and receptors in plants that translate drought stress hormone reception, atmospheric CO2 sensing and salinity stress to specific resistance responses in plants. Some of recent research advances are being used in the biotechnology industry with the goal of enhancing stress resistance of plants and improving crop yields. (Samantha Landgrave - CRSP Regulates Stomatal Development in Response to High and Low CO2) (Rachel Darko – Isolation of salt-sensitive mutants through a genomic-scale artificial microRNA mutant pool in Arabidopsis and characterization of salt-responsive phenotype in rack131-1)  (Deborah Fadoju – Arabidopsis Mutant Screening for Phenotype that Confers Resistance to a Small Molecule that Inhibits ABA signaling by Activating Effector Triggered Immunity)

Brian Zid

While mRNA localization is an important and well-studied question during growth and development, it is less clear how it is regulated during more dynamic conditions, such as during stress. Our previous research found that mRNA localization is controlled in a distinct manner during glucose starvation in yeast compared to previously published results, as the localization signal was not inherent to the RNA but instead encoded by promoter elements in the nucleus. This project will explore if there may be general principles of mRNA localization during stress by investigating the control mechanisms of mRNA localization in other stresses. This will involve culturing yeast, cloning, and fluorescent microscopy, to identify whether cis-sequences in the RNA or something outside the RNA controls localization during osmotic stress in yeast. (Tanvina Ria – Control of Messenger RNA localization under stress)

Biological Sciences – Ecology, Behavior, and Evolution

David Holway

Summer research in the Holway lab includes two projects aimed at understanding how climate change affects interactions between plants and pollinators. The first project will use data on native bees collected before the most recent California drought (2011-2012), during the drought (2013), and after the drought (2015 and 2016) to evaluate the effects of this major climatic disturbance on populations of native bees in endangered coastal sage scrub ecosystems. Students will participate in sampling, curating, and identifying bee specimens, as well as learn analytical techniques for comparing pre-drought and post-drought bee assemblages. The second project will investigate how the interactive effects of climate warming and drought affect the bee pollination of squash plants. We will grow squash in the field (at the UC San Diego Biology Field Station) under varying temperatures and precipitation, and monitor daily plant growth, flowering, pollination, and fruit production throughout the summer.  Students will participate in data collection on plant-pollinator interactions and learn techniques to quantify pollinator behavior, pollen transfer and plant reproduction.

Sergey Kryazhimskiy

How do mutation rates change along the genome? Genetic mutations cause cancer and many other diseases, allow viruses like influenza to evade our immune system, and drive adaptation – for example, many bacteria evolve resistance to antibiotics by acquiring certain mutations in their genomes. Why, how often, and where in the genome do mutations happen? We know that mutations are rare random events, such that out of approximately 3 billion base pairs (bp) in the human genome only about 35 bp are usually different between the mother and the child. We also know that some bits of the genome are more likely to mutate than others, but precise estimates of how mutation rates vary along the genome are absent in any organism. We are developing a method for making such estimates in baker’s yeast (because it is easier to work with than many other organisms). A summer student would work on this project together with a postdoc in the lab. They will learn how to work with microbes, how to sequence the genome, and how to analyze sequencing data.

James Nieh

Research in the Nieh lab at UCSD focuses on two areas: honey bee foraging communication and honey bee health.

1.  Honey bee foraging is essential for colony life, and we therefore study how colonies regulate foraging communication at individual and colony levels. Honey bees are superorganisms because they are so highly social that individual bees can function, to some degree, like cells in a multicellular organism. This opens fascinating research possibilities because the behaviour of individual bees can easily be altered to test hypotheses about colonial organization, particularly self-organization. The Nieh lab is currently focusing on how inhibitory communication (the stop signal) helps to regulate colony foraging. Much as a balance of inhibitory and excitatory signaling is necessary for proper brain function, inhibitory signaling is also important in bee colonies. However, we still know very little about such signaling in superorganisms. Help us learn more and understand how complex, cooperative systems self-regulate and deal with intrinsic and extrinsic noise and environmental variability.

 2.  Our lab focuses on two aspects of honey bee health, which has emerged as a major concern. We examine two different factors: pesticides and infection by a fungal-like pathogen, Nosema ceranae. (1) Our pesticide work focuses on how insecticides that target insect nicotinic acetylcholine receptors affect complex bee behaviors like communication and learning. Such pesticides are widely used, and neonicotinoid pesticides are now highly restricted in the European Union. However, relatively little is known about the complex cognitive effects of these pesticides.  (2) Our disease research focuses on how we can activate the honey bee immune system to fight Nosema ceranae, a widespread disease that affects a majority of managed US honey bee colonies. The major treatment for this disease is an antibiotic, but there is evidence that antibiotic resistance is growing. New treatments are needed, and we are studying how immune-priming (analogous to vertebrate vaccination) may provide resistance by activating the Toll AMP pathway.

 

Scott Rifkin

Roundworms are one of the preeminent organisms used for biological research, particularly in genetics, neurobiology, and developmental biology. After hatching from an egg, a worm rapidly develops through four larval stages on its way to adulthood.  However, if conditions are unfavorable, it can pause development or even develop into and persist in an alternative third larval stage for a long time.  We are developing a method for continuously monitoring a worm's development throughout its life.  We will then use this method to compare the developmental rates of different strains and species of roundworms and test the effects of specific environmental conditions such as food restriction, pheromone, and temperature on the timecourse of development.  A summer student would learn to grow and handle worms, learn to extract data from images, and analyze the data statistically to answer questions.

Biological Sciences – Neurobiology

Brenda Bloodgood

Learning requires a select population of neurons to convert transient synaptic signals into long lasting changes in neuronal function.  In my lab we study how the activity dependent transcription factor Npas4 regulates gene expression to facilitate cellular and circuit plasticity associated with learning. Npas4 is expressed in neurons that are highly active and functions to regulate inhibitory synapses that are made onto the active neuron. Potential STARs students would contribute to ongoing studies aimed at identifying the interneurons that form Npas4-regulated synapses and molecules that mediate this plasticity in the mouse hippocampus. This would involve mastering biocytin-DAB reactions, Neurolucida reconstructions of biocytin labeled neurons, immunostaining, and confocal microscopy. The results of these experiments will provide fundamental insight into how activity dependent regulation of the genome alters inhibitory circuity to shape the computations performed within the hippocampal microcircuit. (Grant Higerd - Activity – Dependent Regulation of Inhibitory Circuitry in the Rodent Hippocampus by NPAS4)

Chemistry and Biochemistry

Seth Cohen

The design, synthesis, characterization, and evaluation of new metal-organic frameworks (MOFs) is the goal of this project. MOFs are a class of materials that combine organic ligands and metal ions to generate porous materials with defined topologies. Our focus for several years has been on the development of postsynthetic methods for the functionalization of MOFs. Postsynthetic methods, such as postsynthetic modification, postsynthetic deprotection, and postsynthetic exchange are useful approaches to altering the physical properties of MOFs and generate MOF materials with new properties, including catalytic function. More recently, we have developed an interest in the interface between MOF and polymer materials, including a new hybrid we describe as polyMOFs. (Pablo Quijano Velasco - Synthesis of polyMOF with block copolymer ligand)

Gourisankar Ghosh

My laboratory focuses on two major research areas: 1) investigation of the mechanism of gene regulation by the NF-kappa B (NF-kB) family of transcription factors, and 2) investigation of the role of serine-arginine (SR) family of splicing factors in metazoan pre-mRNA splicing.  Our approach integrates x-ray crystallography, biochemistry and molecular genetics. NF-kB regulation has been the major focus for over twenty years.  We have determined x-ray structures of several protein:DNA and protein-protein complexes relevant to NF-kB signaling.  These structures and correlated biochemical and cell-based studies have helped us to explain how deregulation of NF-kB activity promotes cellular transformation. My research was expanded to include splicing regulation with special emphasis on SR proteins, SR protein kinase and assembly of the spliceosome.  Our works in this area have been instrumental for better understanding of how the phosphorylation and dephosphorylation of the SR proteins facilitate spliceosome assembly at the correct splice sites across the intron. These works emphasize on how the spliceosome assembles on sequences with apparently minimal distinguishable features within the intron and what causes inappropriate assembly that might lead to abnormal cell growth and proliferation. (Chase Musson - Structural Analysis of Immune Signaling Pathway Protein Complex NF-KB p100/RelB) (Crystal Monsale – The Mechanistic Interactions of GST – tagged IkB-gamma, His-tagged Reg gamma, and His-tagged p68 protein)

 

Kamil Godula

Our research lab is interested in developing chemical approaches to study how carbohydrate molecules presented on the surfaces of cells encode biological information. As well, we create new nanotechnology tools to harness the biological functions of these biomolecules to influence cellular functions. One major area of research involves the study of glycoproteins, called mucins. Viruses, such as Influenza A, use mucins to gain entry into host cells. STARS scholars visiting our lab participate in creating nanoscale materials that mimic mucins and use them as a tool to unravel the mechanism through which Influenza A viruses interact with host cells during infection. A second project area in our lab that STARS scholars can participate in focuses on tailoring carbohydrate structures on the surface of stem cells using chemical methods. Cell-surface glycoproteins engage growth factors, which, in turn, trigger signaling pathways involved in the activation of genes and cell differentiation.  By gaining control over the activity of growth factors at the cell surface, we aim to direct the outcome of stem cell differentiation. (Joel Beazer - Use of heparan sulfate proteoglycan mimetics to enhance growth factor signaling in mESCs on cellular microarrays) (Ashley Litton - Synthesis of Epoxide Monomers for Polymerization and Development of Mucin-Like Glycopolymers) (Daisy Monsivaiz – Remodeling the Glycocalyx of Stem cells derived from Embryoid Bodies, using NeoPG’s)

Tadeusz Molinski

The Molinski laboratory studies the chemistry – isolation, structure elucidation and synthesis – and chemical biology of marine natural products. MNPs are organic molecules of highly diverse molecular structures that are produced by marine invertebrates and microbes, and exhibit great potential as drug leads for a range of therapeutic needs, including cancer and infectious disease.

The STARS student will be engaged in discovery, purification and structure elucidation of novel natural products from Porifera (marine sponges) and Urochordates ('sea squirts') or microbes (cyanobacteria).  Expected outcomes include training and acquisition of laboratory skills in analytical and semi-automated ('robotic') preparative chromatography,  nuclear magnetic resonance spectroscopy and mass spectrometry, and associated organic spectroscopic techniques (infrared spectroscopy, polarimetry, circular dichroism), together with design-planning and execution of multi-step organic synthesis for high-yield targeted synthetic compounds that mimic the 'minimum pharmacophores' in biologically active MNPs of more complex molecular structure.  Additional outcomes may include – as happens in the Molinski lab – discovery of totally new molecules from Nature, contributing to preparation of tabulated results for manuscripts, and possible co-authorship on a scientific paper. (Maria Cabrera - Exploring Protease Inhibition in Natural Products Isolated from Marine Sponges) (Kyle Planck - Isolation of Bioactive Natural Products from Marine Invertebrates) (Jocelyn Macho – Isolation of Antifungal Terpenes from Marine Spongers)

Joseph O’Connor

The goal of this work is to develop a radically new approach to cancer therapy based upon metal-containing drugs that will destroy tumor cells by perturbing iron homeostasis within the cells. This laboratory experience will involve the synthesis, isolation, purification and study of novel organoiron complexes.  As a prerequisite the student should have at least one undergraduate laboratory course, preferably an organic chemistry laboratory course.  The student will learn modern laboratory techniques for the synthesis, isolation, and characterization of organometallic molecules.  Hands-on experience will be gained in the use of NMR, IR, and UV-vis spectroscopy for the characterization of molecules.  The student will also be introduced to characterization methods such as high resolution mass spectrometry and X-ray crystallography. (Bernardo Jordan - Cycloaromatization of Dienynes and Enediynes via Thermal Activation by Halogenated Solvents) (Ornella Mboning - Synthesis and Characterization of Benzoyl ferrocenes Derivatives) (Christian Sanchez, Austin Roberts)

Francesco Paesani

The Paesani group is interested in developing new theoretical methods and next generation software at the intersection of quantum chemistry, statistical mechanics, and computer science to model complex molecular systems. The methodologies developed by the Paesani group have recently been recognized with the Early Career Award in Theoretical Chemistry of the American Chemical Society. Current research projects include the modeling of chemical processes at interfaces for applications in materials research, energy, environmental chemistry, and biophysics. STARS students can be involved in: 1) Molecular simulations of salt solutions in porous materials for water desalination, 2) Computer modeling of proton conduction in metal-organic frameworks for fuel cell applications, 3) Calculations of linear and nonlinear multidimensional vibrational spectra of water around biomolecules.

STARS students will acquire a solid foundation in theoretical, physical, and computational chemistry. The interdisciplinary nature of all projects provides an extraordinary opportunity to establish bridges and inter-connections between fundamental laws of physics and the properties of molecular systems. STARS students will learn how to apply their knowledge of fundamental principles to the development of new theoretical and mathematical models for describing molecular processes as well as how to implement these models into efficient computer codes using modern programming techniques. The possibility to work at the interface of different disciplines will prepare STARS students for a wide range of scientific careers and will significantly broaden their scientific background and enhance their competitiveness in today’s computer-driven job market.

 (Gerardo Campos Villalobos - Structure, Dynamics and Vibrational Spectra of Water layers on Graphene) (Geovani Montoya – Many-Body Molecular Dynamics Simulations of Ionic Solutions)

Kim Prather

As part of the Center for Aerosol Impacts on Climate and the Environment (CAICE), the Prather Research Group is involved in a variety of projects centered on understanding the production and climate impacts of sea spray aerosols (SSA). With the invention of the Marine Aerosol Reference Tank (MART), focused lab studies on the chemistry of nascent sea spray aerosols are now possible and currently being pursued. Examples of lab experiments in our lab include:

  • Chemical characterization of sea spray and seawater during phytoplankton bloom mesocosm experiments: identifying chemical and biological changes in seawater that lead to changes in SSA composition
  • Heterogeneous reactivity with nitric acid and cloud-nucleating ability of lipid-containing aerosols
  • The impact of enzymatic activity on the chemical composition, phase, morphology, and reactivity of sea spray
  • Understanding the surface properties and dynamics of single-surfactant monolayers and bubble interfaces

(Ramon Gonzalez Perez – Investigation of Marine Secondary Organic Aerosol Formation)

Alina Schimpf

The development of high-surface-area functional materials is advantageous for many emerging technologies including adsorption, catalysis, energy conversion and storage, and drug delivery. Inorganic frameworks composed of polyoxometalate clusters linked by transition metals offer access to ternary metal oxide compositions not readily accessible via other synthetic strategies. We aim to exploit this synthetic versatility to design porous metal oxide semiconductors with precisely tunable electronic properties. One strategy for tuning the material properties will be to change the transition-metal linker. The goal of the undergraduate researcher will be to determine the synthetic conditions (precursor identity and concentration, pH, ionic concentration, solvent identity) necessary promote the growth of frameworks with various transition metals. The materials produced will be characterized using electronic absorption spectroscopy and x-ray diffractometry.

Wei Wang

My group is working on computational epigenomics. Potential projects include analysis of transcriptomics data and histone modification data in human and mouse to understand epigenetic regulation in development.

Wei Xiong

There are great interests in surfaces and interfaces, because of their ubiquitous potential applications to fields such as heterogeneous catalysis, biocompatibility, adhesion, antifouling, and surface charge transfer. Among techniques to mimic the surface environments, self-assembled monolayers (SAMs) provide a method to synthesize organic surfaces with known, reproducible structures, thus are widely used in forming organic surfaces on metal or metal oxide substrates. Critical properties of SAMs, including surface coverage, packing density, wettability, and electrical resistance are all related to molecular orientation on the surface. In this project, we are interested in synthesizing the SAMs of different organic thiolates on transition metal surface (primarily Au and Ag) and study the surface orientation of molecules with infrared reflection absorption spectroscopy at different incoming light polarization. Infrared spectroscopy characterizes the vibrational transitions of surface molecules. When using different polarization incident light to characterize the vibrational modes, their absorption intensities vary as a function of polarization, from which we are able to extract the tilt angle of vibrational modes to surface normal and thus determine the surface orientation of molecules. Students will get a great chance to practice the synthesis of SAMs, and gain instrumental skills to characterize them, like the operation of FTIR and the interpretation of IR spectra. Students will also learn post-experimental data analysis with Matlab. (Eduardo Gutierrez Lopez- Adsorbate-Substrate Interaction in Metal Surface Functionalization Employing Molecules with Thiol Group.)

Joel Yuen-Zhou

The Yuen-Zhou group is devoted to research at the interface of chemistry, physics, and materials science. Our present theme of research is "molecular photonics". Summer students in our group will work on constructing toy models for materials that can transport nanoscale light or charge in controlled manner, recreating ideas from "topological insulators" in the context of soft-materials. The students will have a strong background in physics (quantum mechanics at the level of the textbook by Griffiths, statistical mechanics at the level of the textbook by Reif), mathematics (differential equations, linear algebra), and should have basic programming skills.

Brian Zid

While mRNA localization is an important and well-studied question during growth and development, it is less clear how it is regulated during more dynamic conditions, such as during stress. Our previous research found that mRNA localization is controlled in a distinct manner during glucose starvation in yeast compared to previously published results, as the localization signal was not inherent to the RNA but instead encoded by promoter elements in the nucleus. This project will explore if there may be general principles of mRNA localization during stress by investigating the control mechanisms of mRNA localization in other stresses. This will involve culturing yeast, cloning, and fluorescent microscopy, to identify whether cis-sequences in the RNA or something outside the RNA controls localization during osmotic stress in yeast.

(Tanvina Ria – Control of Messenger RNA localization under stress)

Cognitive Science

Gary Cottrell

We will be looking for undergraduates who can program, and are interested in working with a group that does machine learning/cognitive science. The set of projects in our lab are always in flux, but they generally involve training neural networks, designing human subjects experiments on amazon mechanical turk, and/or making cognitive models. (Vijay Chaudhary - Fine-grained categorization using a bottom up attention model) (Jacqueline Castro – Measuring Object similarity Mapping Emotional Faces and Words, Lisa Garcia)

Seana Coulson

Project 1: Gesture is a prominent feature of face-to-face communication, but researchers have only just begun to explore the cognitive and neural basis of gesture comprehension. Research in our lab has shown that people vary in their ability to take advantage of the information in co-speech gestures and related some of that variability to working memory capacity. We hypothesize that kinesthetic working memory, that is, a memory system for encoding body movements, is also important for gesture comprehension. The proposed project will compare the importance of verbal and kinesthetic working memory for gesture comprehension in a dual task paradigm in which the primary task is gesture comprehension, and the secondary task involves memory for either verbal (a linguistically encoded series of digits) or kinesthetic information (arm and hand postures). Results will reveal the relative importance of these different working memory systems in gesture comprehension, and have implications for education.

Project 2: Little is known about the cognitive and neural basis of gesture comprehension. Research in our lab, however, has shown that people vary in their ability to take advantage of the information in co-speech gestures and related some of that variability to visuo-spatial working memory capacity. The proposed project will measure participants event-related brain potentials in a dual task paradigm in which the primary task is gesture comprehension, and the secondary task involves memory for visuo-spatial information (a sequence of dot locations in a grid). By identifying the EEG indices of gesture comprehension under varying degrees of visuo-spatial memory load, these results will enhance our understanding of exactly how brain systems involved in gesture comprehension recruit visuo-spatial processing resources. (Karen Garcia - Verbal working memory and gesture comprehension: An event-related potentials (ERP) study) (Ashlynn Duncan - The role of kinesthetic and visuo-spatial working memory on gesture comprehension)

Gedeon Deak

The Cognitive Development Lab (cogdevlab.ucsd.edu) investigates social development and learning in infant-parent, child-parent, and adult-adult dyads. We integrate EEG, ECG (cardiac dynamics), motion-capture, and video-behavioral data to discover brain-behavior dynamics during social exchanges such as game-playing, object exploration, and problem solving. One of our goals is to discover the action contingencies nested in parents' natural behaviors that serve as a teaching signal for infants. Another focus is to reveal how brain cortex responses to expected or unexpected events, like rewards or feedback, affect collaborative interactions. Student researchers may be involved with data collection or data coding and analysis, and will gain familiarity with one or more of the following methods: EEG, ECG, eye gaze tracking, machine coding of human action, micro-behavioral analysis, or motion tracking. Upper-division coursework in neuroscience, biology, and/or human development is required; familiarity with Matlab or Python is preferred. (Vanessa Carlos)

Eran Mukamel

Analysis of gene expression regulation in the developing brain.  Our lab’s goal is to understand how healthy brain cells develop during early life, and how disruption of that developmental process can lead to neuropsychiatric disorders.  To do this, we are focused on the brain epigenome, a set of molecular modifications to brain cells’ genetic material that enable fine-tuned regulation of their behavior. By using statistical and computational methods to analyze large sets of genomic and epigenomic data, we test hypotheses about the roles of specific epigenetic modifications in brain function.  This project will involve analysis of RNA-Seq and/or DNA methylation data sets collected from mammalian brain cells.  The student should have some background in computer programming and/or analysis (e.g. Matlab, Python or R); knowledge of genome biology is desirable but not necessary.

Education Studies

Thandeka Chapman and Makeba Jones

The K-12 Ethnic Studies Movement in California seeks to embed Ethnic Studies curricula at all grade levels. In San Diego, the San Diego Unified School District Board of Education approved of a resolution to incorporate Ethnic Studies across K-12 curricula in the district. A pilot 9th grade course is currently being taught at one high school that serves a low-income community primarily comprised of African American and Latinx families. Professors Makeba Jones and Thandeka K. Chapman from the Department of Education Studies are conducting an evaluation of the course. Our guiding research question is “What impact did the Ethnic Studies pilot course have on student performance, mindset, and critical understanding.” We are collecting a range of data from approximately 100 participants - academic and behavioral outcomes such as grades and attendance, student focus group interviews, parent interviews, and all student assignments. We are requesting two undergraduates to work on analyzing the multiple sets of data. This is a great opportunity to learn how research analyses can impact what happens in classrooms and in schools that serve students of color. Undergraduate applicants should be interested in learning more about social science research, race-based theories of research, and equity and access for students of color in education. Undergraduates interested in issues of equity and education reform will find the experience powerful.

Beth Simon

EDS is looking for undergraduate researchers to help conduct research on a new software platform for educating kids under 13 in creating, sharing, and collaborating on digital artifacts, focused around coding. Though there is research on teaching and learning in the digital space for middle school and high school students, focusing on elementary aged students who are underserved is lacking. STARS students will have the opportunity to participate in ongoing research around engaging children under 13 in a safe, online community, promoting learning, and enhancing collaboration techniques with popular coding software, such as Scratch. Furthermore, STARS students will have the opportunity to work with a GitHub engineer to enhance the software platform based on research findings. 

Ethnic Studies

Ross Frank

Dr. Frank works broadly on Native American, history, culture, and epistemology.  One of my research projects is with Plains Indian Ledger Art (plainsledgerart.org), and I also do work with the Kumeyaay, Luiseño, Cupeño, and Cahuilla tribes/bands/nations in the San Diego area today.  I am interested in representation of Native American through material culture - items that Native American communities produced and still produce, and that also leads me to Museum studies. (Sedna Villavicencio - Decolonizing the Museum of Man: A History of Museums, Anthropology and Racism of American Indians)

         

Jacobs School of Engineering (JSOE) - Bioengineering

Karen Christman

For more information about Dr. Christman’s research, please visit: http://christman.eng.ucsd.edu/research

(Gerardo Sandoval - Processing Soluble Extracellular Matrix with Greater Yield and Practicality) (Corina Espelien – Delivery of siRNA by injectable  hydrogels, Julian Garcia – The Synthetic Poly-ethylene glycol)-oxime Hydrogel Does not Exhibit Cytotoxicity or Cellular Interaction, Stacy Van, Gustavo Chata)

Francisco Contijoch (PI Elliott McVeigh)

The Cardiovascular Imaging Laboratory (cvil.ucsd.edu) uses medical imaging such as MRI and CT to improve our understanding of cardiovascular physiology, improve diagnosis of patients, and help monitor disease progression and responses to treatments. We recently developed a techniques to measure myocardial function in a novel way and are interested in comparing the results of this technique with other  standard measures of function. The student would measure both new and standard measures of function in clinically acquired images to explore the potential of this method to improve clinical care. The datasets will include patients with normal function as well as patients with a variety of cardiovascular diseases including myocardial infarction, congenital heart disease, and aortic valve stenosis. This project could advance our understanding of these disease as well as a result in a new way for clinicians to evaluate their patients.

Adam Engler

Cancer cells within a tumor or a cell line in culture are very heterogeneous. They exist in different states and only a small fraction are able to form secondary tumors. Biological markers that clearly identify these cells are limited, which complicates their isolation and further study. However using physical rather than biological characteristics, we have identified cation-mediated changes in attachment strength between metastatic and non-metastatic mammary epithelial cell lines over a concentration range found within tumor stroma. Metastatic cells exhibit remarkable attachment strength heterogeneity only in stromal-like conditions, unlike their non-metastatic counterparts who exhibit stronger, cation-insensitive attachment. This heterogeneity is the result of increased sensitivity to cation-mediated focal adhesion disassembly in metastatic cells. Less cation-sensitive metastatic cells maintain their phenotype over several days in culture but stochastically repopulate the entire attachment strength range within one month. This metastatic subgroup also exhibits less migratory and invasive behavior, similar to non-metastatic cell lines. As with adhesion, they regain invasiveness after 2 or more weeks due to stochastic state transitions. Attachment strength heterogeneity and phenotypic stochasticity was observed across multiple cancer cell lines (mammary and prostate), suggesting that attachment strength may serve as a general marker of highly metastatic cells. (Leigha Jarett – Effects of six growth factors on the proliferation and differentiation of human skeletal muscle progenitor cells)

Juan Carlos Lasheras

Neutrophil migration is essential for effective immune responses to injury or infection. Although many studies have focused on the molecular signaling pathways involved in neutrophil migration, the cell shape changes necessary for the process to occur have not been fully characterized.  To address this, the proposed summer project is focused on investigating changes in neutrophil morphology during 3-dimensional neutrophil migration. The student will learn techniques in cell culturing, confocal & fluorescence microscopy, biomaterial fabrication, and image processing. Results from this study will provide insight into the different morphological phases of neutrophil cell motility in confined environments.

Robert Sah

The goal of the Cartilage Tissue Engineering (CTE) lab is to improve the treatment, diagnosis, and prevention of musculosksletal maladies asssociated with growth abnormalities, injury, or aging, through answering scientific questions and developing engineering solutions related to cartilage. Our research focus areas are the biomechanics and mechanobiology of the cartilage in the synovial joints and also in the growth plate. Our studies of human joints, tissues, and fluids seek to delineate the natural sequence of events. Our studies of tissue models examine the mechanisms by which mechanical, chemical, and biological factors modulate cartilage metabolism, and lead to tissue growth, maintenance, or deteriration. Our studies of engineered tissues, targeting cartilage, bone, and their interface, seek to develop translatable fabrication methods and treatments for damaged cartilage and provide a platform for understanding disease and testing interventions. Our studies of engineered fluids seek to understand the physiology of the lubricating and regulatory nature of synovial joint fluid. Our studies of pre-clinical and clinical translation seek to determine whether and how engineered materials can effectively treat damaged cartilage. We use a variety of methods, including those of biomechanics, mechanobiology, tissue engineering, regenerative medicine, imaging, image processing, molecular biology, cell biology, biochemistry, bioreactor engineering, and bioseparation engineering. (Takeyah Campbell - Vascular Transport Pathways in the Epiphysis using Digital Volumetric Imaging; James Karchner - Tracking Cells for Bone Repair) (Juan Pham – Comparison of cartilage repair in the knee joint between empty osteochondral defects and autografts, Jenny Muan – Determining the Effect of Sliding, Loading, and Lubricant of the Articular Cartilage Wear on the Rabbit Hemi-Condyle, Elelbin Ortiz)

Peter Wang

Live-cell imaging and analysis are important in biomedical research and applications. In our research, we have developed Fluocell for the visualization and quantitative analysis of target molecular activities in live cells. Fluocell is specifically designed for the quantification of time-sequence and multi-channel FRET image data. It has been widely applied to the quantitative analysis of molecular live-cell assays. Further optimization of Fluocell functionality is also desired. For example, Fluocell can be improved to allow tracking and quantification of multiple objects during the time course of imaging. Undergraduate researchers are needed to assist on applying Fluocell for the quantitative analysis of FRET imaging results obtained in our lab, as well as programing in MATLAB to further improve the functionality of Fluocell. (Christopher Blackburn – EGFR/PDGFR Internalization Kinetics of Fyn Kinase Downstream Activation Pathways Constructed in an ODE Model using MATLAB)

Jacobs School of Engineering (JSOE) - Computer Science and Engineering

Vineet Bafna

I have many projects in 'personalized genomics', relating to the mining of genetic information to better inform about diseases, and genetic health. Students should be comfortable, or willing to learn Python.

Jacobs School of Engineering (JSOE) - Electrical and Computer Engineering

Massimo Franceschetti

The project concerns signal analysis and software development in conjunction to musical signal processing. The student will learn applications of the theory of Fourier transforms and spectral analysis related to the analysis of musical signals. The project is open ended and input from the student is welcome. Ideally, the student will develop a set of examples showing application of the theory learned in class to real signals. The student could explore similar material taught in the music department and come up with methods from engineering that may help develop such material further. This project will serve the student as preparation for research in signal analysis, develop mathematical skill, and understand their application to real systems. As a pre-requisite the student should have taken and be excited about the class ECE45 (circuits and systems) at UCSD or an equivalent class in signals and systems at another college/university.

Tara Javidi

Project 1: The innovative use of spectrum sensing for cognitive radio is a methodology that aims to meet the demand for higher data rates in wireless communications by opportunistically exploiting traditionally under-utilized spectral resources. In wireless communication networks, primary users are allocated and licensed to occupy a frequency spectrum. In reality, these primary users occupy less frequency bands than those allocated, thereby leaving valuable spectrum unused. This is where cognitive radio technology comes in, detecting the underutilized spectrum holes, and opportunistically filling them with secondary (non-primary) users.  In order to minimize interference between primary users and secondary users, spectrum sensing for cognitive radio involves the fundamental problem of determining whether a frequency band is available or not, before it can occupy it. Multi-band spectrum sensing has traditionally offered a solution that efficiently detects these spectral opportunities by simultaneously searching multiple spectral frequency bands in sub-channel groups. This research project explores a further optimization of multi-band spectrum sensing for cognitive radio by making connections to the literature on group testing and noisy search. Results can be obtained by creating a simulation program on Matlab, and plotting the results. Ongoing research for this project includes adaptation to a multi-target search, and research on a time varying, or moving, target as well. 

Project 2: A Lightweight Low-Energy sYstem for disruption tOlerant sOcial message Passing (AlleyOop) is a secure delay tolerant social networking application written in Swift for iOS which allows users to communicate when Internet is slow or non-existant. The application serves as a testbed evaluator for delay tolerant and ad hoc networking protocols. AlleyOop also allows nodes to post messages to notable social media platforms such as Facebook and Twitter, when Internet is available. Social interactions, message delivery statistics, and locality will be captured by AlleyOop Social and compared to simulations results. An “alley-oop” in basketball is a play in which one player throws the ball near the basket to a teammate who jumps, catches the ball in mid-air, and immediately puts the ball in the hoop. The alley-oop combines elements of teamwork, pinpoint passing, timing and finishing. In a similar way, the AlleyOop Social app allows socially associated users to knowingly, or unknowingly, behave as a team to deliver messages. The sender broadcasts encrypted messages, and when near other users, the other users catch the message and assist in delivery to the destination. A summer researcher will assist with networking protocol implementation, user interface (UX) design, as well as evaluation of protocols.

(Julian Land – Noise simulation: visual target search a with noise dependent observations for adaptive and non-adaptive methods)

Yuhwa Lo

Investigate the imhomogeneity and diversity of biological systems including tumors and neural disease samples with a resolution at the single cell level.  Will relate the phenotype and genotype to help identify their connections and cell behaviors and effects on disease formation and progression.  A variety of engineering technologies involving nanotechnologies will be employed for such studies.

Siavash Mirarab

Phylogenetic trees show how species have emerged from common ancestors through millions of years of evolutions. Scientists are now able to reconstruct these evolutionary histories, the so-called tree of life, by studying the DNA of present-day organisms. The inference of phylogenetic trees is a computational task and modern phylogenetics draws on ideas from diverse fields, such as discrete math, algorithmic design, statistics and probabilistic inference, graph theory, and more. In this project, we will implement new algorithms or improvements to existing algorithms for phylogenetic inference. The project will involve implementing new algorithmic ideas, testing them in simulation studies, and participation in analyses of real biological datasets. Ideal candidates would have a good background in programming; advanced programming skills will also be helpful. Background in biology is not required, but interest and ability to learn are both essential.

Tina Tse Nga Ng

This project aims to develop short-wavelength infrared photosensors by using a new generation of narrow bandgap conjugated polymers. The polymer semiconductors are processed by solution processing techniques and allow printing deposition to bypass the limitations of die transfer and bonding in conventional devices. The proposed research will involve fabrication of photosensors and device characterization to identify the fundamental constraints in the exciton dissociation and charge collection processes as polymer bandgaps are reduced. The resulting knowledge will be applicable not only to infrared sensing applications but also to other areas including photovoltaics and optical communications, and will be essential to theoretical efforts to rapidly predict better photo-active polymers. (Carolina Salinas - Near-infrared photodetectors, based on low cost flexible organic semiconductors)

Michael Yip

Project 1: Surgical assistants wearing the augmented reality headsets will be able to see “under the skin” during minimally-invasive surgery through registered stereo-endoscopic images controlled by the surgeon. Registered, 3D CAD overlay of instruments will provide accurate poses of instruments normally obstructed when inserted through the ports in the body. With holographic views of the inner cavities and surgical instruments available to surgeons and the assisting surgical team, we expect to see significant improvements in coordination of tasks, improved environmental understanding, safe instrument handling. Mixed-reality therefore can provide the compelling visual feedback for improving how operating surgeons work cohesively as a team. Students with strong CS backgrounds / computer vision experience are encouraged to apply.

Project 2: We will be designing and building a highly-articulated, snake robot, with the aim that this will be used for colorectal endoscopy. Currently, this procedure is performed using handheld endoscopes, with a simple bending articulation of the tip of the device. Without direct control of the full shape of endoscope, the devices tend to push and scrape against colon walls. This can lead to loops forming on the endoscope, resulting in distension and visceral pain. The proposed work will involve designing, building, and testing a robot with snake-like robotic spines that can match the complex shape of the colon anatomy as you insert it into the body. Students with strong ME or robotics backgrounds are encouraged to apply.

Project 3: Haptic feedback for surgical procedures, in conjunction with visual and auditory feedback, provides a natural, immersive environment for minimally invasive procedures. Haptic feedback has furthermore been shown to improve performance for teleoperated robotic laparoscopy, reducing the learning curve for surgeons, improving accuracy, and better-regulating interaction forces with tissue. Currently, minimally-invasive surgery is unable to provide haptic feedback to the clinician, who is then forced to use only visual feedback. This project involves developing a new method for measuring and returning haptic feedback to surgeons, using a combination of embedded sensors and machine learning algorithms. Students will be involved in designing, building, implementing, and testing these sensors, as well as implementing machine learning algorithms for them.  Reintroducing haptic feedback to MIS surgeons would significantly improve their abilities to identify lesions, manipulate soft tissues, and recognize constrained instruments, thereby improving their ability to perform surgical tasks more effectively and accurately, reduce surgical margins, and improve clinical outcomes. (Josh Henry - Electronic Braille display using super-coiled polymer actuators)

Jun Zhang (PI Michael Yip)

Robotic artificial muscles are ideal actuators for applications in safe human-robot interaction, biomimetic robots, and robot prostheses and orthoses. They offer a balance of actuation performance, power-to-weight ratio, and inherent compliance in form factors not observed in any other type of actuator science. However, their full utilization is often challenged by limited strain and relaxation speed. The super-coiled polymer (SCP) actuator is a recently discovered artificial muscle that demonstrates significant mechanical power, large contraction, and good dynamic range in a muscle-like form factor. There has been a rapid increase of research efforts devoted to the study of SCP actuators. However, since SCP actuator is a recent discovery, it is still not clear about how to design and control SCP-actuated robots. In this study, we will work on designing, testing, and control of an SCP-actuated mobile robot. The student will work with a postdoctoral researcher and other undergraduate students along this research line. The expected methods require knowledge about CAD, 3D printing, circuit and PCB design, real-time data acquisition and processing, and control systems. More knowledge about Mechanical Engineering and Electrical Engineering will be helpful. We will first review existing papers and propose design ideas. In order to make the robot, extensive work on circuit and prototyping will be needed. Furthermore, the system will be tested by working on real-time data analysis and implementation. Feedback control will be employed such that the system will produce desirable movements. This work would enable roboticists to design and control artificial muscle-powered robotic systems.

Jacobs School of Engineering (JSOE) - Mechanical and Aerospace Engineering

Jorge Cortes

Work on distributed robotics at the MURO Lab (http://muro.ucsd.edu) designs, analyzes, and implements motion planning strategies and distributed coordination algorithms on multi-robot networks performing

spatially-distributed tasks. We have a set of ground (Turtlebots) and aerial (Parrot quadrotors) vehicles, and we rely on methods from graph theory, dynamics, and control combined with open source software

programming.  Several project opportunities exist to enhance the range of current capabilities in the lab. These include the implementation of distributed methods for self-localization with onboard cameras, 3D formation control strategies with heteregenous teams, and human-swarm interaction structures that enable rapid deployment of robot teams. (Ashim Neupane - State Optimization using Extended Kalman Filter; Bryan Yang - Quadcopter Control Systems - Sliding Mode Controller with Auto-Tuning PID Controller)

Antonio Sanchez

The safe storage and transportation of reactant gas mixtures requires conditions that ensure a negligibly small reaction rate, achieved in storage vessels and transport pipes by lowering sufficiently the wall temperature. The seminal investigation of this problem is due to Frank-Kamenetskii (FK}, who studied a reacting mixture undergoing an exothermic chemical reaction in a centrally symmetric closed vessel with constant wall temperature. The results of the FK analysis associated with the storage of reactants will be extended here to investigate safe transport in pipes, where the temperature is governed by the competition of the heat released by the chemical reaction and the heat losses to the wall, characterized by a Damkohler number D. A slowly reacting flameless mode of combustion is found for values of D below a critical value Dc,  when the heat losses to the wall are able to limit the temperature rise, in such a way that the reaction rate does not change in order of magnitude from its near-wall value. Since the overall heat-release rate is proportional to the volume of reacting gas while the heat-loss rate to the wall is proportional to the wall surface, for a given wall temperature there exists a limiting size, corresponding to a critical value D=Dc, above which a slow reaction cannot be maintained, and is replaced by a localized temperature runaway that leads to the formation of a flame. Ignition events will be analyzed to determine the explosion distance for supercritical cases D>Dc, as well as the slowly reacting mode of combustion established downstream the transition region in subcritical configurations with D<Dc. Unlike the classical FK analysis, our investigation will employ realistic ignition chemistry for hydrogen-air and methane-air mixtures. The student will become familiar with the conservation equations governing chemically reacting flows. The work will involve numerical integration of ordinary differential equations, which will be performed with use made of MATLAB. The research is expected to both increase fundamental understanding and provide quantitative information of interest in connection with safety aspects of fuel transport. (Miguel Becerra - On the Effects of Buoyancy–Driven Motion on the Ignition Limits of Gaseous Reactive Mixtures in Porous Media)

Juan Carlos Lasheras

Neutrophil migration is essential for effective immune responses to injury or infection. Although many studies have focused on the molecular signaling pathways involved in neutrophil migration, the cell shape changes necessary for the process to occur have not been fully characterized.  To address this, the proposed summer project is focused on investigating changes in neutrophil morphology during 3-dimensional neutrophil migration. The student will learn techniques in cell culturing, confocal & fluorescence microscopy, biomaterial fabrication, and image processing. Results from this study will provide insight into the different morphological phases of neutrophil cell motility in confined environments. (Lidia De Barros – Investigating the migration of leukocytes in confined environments)

 

Michael Tolley

Project 1: Soft pneumatic actuators (SPAs) are an alternative to rigid actuators such as motors. Structurally, they expand like balloons, but are fabricated to produce a force or torque. SPAs are typically made out of silicone elastomers, and may be able to support more mass by incorporating a bioinspired, bone-like structure. The goal of this research is to determine if we embed bone-like structures into SPAs, will the resulting force and torque increase compared to bone-less SPAs? This research is important to identify what parameters optimize the force, torque, displacement, and bend angle produced by SPAs with structural reinforcement. The STARS student will be designing, fabricating, and characterizing SPAs. Recommended Experiences: SolidWorks, or similar CAD.

Project 2: Artificial muscles are a key component of bioinspired, soft robotics. Our lab is developing dielectric elastomer actuators (DEAs) to serve as muscles for soft robotics. Layers of stacked DEAs are well-suited for artificial muscles due to their fast response time and high efficiency. Two key issues in fully utilizing DEAs for soft robotics are the high voltages required to stimulate actuation and the ability to fabricate many identical, defect free layers of actuators. Our lab is drawing upon advances in microfabrication to address these issues by utilizing spincoating and laser cutting to form and pattern multiple, thin layers of DEAs for robust actuation in soft robotic systems. The goal of this research project is to design, fabricate, and characterize a stacked DEA that can actuate a limb for a soft robot.

Nathan Adera - Soft Torsional Sensor for Emedding into Artificial Skin) (Alejandra Martinez – Light Tensegrity Systems)

Jacobs School of Engineering (JSOE) - NanoEngineering

Zheng Chen

Advanced technologies for efficient energy generation, storage and utilization is essential to mitigate the global energy challenge. Traditional energy materials and devices have approached their limits, while higher capacity and efficiency, longer lifetime, and reduced cost are needed for future applications (e.g. electric vehicles, smart grid). Next-generation batteries such as Li-metal and Na-metal batteries hold great promise because of their significantly improved energy density (by 3~6 times) compared with today’s Li-ion batteries. However, the use of new materials and new chemistry poses great challenges in terms of cycling stability and safety. This project will involve electrode preparation and electrochemical measurement to study different functional materials (nanostructures, polymers) for Li-metal and Na-metal batteries. The goal of this research is to understand the basic electrochemical phenomena and design advanced metal batteries for improved cycling stability and safety properties.

Shirley Meng

Please see Dr. Meng’s website for research projects: http://smeng.ucsd.edu

Kesong Yang

Hybrid organic-inorganic perovskites based on the metal halides have emerged as one class of promising light-harvesting materials for the next-generation solar cells because of their exceptional properties such as an appropriate band gap, high absorption coefficient, long carrier diffusion length, and high carrier mobility. A number of theoretical efforts have been made to interpret the underlying mechanism of the high power conversion efficiency in this class of materials, though a full understanding of its working mechanism is still not fully achieved. This project aims to elucidate the surface and defect properties of organohalide perovskites such as CH3NH3PbI3 using first-principles electronic structure calculations, within the software package Vienna Ab-initio Simulation Package (VASP). The outcome of this project will be able to address the fundamental surface and defect-related materials properties, yield several fundamental materials design principles and engineering strategies for achieving long-term stability and high performance in the organohalide perovskite-based solar cells.

Jacobs School of Engineering (JSOE) - Structural Engineering

Veronica Eliasson

In this project the STARS student will work alongside a Structural Engineering PhD student on an experimental project. The goal of the project is to understand fracture initiation and propagation in polymeric materials of interest to a variety of naval applications. For example, a ship will experience highly dynamic loads due to wave slamming events, and therefore one must understand how new types of materials behave under extreme loading conditions. Furthermore, it is important to know if a material degrades or not when it has been in contact with seawater for an extended time period. High-speed photography will be used to study how the fracture behaves as the sample is impacted with a projectile launched from a gas gun. The samples will be conditioned in seawater for extended durations before the impact experiment. Different visualization techniques will be incorporated to study the fracture behavior and therefore it is a benefit if the STARS student has an interest in photography and hands-on work. A plus if the STARS student is somewhat familiar with Matlab.

Ken Loh

The aim of my research is to engineer multifunctional materials that can safeguard critical structural and human assets. Our approach is to develop new materials, which often involve the use of nanomaterials and scaling them up to large-scale manufacturing and applications. These materials are engineered to possess different functionalities such as sensing, actuation, and/or energy harvesting. As part of this effort, we also develop and implement computational schemes and signal processing techniques that can enhance the capabilities of these materials. The purpose of doing so is to detect damage or defects in materials or simply to gain a better understanding of the structure (in the most general sense) being monitored. For example, we have investigated carbon nanotube-latex paints that can be applied onto bridges, aircrafts, and/or naval vessels that can pinpoint the location and severity of damage due to cracks or corrosion. Another example is to develop flexible fabric-like material that can monitor the performance and physiological well-being of humans, such as first-responders, patients, or military personnel. I'm hoping to recruit students that are interested in working on hands-on experimental research (fabrication/testing of new materials) or to conduct numerical studies (modeling or implementing signal processing algorithms). 

(Jonathan Ambrose Torres - Multifunctional and Self-Sensing Soft Robotic Structures)

 

Pharmacology

Nicole Purcell

My research focuses on the role of PHLPP in pathophysiological disease processes, in particular, cardiac hypertrophy and stroke. We have found that a newly discovered phosphatase, PHLPP, negatively regulates Akt activity and survival in the heart. My research focus is to further understand through removal of PHLPP, its isoform specificity for Akt and target substrates following cardiac injury and regeneration and determine the potential for PHLPP as a target for therapeutic strategies to improve cardiac function. Studies in this area use in vitro cell culture systems (i.e. NRVM, AMVM and cardiac stem cells) and in vivo transgenic and knockout mouse models for phenotypic and morphometric analysis of cardiac hypertrophy and failure at baseline as well as after cardiac interventions (i.e. TAC, MI and I/R). A second area of interest in my laboratory involves investigating the role of PHLPP in astrocyte signaling and cerebral ischemia.  In the course of a stroke, the brain is highly affected by the loss of oxygen, glucose, and other nutrients, which in turn, initiates intracellular signaling cascades that are both deleterious and beneficial to the brain.  This project uses PHLPP gene-targeted mice and primary astrocytes to investigate novel mechanisms associated with signaling pathways leading to cell death and in particular the hypothesis that astrocyte viability is important to neuronal survival during stroke. (Roseline Azoro - The Effect of Removal of Pleckstrin Homolog Domain Leucine rich repeat Protein Phosphatase 2 (PHLPP2) on Cardiac Hypertrophy) (Cynthia Nguyen – Regulation of GRK5 by PHLPP2 in Cariomyocytes)

Physics

Adam Burgasser

Prof. Adam Burgasser is seeking 1-3 research students to work on the SpeX Prism Library Analysis Toolkit (SPLAT), developing analysis tools to investigate low-resolution near-infrared spectra of low-temperature stars and brown dwarfs. You will learn how to reduce and analyze astronomical spectral data, organized astronomical information into web-accessible databases, and help develop software in Python to search for and characterize rare populations, including metal-poor subdwarfs, young planetary-mass brown dwarfs, and spectral binaries.  Interested students should have some programming experience (not necessarily in Python). (Christian Aganze (2015) – Searching for Distant Brown Dwarfs in WFC’s Parallel Fields, Adrian Suarez – Understanding the Lowest Mass Stars and Brown Dwarfs: Characterizing a Binary at the Hydrogen Fusion Boundary, Christian Aganze (2014) – characterization of the M Dwarf Binary System GJ 660 1.AB Separated by Over 120 A.U.)

Eva-Maria Schoetz Collins

We seek a student to help with a project studying the role of the extracellular matrix for Hydra regeneration from cellular aggregates. Hydra is a freshwater polyp with amazing regenerative potential: One can dissociate the animal into single cells, reaggregate the cells, and they will autonomously regenerate into a new animal in just a few days. The student will assist graduate students in the lab in assaying the role of extracellular matrix in this process by measuring the timing of matrix production, imaging matrix formation, probing and manipulating the mechanical and biochemical properties of the matrix. Molecular biology and programming experience in Matlab preferred but not necessary.

(Simeon McKelvey - Investigating the Role of Physical Forces in the Cell Organization of Biological Systems) (Karla Fernandez – Acetylcholinesterase Iocalization and function during neurodevelopment in the planarian Dugesia japonica, Cindy Khuu – Diversity in Planarian Stem Cells)

Kaixuan Ni

Abundant cosmological evidence supports that the matter content of the Universe is dominated by dark matter, which so far is indicated only through their gravitational effect. Whether dark matter interacts with the visible part of the Universe besides gravity is still a mystery in modern physics. Several large experimental programs in the world aim to search for dark matter using sensitive detectors located at deep underground laboratories. The XENON1T experiment is the upcoming largest dark matter search experiment using 3.5 ton of ultra-pure liquid xenon at Gran Sasso Underground Laboratory in Italy. The summer research project provides participants an opportunity to learn about the dark matter problem. They will also learn the experimental techniques, build parts of the detector system, and develop analysis tools to search for dark matter using XENON1T. The students will develop algorithms and software techniques to sort out signals from background and noises in waveforms from the detector for both calibration and dark matter search data; develop experimental techniques to achieve and analyze ultra-low background and ultra-pure operation condition of the dark matter experiment. Dark matter search is a frontier research topic to solve the most fundamental physics problem. The summer program will not only allow the students to learn the most fundamental physics problem in the cutting-edge dark matter research, but also allow them to learn the technical methods to prepare for graduate school research.

(Rebekah Shtayfman - Analyzing the Sensitivity of XENON1T, the Dark Matter Detector)

 Psychology

Adam Aron

Our lab www.aronlab.org is happy to host a summer STARS student in 2017 who is interested in psychology/neuroscience, especially the intersection. For the summer of 2017 our postdoc, Francesco Marini, will be running a behavioral, and possibly cognitive neuroscience, experiment with which an undergraduate student from the STARS program could provide great assistance. The experiment will investigate a facet of response control - i.e. how humans control inappropriate responses (see example projects at http://aronlab.org/research/). Methods involve using a computerized task to measure behavioral performance (and possibly neural data such as EEG). The volunteer will be involved at all stages of the experiment. This is includes: Recruitment: The lab assistant will have to utilize methods of recruitment such as putting out flyers, contacting previous subjects through email, and scheduling study time slots through SONA (the online subject recruiting platform for students at UCSD).  Data Collection: After recruiting participants, the lab assistant will also be responsible for running these subjects through the behavioral paradigm (the computerized task). This is a crucial part of our data-collection and requires that the student be completely familiar with the task, so that they are able to give precise task instructions to the participant. The student will have to implement the computer task using Matlab (they will be given instruction on how to do so). Data analyses: Along with the postdoc, the student will be involved in the data analysis process. This will enable the him/her to learn the many facets involved in developing behavioral parameters and researching statistical data. Reporting Results: Either through powerpoint presentation to the lab members, or through group discussion, the student will have to present the experiment as well as any significant data results. The student will receive guidance in preparation for such tasks from the postdoc, lab manager, and the principal investigator (Adam Aron). We are looking for a motivated and diligent student who is interested in cognitive neuroscience and/or psychology. If the student has previous experience with Matlab, it would be a plus, but it is not a requirement. 

(Marina Nakhla - The Effects of Surprise on Visuomotor Working Memory)

David Barner

The Language and Development Lab is interested in how children learn language and develop an understanding of objects and events in the world. Current research projects in the lab investigate a broad range of topics, from how children acquire words and concepts about logic, number, color, and time, to how children make pragmatic inferences in conversation. Summer research students will have the opportunity to work on an existing project under the supervision of a graduate student, postdoc, or lab coordinator. Students will run experiments in preschools, museums, or in the lab with children (e.g. 18-months-old to 5-years-old) or adult controls; enter and code data using various computer software; recruit families via phone, email and at external sites; design stimuli; and participate in weekly lab meetings.

(Desia Bacon - First Color Word Learning in Toddlers)

Timothy Brady

My lab is interested in the precision with which people can remember information in long-term memory. When you are asked to remember a property of a visual object (e.g., what color was that car you saw?), how much does holding it in mind for a longer time hurt your memory? Does your memory get worse primarily because all of your memories get noisier and less precise, or because some memories are lost completely but others are preserved almost perfectly? This summer STARS project will focus on using psychophysical methods with human adults to examine visual long-term memory precision. You'll get to do some programming in MATLAB; run people in experiments; and analyze the data in Excel and MATLAB. The experiments will vary from simple examinations of memory precision to questions about what memory looks like when people have false memories. Data analysis will vary from simple measures of people's average errors to complicated Bayesian fits of probabilistic mixture models.

(Crystal Ruedas - Interference in Visual Working Memory)

Rosanne Rademaker (PI John Serences)

The brain contains roughly 80-100 billion brain cells, each connecting with up to 10.000 others. Critically, the vast majority (~99%) of connections do not come directly from the senses, but connect locally from one cortical cell to another. With an architecture so heavily skewed towards representing the extra-sensorial, it is easy to imagine how perception involves much more than meets the eye – literally. It is therefore not surprising that basic perception is very much shaped by cognition. For example, attention to only a subset of the sensory world (i.e. look only for ‘red’ things when searching for your red-sweater wearing friend in a crowd) will help enhance the thing you attend to; expectations of what the visual world should look like (i.e. expecting light to come from above) help you interpret ambiguous sensory information, and short-term memory can be used to temporarily store sensory information that is needed to achieve cognitive goals. Research objective Many studies are ran in the lab at any given time. The general objective is always to study how the healthy human brain sees & hears, and how cognitive factors impact basic aspects of visual & auditory perception. Expected methods In the lab we use behavioral tasks, Electroencephalography (EEG), and functional Magnetic Resonance Imaging (fMRI). In the near future we expect to also record intracranial data from human patients. For most of our analyses we use Matlab (a programming language) and neuroimaging-related software. importance Increasing our understanding of the fundamental brain processes that govern basic human perception will help increase our understanding of what happens when these processes break down in major cognitive disorders such as autism or schizophrenia. Such knowledge might ultimately provide clinicians the necessary knowledge to diagnose and treat disease.  

Timothy Rickard

At the Cognition and Cognitive Neuroscience Laboratory, we investigate how human beings learn and how learning can be made more efficient and more effective.  This work encompasses such topics as human learning and knowledge representation, memory retrieval processes, acquisition and transfer of skills, and educational practice.  The summer STARS student will assist in the development of an experimental research project related to human learning and memory, contribute to data collection and analysis for that project, and present the results at STARS and related conferences.  Throughout, there will be opportunities to learn about experimental design and programming, research methods, data analysis, and other facets of graduate-level scientific research.  Possible research project topics are diverse and input from the STARS student is encouraged; in recent years we have investigated the optimization of learning in arithmetic, spelling, and other domains, the role of sleep in learning and memory, skill-training programs, testing effects, and the cognitive processes underlying recall from long-term memory. (Joshua Lozano - Recognition vs. Cued Recall: Which is More Optimal for Test-Enhanced Learning?)

Adena Schachner

The Mind and Development Lab (madlab.ucsd.edu) investigates children's social and cognitive development. We are interested in how infants and children learn about their social world, by making inferences about the hidden contents of others' minds (like goals, preferences, or beliefs). In particular, we are currently studying how infants, children and adults understand other's intentional actions, and reason about the objects they own and create. Our work has also focused on music cognition, particularly the origins of our capacity to move in time with a beat. Student researchers may be involved with data collection (including recruiting and conducting studies with families of infants, children, and adults), data coding and analysis, weekly lab meetings and reading groups.

Viola Stomer

My lab (http://stoermerlab.ucsd.edu/) is interested in understanding the cognitive and neural mechanisms of visual attention and multisensory processing. Our research is focused on the question of how attention helps us select and process information efficiently. Furthermore, we are interested in the role of attention in integrating events from different sensory modalities (sight, sound, touch). We use both behavioral and electrophysiological methods to study these questions in healthy human participants. This summer STARS project will focus on examining how visual and auditory attention interact. As a student researcher, you’ll get to do some programming in Matlab, run participants in both behavioral and electrophysiological (EEG) experiments, and analyze data in Excel and Matlab. You will work closely together with the PI and a PhD student.

Caren Walker

The Early Learning & Cognition Lab, under the direction of Dr. Caren Walker, seeks to understand how children build early theories and learn and reason about the causal structure of the world. We use a model of the child as a "scientist," forming implicit hypotheses and then testing and rationally revising those hypotheses based on incoming evidence. Although children are excellent at scientific reasoning in informal learning contexts, they often find explicit scientific inquiry skills in formal pedagogical contexts quite difficult. Our current line of work explores a variety of techniques in order to facilitate these early skills. One set of studies we will be pursuing over the summer is the use of counterfactual reasoning to boost children's ability to evaluate evidence. We will also be examining children's early ability to entertain multiple possibilities and reason about abstract relationships. All studies will take place in the context of short games, designed to be engaging for young children.

School of Medicine

Hannah Carter

Hundreds of common inherited alleles have been associated with susceptibility to developing cancer later in life. We are interested in better understanding the relationship between these variants and the characteristics of tumors. For this project, the student will use statistical methods to analyze the relationship between inherited risk alleles and characteristics of tumors. Specifically, the student will apply established methods to evaluate groups of cancer patients partitioned based on the number of minor alleles at a particular locus and evaluate statistical correlation with measures that we commonly use to describe tumors such as number of driver mutations or expression-based subtype. This project investigates whether we can obtain additional information from germline cancer predisposition alleles beyond a measure of increased risk of developing disease. (Andrea Castro - Integration of Protein Network Analysis in Machine Learning Classification of GOF and LOF Mutations in Cancer; Alexis McDonald - The Role of Genetic Variation in Helping the Immune System Fight Cancer)

John T. Chang

Our laboratory is interested in cell polarity as a central theme in regulating the fate and function of a wide range of cell types across many different organisms.  In particular, we are interested in how rare progenitor cells continually produce terminally differentiated cells while also preserving a self-renewing lineage. One potential solution is an evolutionarily conserved mechanism called asymmetric cell division, during which a dividing cell imparts unequal inheritance of its components to its two daughter cells, making them different from inception. In the mammalian immune system, T lymphocytes face a similar need for simultaneous differentiation and regeneration. During a microbial infection, a naive lymphocyte, so called because it has never encountered its foreign antigen, must give rise to two distinct classes of cellular progeny. One daughter cell undergoes terminal differentiation into effector cells, which play a critical role in the elimination of an invading microbe. The other daughter cell gives rise to long-lived memory cells, which are capable of regenerating both subsets of progeny upon re-infection. We have recently found that a T lymphocyte undergoing an immune response against a microbial pathogen appears to divide asymmetrically, giving rise to effector-fated and memory-fated daughter cells. The goal of our research is to understand how T cells use asymmetric cell division to balance the demands of terminal differentiation and self-renewal, using cutting-edge methods including immunofluorescence microscopy, animal models of infection and autoimmunity, multi-color flow cytometry, and single-cell RNA sequencing techniques. The importance of the work is that defining the mechanisms regulating asymmetric cell division will contribute to our understanding of a multitude of diverse processes, including embryonic patterning, organ formation and function, stem cell and tissue regeneration, immunity, and cancer. (Gianna Casteleiro - The role of β1 integrin in regulatory T-cell homeostasis; Jocelyn Olvera - Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification)

Alon Goren

My group’s research focuses on epigenomic mechanisms, and merges basic biology, technological innovations and computational analyses. Our major interest is in developmental-epigenomic questions, and includes the employment and development of tools to study chromatin in uncharted settings, such as investigating the organization of chromatin regulatory networks during mouse embryogenesis. This is a terrific opportunity to get to the field of genomics. I believe in hands on experience, and that the future of biology is in the merging of experimental and computational approaches. The student will be involved in experimental design, running wet lab experiments and computational analysis using publically available tools. Ideally the candidate will have background in molecular biology and computation (e.g. Unix and R).

Dan Kaufman

Briefly, the project in my lab would involve using human pluripotent stem cells to better understand human blood cell development. Projects involve both derivation and characterization of hematopoietic stem cells (HSCs) and lymphocytes (T cells and NK cells) that can be derived from human pluripotent stem cells. One main goal is to use these cells to produce new anti-cancer therapies by specifically targeting lymphocytes to better kill tumor cells. These studies involve a variety of research methodologies including cell culture, molecular biology, flow cytometry, and mouse work.

Miguel Lopez Ramirez (PI Mark Ginsberg)

Cerebral cavernous malformations (CCMs) are cerebrovascular malformations that affect the central nervous system. CCMs cause epilepsy and strokes, leading to significant morbidity and mortality. CCMs affect ~1/200 humans and there is no pharmacologic therapy. Our pre-clinical study provides evidence that genetic inactivation of the gene Ccm1 inhibits expression of anti-angiogenic proteins that contributes to brain vascular anomalies and the pathogenesis of CCMs. Our research is using mouse and zebrafish genetics in combination with histology, primary cell cultures,  molecular cell biology and bioinformatics tools. The ultimate goal of our research is to better understand the biology of CCMs to provide non-invasive, safe, and effective therapies to cardiovascular and neurological diseases.

Sreejith Nair (PI Geoff Rosenfeld)

Background: Less than 2% of human genome code for proteins. Strong evidence suggests that the remaining non-coding part of the genome also contribute significantly to overall health and disease states of the organism. One important non-coding modulator is long non-coding RNAs  (lncRNA) that plays diverse roles in development and diseases. In this project we examine the physiological and biochemical role of a long non-coding RNA specifically expressed in Estrogen receptor a positive breast cancer cells. Research Objective: DSCAM-AS1 is a long-noncoding RNA expressed specifically in ERa positive breast cancer cells. In this project we will examine the phenotype of DSCAM-AS1 knockout cells.  The main objective of the study will be to unravel the mechanisms through which the lncRNA function in gene regulation and chromosomal structure. Methods: We will use cutting edge molecular biology techniques, various imaging methodologies along with genome editing tools to address these questions. Importance: Previous studies have shown the important role of DSCAM-AS1 in breast cancer development and therapy resistance. Understanding the mechanisms by which this lncRNA is involved in cancer development will help us to develop novel approaches to treat the condition.

Francesca Telese

Dr Telese’s research program is focused on the epigenetic regulation of higher cognitive behaviors, including learning and memory. Her experimental approaches include a wide array of next-generation sequencing methodologies to dissect the complexity of gene-environmental interactions by analyzing changes in transcription and in epigenetic marks associated to different behaviors. A major focus of her research involves the molecular characterization of conditional knock-out models targeting several epigenetic regulators, including histone demethylases, transcription factors, and co-repressor complexes. Ongoing work is directed towards developing novel genome-wide tools to analyze cell-specific and circuit-specific epigenetic pathways in the brain.

Gene Yeo

Methodological and technical advances have enabled the insight that the three-dimensional arrangement of the cell’s chromatin – and nearby RNA and proteins – within the nucleus is non-random.  Instead, the relative localization of a genomic locus may affect the transcriptional activity of genes in that locus. It has become clear that nuclear subcompartments play a critical role in controlling transcriptional output and post-transcriptional processing by anchoring portions of the genome within nuclear regions of highly specific protein and RNA composition, such as transcription factors and splicing complexes. These processes may play a critical role in normal development and their dysfunction may contribute to or cause disease. Using stem cells, we seek to characterize the molecular constituents of these nuclear bodies during differentiation and in models of neurodegeneration. We will combine several cutting-edge technologies in pluripotent stem cell genetics, genomics and molecular biology, to help identify the four-dimensional nucleome (4DN), i.e., the RNA, DNA and protein composition of three nuclear bodies (speckles, paraspeckles and Cajal bodies) in induced pluripotent stem cells (iPSCs) and their differentiated progeny (motorneurons and muscle cells). This unique combination provides an exciting opportunity for two highly motivated interns to support this effort. Depending on his/her interests and skillsets, the intern may choose to contribute to all aspects of this project or take on a specific role, such as being responsible for stem cell culture activities and differentiation, cell line generation by genome editing, or contributing to sample preparation and analysis. (Enrique Amaya-Perez - A Cre-loxP-based method for the generation of large genomic duplications via CRISPR/Cas9 genome editing)                                                                                              

School of Medicine – Biomedical

Tsung-Ting Kuo (PI Lucila Ohno-Machado)

Project 1: In the era of big data, the need to search, view and use the datasets for biomedical and healthcare studies becomes increasingly enormous. Although the existing nation-wide initiatives are proposed to support data sharing, there are still several burdens that prevent the sharing of datasets. In this research project, we target the development of a Blockchain-based technology to improve healthcare data sharing. We believe by accessing the shared datasets, researchers and reproduce important clinical results, evaluate new technical methodologies, and discover new biomedical findings on the shoulder of the giants.

Project 2: Cross-institution interoperable predictive modeling can advance research and facilitate quality improvement initiatives. However, state-of-the-art distributed privacy-preserving predictive modeling frameworks are still centralized, which carries several risks. In this research project, we aim at developing novel privacy-preserving machine learning algorithms on Blockchain networks to learn better models. We believe it is critical to exploit the wide-range of existing predictive modeling methods to further improve the predictive power of the cross-institutional machine learning models.

Project 3: With the wide adoption of electronic health record systems, cross-institutional predictive modeling is becoming increasingly important. However, most existing privacy-preserving machine learning methods that have been used to build predictive models given clinical data are based on centralized architecture, which presents security and robustness vulnerabilities. In this research project, we focus on developing new privacy-preserving predictive modeling algorithms based on the Blockchain technology, to deal with complicated real-world research networks. We believe the development of such algorithms is important to provide a foundation to mitigate the complexity of machine learning introduced by complicated research networks.

School of Medicine – Neuroscience

Tim Brown

Research projects in my laboratory focus on structural and functional changes in the brain during childhood (measured using neuroimaging) and how they relate to cognitive and academic skill development and clinical disorders. For example, recent research with undergraduate students has focused on children’s language, math, and reading abilities and how individual differences in these skills might relate to white matter tissue properties, cortical surface area, or regional brain activity measures. I particularly like to work with students in research who might not have had much exposure to it, including students from disadvantaged or underrepresented backgrounds. Since I myself grew up in a somewhat rural part of Arizona, I especially enjoy working with Native American students. (Brittany Ketchup)

Tom Hnasko

Our lab is exploring how VTA glutamate neurons contribute to behavioral reinforcement.  You will contribute to an experiment where VTA dopamine or VTA glutamate neurons are selectively killed using a genetic tool.  You will study how these mice respond to drugs of abuse like cocaine after the cells have been killed.  The project will include performing and analyzing mouse behavior, histology, microscopy. For more information about Dr. Hnasko’s research, please visit: https://neurosciences.ucsd.edu/research/labs/hnasko/Pages/default.aspx

Chitra Mandyam

Neural stem cells persist in the adult hippocampal subgranular zone and mature into hippocampal granule cell neurons (a process known as hippocampal neurogenesis). Neurogenesis may play a significant role in brain repair and recovery from a number of insults. Withdrawal and relapse are integral parts of the addiction cycle, and withdrawal from intravenous methamphetamine self-administration (Meth SA) enhances reinstatement to Meth seeking in male and female rats. It is therefore essential to determine whether withdrawal from Meth SA alters the process of hippocampal neurogenesis and whether this alteration is required for enhanced relapse to Meth seeking in an animal model of Meth addiction. The student intern will assist the postdoctoral fellow to determine whether withdrawal from Meth SA differentially alters the neurogenic capacity of neural progenitor cells in the granule cell layer of the hippocampus in adult male and female rats. We will use techniques such as retroviral labeling to label newly born granule cell neurons and perform 3D structural analysis on these neurons. We will use state-of-the-art software Neurolucida and NeuroExplorer from MicroBrightField to determine these issues. The overall goal of the summer internship will be to assess if withdrawal from Meth SA differentially alters the structural plasticity of newly born versus preexisting neurons in the granule cell layer in the dentate gyrus of the hippocampus in male and female rats. Preclinical rodent models of intravenous Meth SA will be used. Students majoring in Biochemistry or Neuroscience preferred. Students should have an interest in performing animal behavior such as methamphetamine self-administration, biochemical experiments including immunohistochemistry and should be interested in performing extensive microscopic analysis. Students with experience in animal handling, pipetting, tissue handling are desired.

Doris Trauner

Individuals with the genetic lysosomal storage disorder nephropathic cystinosis have a specific cognitive profile including visual spatial and visual memory impairments. It is not known whether the renal disease alone could account for the observed cognitive differences. This study will examine cognitive differences between individuals with nephropathic cystinosis and those with renal disease of other causes using standardized neuropsychological tests. This study is important in determining whether the cognitive profile in cystinosis is unique to that genetic condition and thus possibly related to the effect of the aberrant gene on brain development. (Alfredo Bolanos – A closer look at white matter tract integrity in patients with perinatal stroke through diffusion tensor imaging)

Eric Zorrilla

The Zorrilla laboratory seeks to understand the neural substrates of motivated behavior and of the regulatory control of energy balance using interdisciplinary techniques that span molecular, biochemical, neuroanatomical, pharmacological, physiological, behavioral and statistical methods. We are particularly interested in genetic, epigenetic and neuroadaptive differences in the neurobiology of reward and stress circuits that subserve the control of food intake as well as other appetitive (reward-driven) and stress-related behaviors. The summer project will seek to identify addiction-like neuroadaptation of stress- and reward-regulatory neurocircuitry that results from cyclic binge-like intake to highly palatable food.  The project will involve neuroscience approaches that may include optogenetic, DREADDs, immunohistochemistry, in situ hybridization, quantitative PCR, Western blotting, and behavioral techniques. Results from the project aim to be therapeutically relevant to the increased incidence of obesity, binge eating disorders, alcoholism and drug addiction and stress-related psychiatric disorders in Western societies.

School of Medicine – Pathology

Nigel Calcutt

Neuropathy is the most common complication of long-term diabetes and there is currently no FDA-approved therapy for this condition. Corneal confocal microscopy (CCM) is emerging as an iterative, non-invasive and sensitive technique for both diagnosing peripheral neuropathy and following the progression of sensory nerve degeneration. CCM also has the potential to be used to assess efficacy of therapeutic interventions that are developed in preclinical studies prior to clinical use. The goal of this research is to test the hypothesis that diabetic peripheral neuropathy in the cornea can be reversed by topical application of growth factors. The student will establish colonies of control and diabetic mice, monitor corneal nerves until neuropathy is detected then instigate daily topical treatment with growth factors and use CCM to track reversal of neuropathy. Prior studies have shown that mouse models of diabetes develop loss of corneal nerves in a manner that replicates the human condition and that this can be prevented by topical insulin treatment. The aim of this research project is to use this preclinical system to investigate the capacity of novel therapeutics to reverse established neuropathy with the intent of providing support for the advancement of effective therapies to clinical trial and ultimately, clinical practice. (May Madi Han - New Topical Cream Treatment against Diabetic Peripheral Neuropathy: Muscarinic Subtype 1 Acetylcholine Antagonist as an Enhancer of Nerve Growth in Diabetic Peripheral Neuropathy)

Jonathan Lin

Tauopathies are devastating neurodegenerative diseases that include Alzheimer’s disease, Progressive Supranuclear Palsy, and Chronic Traumatic Encephalopathy.  Recent studies have identified a novel gene, EIF2AK3/PERK, as being a risk factor in patients with tauopathies.  The EIF2AK3/PERK gene encodes a kinase with numerous coding and non-coding variants in the human population.  Several of these EIF2AK3/PERK variants are associated with increased risk for tauopathy, but the function of these variants and how they cause neurodegeneration are unknown.  The goal of the STARS project is to test the function of human EIF2AK3/PERK alleles in cells obtained from patients with tauopathies.  The student will use stem cell, molecular, and biochemical approaches to identify differences between EIF2AK3/PERK alleles.  These studies will reveal how EIF2AK3/PERK contributes to neurodegeneration and may lead to development of novel therapies to prevent disease based on targeting this kinase.

School of Medicine – Pediatrics

Kelly Frazer

The Laboratory of Prof. Kelly Frazer at University of California, San Diego offers a STARS student an opportunity to participate in a multilevel project that aims to understand the genetic background of inherited and acquired cardiomyopathies that include Long QT syndrome, sudden death syndrome and arrhythmia. A number of previous studies have identified at least 55 different genes involved in various cardiomyopathies. In our project we are not limited to the protein coding genes but we are aiming to also identify novel non-coding variants that are associated with cardiac disorders. As a tool we are using human induced pluripotent stem cells (iPSC) that we have generated over the past few years from over 200 individuals. We plan to differentiate these iPSC into cardiomyocytes during the next year. To this uniquely large cohort of iPS cells and iPSC-derived cardiomyocytes we are applying phenotypic, physiologic, genetic and bioinformatics studies which will subsequently be implemented in an extensive collaborative project that merges the efforts of several multidiscipline research groups. We are looking for talented and skillful students with biology and/or computational backgrounds that wish to participate in a complex and dynamic research project. The student will work closely with PhD scientists for study design and experimental analysis and learn how to present his/hers data in a written and oral fashion allowing him to complete the scientific training. (Joy Rosa Jackson - Analysis of CRISPR-Edited Genetic Variant Phases in Long QT Syndrome Genetic Lines)

Kyle Gaulton

Diabetes affects over 400 million individuals worldwide, and genetics plays a major role in risk of developing diabetes.  Over 100 genetic risk factors for diabetes have been identified, although the molecular functions of these risk variants are largely unknown.  The goal of this research project is to identify and study the molecular functions of genetic variants that influence type 1 and type 2 diabetes risk.  This project will involve both bioinformatics analyses of genetic and epigenome data to identify diabetes risk variants, and experimental assay in human and rodent cells to determine the molecular functions of these variants.  The results of this project will identify mechanisms of diabetes pathogenesis that will lead to new disease prevention and treatment strategies. 

James Hagood

The Lung Repair Lab (Dr. James Hagood, PI) in the Department of Pediatrics at the University of California San Diego (UCSD) is seeking outstanding students for positions in the summer 2016 to join a dynamic, interdisciplinary team of scientists focused on lung development and lung remodeling in the context of fibrotic lung diseases. (Jose Ramirez - Role of Wnt Pathway in the Regulation of Thy-1 Expression in Lung Fibroblasts) (Monica Del Moral Suazo – Thy-1 as modulator of YAP/TAZ activity in lung fibroblasts)

Project 1: The final and most important stage of normal lung development is the formation of alveoli, the small air sacs where gas exchange occurs. Pulmonary alveolar septation is a dynamic, coordinated process that requires the accurate spatial and temporal integration of signals to develop the intricate alveolar structure. Despite significant progress in our understanding of this process, we still lack a comprehensive understanding of the dynamic regulatory networks that govern it. Thus, while we are aware that the regulation of alveolar septation depends upon integration of numerous signals from multiple molecular pathways (e.g. Wnt, TGF-β, Hedgehog, Retinoid), we have little understanding of how these pathways interact in the complex and rapidly varying spatial microenvironment of the developing lung. In addition, we do not have a detailed understanding of the hierarchy of transcriptional regulation during lung development, including the tightly regulated temporal changes in epigenetic regulation of gene expression.

The Hagood Lab participates in the national Alveolar DevMAP project, whose purpose is to generate a compendium of the dynamic and regional changes in epigenetic marks, microRNA, mRNA and proteins that happen during alveolar septation, and use this compendium to generate a dynamic temporal regulatory model of normal alveolar septation. The Hagood Lab is establishing several methods to determine changes in global DNA methylation, histone modifications and chromatin accessibility during alveolar septation (MEDIP-seq, MRE-seq, targeted Bisulfite sequencing, ChiP-seq and ATAC, to mention some). Samples will be analyzed by Next-Generation Sequencing and/or quantitative RT-PCR.

We welcome summer students who want to learn more about the exciting field of Epigenetics at the theoretical and practical level. Students will participate in the generation of data that will allow a better understanding of the normal pathways involved in lung development. This knowledge may lead to future therapeutic strategies in both pediatric and adult lung disorders, with the goal of maintaining or regenerating alveoli.

Project 2: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal disease with no effective therapy. Many promising drugs have failed in clinical trials because of excessive side effects or difficulty delivering the drug to the scarred, fibrotic lung tissue. This project will translate a novel mechanism for delivery of therapeutics for IPF and other diffuse lung diseases, by taking advantage of an unique mechanism for penetrating the lung endothelial cell (EC) barrier. Aminopeptidase P (APP) is specifically enriched in lung EC caveolae, enabling lung-specific targeting of intravascularly injected APP antibodies (mAPP). These are actively and specifically pumped rapidly across the EC barrier via caveolae to reach the lung interstitial spaces. We are studying the ability of the lung-specific caveolar pumping system to enhance the antifibrotic effects of Thy-1 or rapamycin in vivo in relevant, complementary animal models of pulmonary fibrosis at distinct stages of disease. Students will learn combined knowledge/approaches in cellular, histopathological, and systemic biology.

Project 3: The candidate for this project will explore how the cell responsible for fibrotic scarring, the fibroblast, becomes activated and programmed to cause destructive fibrosis, and how this process can be reversed. Specifically, this project will explore the role of Thy1 receptor and microRNAs in lung injury, repair and cellular remodeling in the context of fibrotic lung disease.

Idiopathic pulmonary fibrosis (IPF) is an incurable fatal disease with increasing incidence and mortality. A final common pathway for the destructive remodeling which characterizes fibrosis is the apoptosis-resistant myofibroblast, which both creates and responds to an altered mediator and matrix microenvironment, thus perpetuating fibrogenesis. In order to contribute to the understanding of fibrogenic reprogramming of lung fibroblasts in vitro and in vivo, we have leveraged understanding of the molecular functions of Thy-1, a cell surface glycoprotein that acts as a context-dependent regulator of cell phenotype. Thy-1 is present on normal lung fibroblasts, but absent from cells located in IPF fibroblastic foci. In our group we are especially interested in the Thy-1/miRNA network implicated in early reprogramming events of Thy1 negative lung fibroblasts after lung injury. In addition, we are interested to explore the role of Thy-1 and miRNA135b in regulating myofibroblastic transformation and survival. Thus we propose to investigate the role of micro RNAs (miRNAs) in cell potency transitions from lung fibroblasts to endoderm progenitors, as a mechanism to replenish alveolar tissue after IPF.

This project engages an emerging area of study in the field with opportunities for mechanistic discovery as well as translational applications in lung disease.

School of Medicine – Psychiatry

Cristian Achim

Over 34 million people worldwide are infected with Human immunodeficiency virus (HIV), and despite effective pharmaceutical therapies, half of these patients will suffer from HIV-associated neurocognitive disorders (HAND). The causes of HAND are variable and most likely multifactorial, including chronic low-level viral replication, chronic viral protein expression, inflammatory gene expression, toxicity of drug therapies, and others. This research project will focus on elucidating molecular mechanisms of chronic neuroinflammation, which is observed in brain tissues of many HAND donors. Specifically, recent findings suggest that the complement system, which plays roles in inflammation as well as synapse formation, is dysregulated in the brains of many HAND patients. The goal of this project is to identify the cellular expression and localization of key complement component genes in the frontal cortex of HAND donors. In completion of this project, the trainee will learn to analyze human brain tissue for gene and protein expression using techniques such as real-time PCR and immnoblotting, respectively. This project will be conducted in the context of a larger project that includes human, animal and in vitro models to investigate how the complement system is involved in neuroinflammation during HAND. Findings from these studies may lead to therapeutic targets that ameliorate the severity of HAND for many HIV+ patients.

Zachary Cope (PI Jared Young)

Children born in the springtime, following gestation during Fall and Winter when daylight (photoperiod) is reduced, are more frequently diagnosed with psychiatric illnesses such as schizophrenia, autism spectrum disorder, bipolar disorder, and depression. While some developmental aspects resulting from reduced photoperiod have already been tested (e.g. vitamin D deficiency), the relationship between reduced photoperiod gestation is likely multifactorial and may even be heritable via epigenetic means. To determine if 1) the effects of short-active photoperiod gestation are exacerbated by reduced synaptic clearance of dopamine and 2) if these behavioral effects are heritable to offspring of parent mice gestated in short-active photoperiod. A generation of dopamine transporter hypomorphic (DAT-HY) mice with ~50% reduced dopamine clearance, and their wild type littermates, have been bred, gestated, and reared under either normal (12 hours light : 12 hours dark) or short-active (19 hours light : 5 hours dark) photoperiod conditions. These mice are currently undergoing a broad phenotyping to assess behavioral domains such as anhedonia (saccharine preference), hyperactivity (behavioral pattern monitor, BPM), sensorimotor processing (prepulse inhibition, PPI), motor coordination (Rotarod), social (social approach) and non-social  (novel object, NORT) recognition, depression-relevant behavior (forced swim task, FST) and risk preference (elevated plus maze, EPM). These mice will then be bred to generate an F1 cohort. In adulthood, these mice will be tested in the same battery of tests to assess if the behavioral phenotypes witnessed in the F0 generation will persist into the offspring. Hypotheses: 1) Offspring of mice bred during a short active photoperiod length will exhibit psychiatry-relevant behaviors of increased anhedonia (saccharine preference), increased activity (BPM), reduced sensorimotor gating (PPI), depression-relevant immobility (FST), and risk-preferring behavior (EPM); and that 2) Mice with reduced DAT levels will exhibit an exaggerated effect as measured by higher effect sizes than mice with normal DAT levels. Alternatively, homeostatic compensation may occur in offspring, resulting in a protective phenotype where these behavioral effects may be inversed compared to the F0 generation. This will also be assessed. Understanding the environmental and genetic factors that underlie psychiatric disorders will be a massive step toward developing targeted therapeutics for people suffering from serious mental illness. These illnesses occur in 6% of the population resulting in pervasive suffering of the patients and their families, not to mention billions of dollars annually in healthcare costs and lost productivity.

Barbara Parry

Our laboratory studies clinical depressions occurring in association with reproductive events in women – premenstrual, pregnancy, postpartum, and menopause. We focus on circadian rhythm studies of sleep and melatonin, using sleep and light therapy to improve mood in these conditions.

Lilia Iakoucheva

For more information about Dr. Iakoucheva’s research, please visit:

http://iakouchevalab.ucsd.edu/

Gregory Light

Psychotic disorders have devastating and often life-long consequences for approximately 2% of the global population. Most psychiatric interventions are implemented in the absence of knowledge about individual variation in important domains of brain function that might influence therapeutic response and outcome. This “one-size-fits-all” approach to treatment is problematic, with treatment failure occurring far too often and incurring substantial cost to the patient, family, therapist and larger social system. To “bend the curve” on the individual outcomes and societal impact of chronic psychotic illness, we must advance our understanding of the neural substrates of the illness features that most strongly contribute to poor outcomes, and use this information to guide mechanistically informed, personalized treatments. My program of research has advanced the use of neurophysiological biomarkers to develop precision medicine trials for psychosis patients that are: 1) effectively delivered in “real-world” community centers; and 2) informed by objective, reliable, validated, and low-cost biomarkers for identifying patients most likely to benefit (or not) from treatments. Findings support large-scale biomarker-guided trials to prevent or ameliorate illness in high-risk cohorts or treatment refractory populations. This program ultimately aims to develop and apply personalized biomarker assessment tools to deliver the “right treatment” to the “right person” at the “right time.”

Dave MacQueen (PIs Jared Young and Mark Geyer)

Impairment of attention is associated with functional disability in patients with neuropsychiatric disorders such as schizophrenia, bipolar disorder, and Alzheimer’s disease. Improving sustained attention/vigilance amongst patients with these conditions remains a critical goal of new medication development.  In humans, vigilance is frequently assessed through the use of a continuous performance test (CPT) and our group has developed a 5-choice variant (5C-CPT) which allows for testing across multiple species (e.g., humans, mice, and rats) using visual stimuli.  Yet, many experimental strains of mice and rats have notoriously poor vision and olfaction is often considered the primary sensory modality for rodents. The goal of this project is to validate a 5C-CPT procedure for mice using olfactory stimuli.  An olfactory 5C-CPT (o5C-CPT) for mice will allow for a direct comparison of attentional performance and the effect of pharmacological manipulations across stimulus modalities (vision and olfaction) in addition to accelerating training times for mice.  Development of the o5C-CPT will be conducted with the use of two fully-automated olfactometers designed for the timed presentation of olfactory stimuli (up to 8 odors) for mice.  The experimenter will be expected to train up to 16 mice to selectively respond to stimuli within the olfactometer using training programs provided by the manufacturer.  The experimenter will receive training on, and will subsequently be responsible for, the processing of data, tracking progression through phases of training, and will collaborate with the research team to develop programming which will extend initial training to a full o5C-CPT procedure suitable for pharmacological testing. 

Victoria Risbrough

Catecholamine-O-transferase (COMT) is an enzyme implicated in the degradation of catecholamines, which are ubiquitous neurotransmitters such as dopamine. In humans a mutation in this gene, named “COMTval158met”, results in a change in the coding sequence of the gene which causes the code for a valine (Val) to be replaced by a code for a methionine (Met). This mutation results in a COMT enzyme that is 40% less effective in degrading dopamine and norepinephrine in human Met/Met carriers. COMTval158met is one of the most well studied mutations related to neuropsychiatric disorders, and has recently been shown to alter brain development in humans, with differences in cortical thickness across Val and Met carriers.  However only animal models can help us assess causality of this mutation with alterations in brain development.  We have developed a mouse line that is “humanized” for COMTval158met.  The mouse gene is deleted and replaced with the human COMT gene carrying either the Val or Met coding sequence. Research objective: Using the “humanized” COMTval158met mouse, we propose to investigate whether carrying the Val/Val genotype induces changes in brain structure and cortical thickness. Expected methods: Structural MRI will have been conducted in COMT-Met/Met and Val/Val carriers to assess cortical thickness, since reduced volume of grey matter is a well-known abnormality associated with PTSD. Diffusion tensor imaging will be conducted to identify microstructural changes. The student will process the DTI images to analyze fractional anisotropy (FA) and mean diffusivity (MD), with a focus on the cortical and hippocampal circuitry, which are altered in humans carrying the COMTval158met mutation.  Importance:  Understanding how common gene mutations affect brain development allows us to identify mechanisms of genetic risk for neurodevelopmental disorders.

Julie Wetherell

For more information about Dr. Wetherell’s research, please visit: www.medexstudy.com

School of Medicine – Public Health

Kiyomi Tsuyuki

Project 1: Double vulnerabilities of violence and HIV among women in Brazil

Background: More than 13 million women in Brazil are victims of intimate partner violence. According to the World Health Organization, Brazil also has the seventh highest rate of femicide worldwide, with nearly one woman killed every two hours. To address this public health problem, the Maria de Penha law was enacted in 2006 in Brazil to provide victims with legal means to prevent IPV and to prosecute IPV perpetrators. However, recent data indicate that even though most women are aware of the law they are not accessing services after IPV victimization. Aims: We use population-based data from São Paulo (n=2,000) and Porto Alegre (n=1,323) to conduct a Latent Class Analysis to classify typologies of violence over the life course (by type of violence [physical, sexual, psychological]; timing of violence [childhood, adulthood, both]; and violence perpetrator [intimate partner, friend, family, etc.]). We then use regression models to identify risk and protective factors for each violence typology and for various levels of the socio-ecological theoretical model (e.g., individual, relationship, community, structural). Given that 98% of women living with HIV in Brazil report a lifetime history violence (79% prior to diagnosis), we will also examine how violence victimization and socio-ecological correlates are associated with HIV risk. Implications: Our bi-national collaboration, combined with an information exchange with key leaders in Brazil, will facilitate the development of a viable socio-structural intervention to prevent violence, connect victims to Brazil’s socialized healthcare system, facilitate access to the legal process offered by the Maria da Penha law, and possibly to integrate violence prevention within extant HIV care services.

Project 2: Neighborhood Environment, Physiological Stress, and Syndemic Substance Abuse, Violence, and HIV/STIs among Black women in Baltimore, MD.

Background: Women who experience sexual violence have up to nine times greater risk for HIV. Black women have the highest HIV incidence rate in the US, and Baltimore, MD (68% Black) has the 9th highest HIV rate in the nation. Neighborhood environment is thought to create a risk environment for co-occurring epidemics (syndemic) of Substance Abuse, Violence Against Women (VAW), and HIV/STI (known as the SAVA syndemic). This study will elucidate how neighborhood risk environment “gets under the skin” to increase women’s physiological stress levels (cortisol), and cause disparities in the SAVA syndemic among Black women in Baltimore, MD. Aims: We use data from women at high risk for HIV (n=400) and their neighborhoods in Baltimore, MD to conduct multi-level modeling that allows us to estimate the distinct effects of neighborhood-level factors (e.g., police violence, % vacant buildings) and individual-level factors (e.g., gender roles, perceived discrimination) on women’s stress levels (cortisol) and SAVA syndemic risk. Implications: This study will be the first to elucidate the relative contribution of neighborhood-level and individual-level risk and protective factors to the SAVA syndemic among Black women, as well as identify amenable socio-structural and neighborhood factors for the development of a critically needed multi-level (e.g., socio-structural, neighborhood, social, individual) intervention to address the SAVA syndemic.

School of Medicine – Reproductive Medicine

 

Hanne Hoffmann (PI Pamela Mellon)

Today, more than 20% of the population performs shift-work, travels across time zones, and has disrupted sleep patterns. These are all factors affecting circadian rhythms and that lead to medical illnesses including diabetes, decreased cognitive capacity, and impaired fertility. Female fertility is particularly sensitive to compromised circadian rhythms causing dysregulation of the hypothalamic-pituitary-gonadal axis (HPG) axis. Formation and correct function of the suprachiasmatic nucleus (SCN), the master pacemaker of the body, is fundamental in establishment of circadian rhythms, and is required for fertility. The SCN orchestrates the HPG axis by coordinating GnRH neuron activity with peripheral tissues and light cycles. Mature GnRH neurons release GnRH in a pulsatile fashion maintaining basal levels of sex steroids and the preovulatory luteinizing hormone surge. I am interested in understanding how compromised circadian rhythms affect hormone release, and fertility. To understand how the SCN controls hormone release and is associated with endocrine-related disorders, such as diabetes and fertility, I use a number of transgenic mouse models in combination with behavioral studies such as wheel running activity and shift-work-like light settings. We following collect blood and tissues to study the molecular mechanism giving rise to infertility. Research questions which we are currently working on include, how disruption of circadian rhythms in adulthood affects hormone release in males and females, and how this relate to diabetes and fertility.

Terra Plank (Miles F. Wilkinson)

Dynamic changes in gene expression are required for a pluripotent stem cell to progressively develop into the multitude of mature differentiated cell types within an organism. The laboratory of Dr. Miles Wilkinson at the University of California, San Diego offers a STARS student an opportunity to participate in a project that aims to understand how post-transcriptional control of gene expression regulates neural development.  Specifically, we are interested in how a conserved and highly selective RNA turnover pathway—called nonsense-mediated RNA decay (NMD)—regulates stem cell pluripotency, proliferation and differentiation decisions. Analogous to how transcription factors control the synthesis of subsets of mRNAs, NMD controls the decay rate of specific subsets of mRNAs.  By collaborating with transcriptional mechanisms, NMD can dramatically up- and down-regulate mRNAs during developmental transitions.   NMD is also of clinical significance, as disruption of this pathway is associated with several human diseases, including intellectual disability and pancreatic cancer.  Using gene knockout experiments coupled with phenotypic and transcriptome analysis in stem cells models of neural differentiation, we are probing how NMD controls the neural differentiation process. Depending on his or her specific interests and experiences, we would tailor an individual project for a STARS student to support these efforts.  The student will work closely with a post-doctoral researcher for technical and experimental guidance, as well as how to communicate the data in both written and oral formats. 

Skaggs School of Pharmacy

Vivian Hook

The overall goal of our research is to define primary peptide and protease mechanisms of human brain diseases to find new drug targets for therapeutics discovery.  This approach is being utilized for discovering new mechanisms as drug targets to address the unmet need for therapeutic agents to treat devastating brain diseases of Alzheimer's disease, Huntington's disease, traumatic brain injury, mental disorders, and neurological conditions.  New disease mechanisms are discovered by advancing knowledge of basic neuronal mechanisms of how the brain cells communicate by neurotransmitters, the fundamental basis of brain function.  Understanding of the normal brain neurochemical communication is necessary to define how dysregulation of communication among brain cells causes serious brain disorders.  Our experimental approaches utilize interdisciplinary technologies in neurochemistry, molecular and cellular neurobiology, computer sciences, and human disease neuronal models.  Scientific design of cutting-edge research is essential to the success of our work to advance new brain mechanisms into drug discovery efforts.  This research strives to have future impact to improve the lives of those suffering from deleterious brain disorders. 

Students should have completed college level courses in chemistry, biochemistry, biology and preferably neurobiology.  Basic knowledge of bioinformatics is utilized in the research.  Specific summer research projects will be organized based on the student's background and experience.

Scripps Institution of Oceanography

Sarah Gille

Standing on the beach, you can watch waves crash against the shore.  The physics of these waves, known as surface gravity waves, is generally well understood.  However, we have lingering questions about how surface waves can influence satellite measurements of sea surface height, and about how waves vary from season to season or from year to year.  The aim of this project is to use buoy observations along with satellite-derived wave data to evaluate wave variability off the California coast and in comparison regions across the world.  We'll compare these observational results with output from a wave model (WAVEWATCH III) forced by winds and ocean currents. These questions are relevant for the future of satellite missions and will broaden our knowledge on how waves can impact the upper ocean. (Angelica Gilroy)

Jenny Hofmeister

Octopus predatory behaviors and their impact on recovering abalone populations:

Octopuses are ubiquitous and important predators in the rocky reef ecosystem. However, little is known about how they move through and utilize their environment. As voracious predators, they have significance impacts on the abundance and diversity of benthic invertebrates, especially populations of endangered and depleted species like abalone. Questions: 1) How does local octopus abundance and density change across seasons, and do these metrics correlate with abiotic and biotic variables? 2) What is the predatory impact of octopus on outplanted juvenile abalone, and how can outplanting methodology help to mitigate these effects? 3) Can octopus deterrents be developed to mitigate octopus predation on outplanted abalone? 4) To what extent is octopus prey handling behavior and drill placement learned, and what components are innate? Methods: These research questions are addressed using a combination of SCUBA field work, lab experiments, and statistical modeling. If an applying student wishes to participate in the SCUBA portions of the study, he or she must already hold an AAUS SCUBA certification through UCSD or an equivalent organization. Octopus densities and habitat characteristics will be monitored using regular SCUBA surveys. In collaboration with the California Department of Fish and Wildlife (CDFW) and the National Oceanographic and Atmospheric Administration (NOAA), several thousand tagged juvenile red abalone will be placed in the environment (outplanted) and survivorship and mortality of these abalone, as well as octopus response, will be closely monitored using SCUBA surveys. Abalone shell coatings that could potentially deter octopuses and an assessment of octopus prey handling behavior will be tested using laboratory behavioral trials. Implications: This research will greatly advance our understanding of octopuses as behaviorally complex and flexible predators, and inform analyses of the evolution of problem solving and advanced cognition. Additionally, all results will be used by CDFW and NOAA to maximize the success of the restoration of the endangered white abalone in Southern California. 

Paul Jensen

Many of the bacteria living in the ocean have the genetic potential to produce antibiotics and other biologically active natural products. Yet under normal laboratory culture, most of these compounds are not produced. This project will employ ecological approaches to trigger antibiotic production in marine bacteria. Challenge assays in which bacteria are cultured with potential competitors will be used as a method of induction. Antibiotic activity will be monitored using these bioassays and the active compounds isolated and identified. The goals are to develop new methods for antibiotic discovery and to demonstrate that they can be effectively employed for this purpose. The results will also provide new insight into the ecological functions of antibiotics in nature. (Emily Aguirre - Chemical Ecology of Naturally Produced Brominated Compounds)

Lisa Levin

There is growing interest in elucidating the forces shaping deep-sea biodiversity, determining how this biodiversity might be affected by human activities such as energy extraction or bottom fishing , and what the consequences are for the functions and services provided by deep ecosystems. Levin Lab research in summer 2017 will examine how deep-sea heterogeneity in methane seepage shapes biodiversity and its services. A research cruise in May-early June 2017will be recovering 7 year old colonization samples and collecting new faunal samples from carbonate rocks and sediment cores from methane seeps and surrounding habitat off Costa Rica (400-1850 m water depth).  This summer we are seeking motivated students to help sort, quantify, identify, photograph and analyze these samples.The research will contribute to better understanding of how chemosynthetic communities interact with the rest of the deep sea, and what this might mean for designation of deep-sea protected areas on continental margins.

Lauren Nadler (PI Ryan Hechinger)

Parasites are increasingly being recognized as important players affecting individuals, populations, communities, and even ecosystems. Some parasite species change their host’s behavior, making the host more likely to be eaten by a predator. This is often in the parasite’s interest, as the predator is the next host in the parasite’s life cycle. This project is studying a behavior-modifying trematode parasite that encysts on the brain of the California Killifish. We know that the parasite makes infected fish 30 times more likely to be eaten by the parasite’s next host, which is a wetland bird. But, we still do not know exactly how many more fishes the birds are able to eat given the parasite’s behavior modification. Hence, this project seeks to quantify how much this parasite actually ‘delivers’ fishes to birds in our coastal wetlands. This work will provide a better understanding of a major component of biodiversity (parasitic species) and will provide information that will increase our understanding of their role in community interactions.

Chiara Romano (PI Greg Rouse)

Seasonal and episodic climate events may enhance the transport of matter from the shore to the ocean. What is the fate of the terrestrial debris and wood that accumulate on the ocean floor? Sunken wood attracts a variety of deep-sea species including distinct and specialized invertebrates and chemosynthetic bacteria. There are numerous species of mollusks that have been discovered on the wood that are able to digest the cellulose. Also there are various polychaete worms and a variety of crustaceans. Very little is still known about this unique community. The summer intern will analyze wood samples collected from various deep-sea sites (400- 1200 m deep) from the Pacific and Atlantic Oceans. We will analyze and compare the extracted invertebrate fauna by means morphological and molecular analyses (DNA sequencing). The results will provide new insight into the deep-sea species diversity and dispersal. These questions are also relevant to investigate the matter and energy exchanges between coastal and deep-sea regions and to understand the potential impacts of episodic climate/oceanographic events on deep-sea.

Ana Sirovic

Blue whales are the largest animal that has ever lived on our planet and they are seasonally common off Southern California. They produce distinctive songs during the mating season, as well as social calls during foraging.  We are using seven years of passive acoustic data to study their presence, habitat use, and response to anthropogenic sound in this area.  Most of the previous work has been focused on songs, as they were easily detected using automatic methods. The summer intern will contribute to this large project by running a new automatic detector that was recently developed for foraging-type blue whale calls on multiple years of data available from the region.  This analysis using the additional call type will expand our understanding of blue whale presence and habitat use off Southern California, which is particularly important as this is one of their primary foraging grounds. (Lynnette Reed - The Effect of Navy Sonar on Blue Whale (Balaenoptera musculus) Calling Behavior in Southern California)

Sociology

Mary Blair-Loy

How does gender matter to the course of professional careers? What is the current state of the Glass Ceiling for women in U.S. corporations? What is the current state of the Stained Glass Ceiling for women in religious leadership? This STARS student researcher’s time will be split between two projects: the first looks at women’s attainment in high-level executive positions in large U.S. corporations, and the second considers women’s attainment in clergy leadership positions in the Episcopal Church. Both projects will give the student researcher the chance to work with unique datasets, maintaining the databases and coding data for analysis. Other duties will include research in the existing sociological literature and thinking creatively about project findings to frame questions for future research. The STARS student researcher will be directly engaged in the nitty-gritty of social science research, working with data and helping to generate research findings while working closely with a faculty member and a graduate student. The student can expect daily to semi-weekly oversight in the form of regular check-ins and at least one longer meeting each week. (Ruben Casillas - Glass Ceiling in the Corporate World) (Janette Govea – Are women underrepresented in executive positions? Does this mean the chances of women in CEO positions seem bleak?)

Kwai Ng

My research focuses on British colonial bureaucracy in the first half of the 20th century. The actual research involves going through some archival materials - minutes, letters, policy documents, biographies etc. Most of the materials should be available in our library or online. The goal is to see what kind of interactions there were between the metropole and the crown colonies in the period of “gradual retreat.” I’m happy to work with students about doing archival work and some qualitative analysis of documents.