2017 Symposium Poster Presentations

2017 SYMPOSIUM POSTER PRESENTATIONS

LIFE SCIENCES

  • Sarah Ackley
    Allison & Aneel Bhusri Scholar
    UC San Francisco - Epidemiology
    PI:Travis Porco

    “Comparing Exponential, Power-Law, and Lognormal Distributions for Predicting Vaccine-Preventable Disease Incidence Pre- and Post-Control”

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  • Benjamin Barad
    ARCS Foundation Scholar
    UC San Francisco - Biophysics
    PI:James Fraser

    “Unraveling the Processive Mechanism of Acidic Mammalian Chitinase”

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  • Andrew Brandon
    Martha & Greg Ryan Scholar
    Lonna Wais Scholar
    UC Berkeley - Plant & Microbial Biology
    PI:Henrik Scheller

    “Optimizing Biofuel Crops through Modification of Cell Wall Composition”

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  • Candace Britton
    Betty & Bruce Alberts Scholar
    Prisca & John Geeslin Scholar
    UC San Francisco - Biochemistry/Molecular Bio
    PI:Alexander Johnson

    “Evolution of Transcription Factor Function”

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  • Caleb M. Bryce
    Marie & Barry Lipman Scholar
    UC Santa Cruz - Ecology & Evolutionary Biology
    PI:Terrie Williams

    “The Effects of Prey and Habitat Heterogeneity on Denali Wolf Movements and Energetics”

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  • Lauren Byrnes
    Deborah Mann Scholar
    UC San Francisco - Developmental Stem Cell Biology
    PI:Julie Sneddon

    “Interrogating Cellular Heterogeneity in Mouse Pancreatic Development Using Single-Cell RNA Sequencing”

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  • Alma Yesenia Ceja
    Maura & Robert Morey Scholar
    Barbara & Richard Rosenberg Scholar SF State University - Biology
    PI:Jonathon Stillman

    “Modeling the Future Distribution of an Intertidal Crab Concerning Global Climate Change”

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  • Witney Chen
    Kayla and Jamie Grodsky Memorial Scholar
    UC San Francisco - Neuroscience
    PI:Philip Starr

    “Fronto-Subthalamic Modulation of Movement Inhibition in Parkinson's Disease”

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  • Helen E. Chmura
    Ray Benton Family Fund Scholar
    UC Davis - Animal Behavior
    PI:John Wingfield & Thomas Hahn

    “Weathering the Storm: Yearly Variation in Migration and Reproduction in Arctic-Breeding Birds”

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  • Mark DeBlois
    ARCS Foundation Scholar
    UC Davis - Earth & Planetary Sciences
    PI:Ryosuke Motani

    “A New Method to Reconstruct the Soft Tissue Margin from Skeletal Elements in Extant Tetrapods with Potential Application to Plesiosaurs and Ichthyosaurs”

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  • Dwayne Evans
    Montgomery St. Foundation Endowment Fund Scholar
    SF State University - Biology
    PI:Pleuni Pennings

    “Tracking the Evolution of HIV-1 in Participants After Discontinuing PrEP Treatment”

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  • Samantha Francis Stuart
    Susan & Dennis Mooradian Scholar
    UC Davis - Pharmacology & Toxicology
    PI:Crystal Ripplinger

    “Aging and Arrhythmias: The Role Of Sympathetic Activation”

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  • Trevor Gokey
    ARCS Foundation Scholar
    SF State University - Chemistry & Biochemistry
    PI:Anton Guliaev

    “Conformational analysis of the fructose-specific transporter GLUT5 via non-equilibrium molecular dynamics”

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  • Brianna Haining
    Diana & Steve Strandberg Scholar
    Ramsay Family Foundation Scholar
    UC Berkeley - Plant & Microbial Biology
    PI:Ben Blackman and Sarah Hakev

    “Setaria Metallica: Interrogating Iron Uptake Through Natural Variation”

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  • Stephanie Holden
    Michele Goss Scholar
    UC San Francisco - Neuroscience
    PI:Jeanne Paz

    “Thalamic Excitability After Traumatic Cortical Injury”

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  • Alli Injaian
    Barbara A. Wolfe Scholar
    UC Davis - Animal Behavior
    PI:Gail Patricelli

    “Growing Up in a Noisy World: An Experimental Study of How Traffic Noise Impacts Tree Swallows”

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  • Monet Andrea Jimenez
    Lakeside Foundation Scholar
    SF State University - Biology
    PI:Diana Chu

    “Defining the Functional Roles of Histone Variant Domains Involved in Sperm-Specific Gene Regulation”

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  • Steven Kubiski
    Marcia & Max Messmer Scholar
    UC Davis - Integrated Pathobiology
    PI:Patricia Pesavento

    “Investigating the Prevalence and Pathogenesis of Canine Circovirus”

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  • Amanda Miguel
    Kimball Foundation Scholar
    Stanford - Bioengineering
    PI:Kerwyn Casey Huang

    “A Single Cell Perspective: the Rcs Stress Response and its Relationship with Cell Shape”

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  • Andrew Norman
    Roche/ARCS Foundation Scholar
    UC San Francisco - Developmental Stem Cell Biology
    PI:Jeremy Reiter

    “Evolution of a Human Gene Enhancer Near the Sonic Hedgehog Transcription Factor Gli2”

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  • Moria Robinson
    ARCS Foundation Scholar
    UC Davis - Population Biology
    PI:Sharon Strauss

    “Effects of a Unique California Soil Type on Plant-Caterpillar Food Webs”

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  • Amber Schedlbauer
    Roulhac Austin, Donna Miller Casey, Carmi Ticehurst & BeBe Trinkner Scholar
    UC Davis - Neuroscience
    PI:Arne Ekstrom

    “The Effects of Electrical Stimulation on Human Memory”

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  • Leah Schwiesow
    Wildcat Cove Foundation Scholar
    UC Santa Cruz - MCD Biology
    PI:Vicki Auerbuch Stone

    “Role of IscR in Blood Survival of Yersinia Pseudotuberculosis”

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  • Charles Seller
    ARCS Foundation Scholar
    UC San Francisco - Genetics
    PI:Pat O’Farrell

    “Embryonic Development of S Phase Length”

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  • Lucas Smith
    Dr. & Mrs. Bernard M. Kramer Endowment Fund Scholar
    UC San Francisco - Biomedical Sciences
    PI:Saul Villeda

    “Beta-2-Microglobulin Regulates the Age-Related Decline in Adult Neurogenesis and Cognitive Function”

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  • Michelle Stitzer
    Eileen D. & Lisa C. Ludwig Endowment Fund Scholar
    UC Davis - Population Biology
    PI:Jeffrey Ross-Ibarra

    “The Impact of “Jumping Genes” on Fitness Differences Between Maize Plants”

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  • Adrienne Stormo
    Roche Molecular Sciences Scholar
    UC San Francisco - Biomedical Sciences
    PI:Scott Oakes

    “Global Protein Interactome of Parkinson's Disease-Associated LRRK2 Sheds Light on Function and Disease”

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  • Jennifer Kateri Teschler
    Dana & Robert Emery Scholar
    UC Santa Cruz - Microbiology & Environmental Toxicology
    PI:Fitnat Yildiz

    “VxrAB Positively Regulates [Vibrio cholerae]i Biofilm Formation”

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  • Eric Velazquez
    Joan Diehl McCauley Endowment Fund Scholar
    UC Davis - Microbiology & Immunology
    PI:Andreas Baumler

    “Mouse Vendor-Dependent Variation in Gut Microbiota Determines Susceptibility to Salmonella Infection.”

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  • Ouwei Wang
    Ji Ing Soong Endowment Fund Scholar
    UC Berkeley - Plant & Microbial Biology
    PI:John Coates

    “Synthetic Biology Approach to Hygiene Control of Escherichia coli Continuous-Flow Bioreactor System”

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Department of Epidemiology
Ph.D. Program

Sarah Ackley

Community needs drive the research agenda in epidemiology, challenging researchers to hone and redirect their focus to solve important problems. Sarah is attracted to infectious disease modeling because it draws on her existing skills, while at the same time challenging her to gain skills in fields that she finds exciting: biology, computer science, and mathematics. For her Ph.D. dissertation, Sarah is using branching process theory with causal inference techniques to determine whether large measles outbreaks in California can be explained with information collected during routine surveillance. The ultimate goal of this research is to improve contact investigations and to better target vulnerable populations for vaccine campaigns. The results of her work will contribute to evidence-based decisions to improve policy decisions in California, nationally, and internationally.

Prediction of future disease incidence in infectious epidemiology is important for public health planning. Previous efforts have found that forecasting incidence for specific small geographic areas is challenging. However, in many cases, it is possible to forecast patterns in the distribution of disease incidence across many such small geographic areas. Theoretically, the incidence of subcritical diseases follows an exponential distribution. We assess the distribution in incidence for vaccine preventable diseases that have been targeted for elimination in the United States. We use longitudinal project TYCHO state-level weekly incidence data for smallpox, measles, rubella, mumps, and polio. Elimination/control was achieved for each of these diseases and we compare patterns both pre- and post-control. Since large, rare events may account for the majority of public health resources devoted to the control of infectious disease, we specifically assessed the role of these events in shaping the distribution of weekly incidence. The Aikake Information Criterion (AIC) was used to compare the following competing distributions: exponential, power-law, and lognormal. The Vuong test provides p-values for comparing these distributions across non-nested models. Pre-control, the exponential distribution confers a better fit than the power-law or log-normal distributions (p<0.001 in both cases). Post-control, the power-law distribution performs significantly better than the exponential distribution (p<0.001). These results indicate that the distribution of disease incidence from routinely collected surveillance data can be used to assess whether disease control has been achieved.

Department of Biophysics
Ph.D. Program

Ben Barad

Ben is interested in understanding the role that protein dynamics play in the regulation of biological function. He has pursued this goal from two angles. The first is the development of new tools for doing analysis of models and data from electron cryomicroscopy, to which end he has written a software package which uses dihedral analysis to provide novel information comparing models with the EM maps from which they were generated. The second involves research into enzymes involved in the recognition and degradation of chitin in mammalian lungs. Outside of research, Ben is obsessed with finding the perfect cup of coffee, a quest that has included learning to roast his own coffee beans.

Chitin is an abundant structural biopolymer utilized by organisms ranging from fungi to insects to squid. Composed of poly-ß-4-linked n-acetylglucosamine, chitin forms a crystalline solid, which is innately recognized and degraded by the mammalian immune system. The mechanisms of chitin recognition, signaling and degradation by the innate immune system are not fully understood. Acidic Mammalian Chitinase, a secreted processive exochitinase that is conserved across mammals, is overexpressed in the lung upon chitin challenge. I am investigating the role of this enzyme in chitin degradation and signaling.

Department of Plant Biology
Ph.D. Program

Andrew Brandon

Andrew first became interested in alternative energy and biofuels as an undergraduate at the University of Tennessee, where he spent 1-1/2 years working in an environmental microbiology lab and was introduced to all the recent advances in bio-energy research. At UC Berkeley, his focus is on gaining a deeper understanding of photosynthesis in a biochemical context and how these processes can be harnessed to produce energy useable by humans. After he earns his doctorate, Andrew hopes to pursue private industry research or possibly a career in academia.

The β-(1,4)-linked xylose homopolymer xylan comprises 20-30% of the biomass of dicot plant species and nearly half the biomass of grasses. It is the most abundant polysaccharide after cellulose in most plants and, thus, one of the most abundant biopolymers on earth. While its role in the cell wall is not entirely known, it is believed to coat and/or crosslink cellulose microfibrils. Mutants in xylan biosynthetic genes have thinner and weaker cell walls. The vessels of these mutants tend to collapse under the negative pressure of water transport, causing a severely dwarfed whole-plant phenotype. Despite its abundance in the cell wall and importance to plant health, the composition of xylan makes it unfavorable for the conversion of plant biomass to biofuels and bioproducts. The xylan backbone is composed entirely of the 5-carbon sugar xylose. Microbial fermentation of 5-carbon sugars is relatively inefficient, and the presence of 5-carbon sugars inhibits the fermentation of abundant 6-carbon sugars like glucose. Additionally, the xylan backbone is heavily substituted with acetyl groups. The released acetate creates a toxic environment for microbial fermentation. So, any engineering efforts that can reduce the amount of xylan in plant biomass can have significant positive impacts on the viability and cost-efficiency of advanced biofuels. Transformation of plants with dominant alleles is an ideal method to engineer a range of bioenergy crops, especially since few, if any, xylan mutants of biotechnologically relevant crops exist. We have therefore explored the possibility of developing dominant supressors of xylan biosynthesis. While xylan biosynthesis is still poorly understood, one pair of homologous enzymes Irregular xylem (IRX) 10 and 10-like has unambiguously demonstrated xylan synthase activity. We have been able to dramatically reduce or abolish this catalytic activity by identifying and mutating highly conserved residues in the IRX10 amino acid sequence. Then, we were able to out-compete the native IRX10 enzyme in a wild-type background by constitutively overexpressing the mutant form, the effect being to suppress xylan biosynthesis and reduce the amount of xylan in the plant to varying degrees.

Department of Biochemistry/Molecular Biology
Ph.D. Program

Candace Britton

Candace is interested in discovering the molecular bases of how organisms evolve. In her current research project she is studying a transcriptional regulatory protein across hundreds of millions of years of its evolution in order to ask how a regulatory protein evolves to coordinate the expression of new sets of target genes. Her data indicate that these regulatory proteins gain intermolecular interactions with other complexes of proteins that are then co-opted to regulate new gene sets. Before joining the Tetrad Graduate Program at UCSF, Candace graduated with a BSc in Molecular Environmental Biology with High Distinction from UC Berkeley.

Transcription factors, the sequence-specific DNA-binding proteins that control transcription, are master regulators of complex processes from development and differentiation to cellular responses to the environment. Because they regulate such important, complex phenotypes understanding how transcription factors evolve is crucial for understanding the molecular basis of how these processes evolve. In my PhD research I am asking how a transcription factor evolves a new regulatory function while maintaining a more ancient one using the yeast homeodomain transcription factor α2 as a model. Whereas ancestrally α2 functioned only in repressing the haploid-specific genes in diploid yeast, more recently it evolved a second function in the α cell mating type where it represses another set of cell-type specific genes (the a-specific genes). In order for α2 to gain the ability to repress a-specific gene transcription, the evolution of three molecular interactions was necessary: two with other proteins, the co-repressors Tup1 and Mcm1, and one with the regulatory DNA at a-specific gene promoters. I discovered that α2’s protein-protein interactions evolved before α2 actually functioned in a-specific gene repression, indicating that cooperative protein-protein interactions can evolve as exaptations in transcription factors.

Department of Ecology & Evolutionary Biology
Ph.D. Program

Caleb Bryce

Caleb’s research interests in animal behavioral ecology and field physiology are united by his commitment to answering critical questions and disseminating results of conservation relevance. His formative undergraduate research in Costa Rica and New Zealand inspired his affinity for fieldwork and dedication to scientific community outreach. Eager to understand how large carnivore physiology drives behavior and trophic interactions in a changing world, Caleb has contributed to cutting-edge conservation science for pumas, wolves, and African lions, with results published in top-tier journals including Science and Ecology. At the same time, he has emphasized outreach, mentoring, and personal leadership skills to continue developing as an effective environmental problem solver.

Animal movement is reliant upon metabolic energy, the fundamental currency of ecology. Yet quantifying the activity patterns and energy demands of large carnivores such as gray wolves (Canis lupus) in the wild has been historically difficult, resulting in an incomplete understanding of the interplay between physiological and environmental factors that affect animal movement and foraging success. To gain insight into the behaviors, travel patterns, and daily energetic expenditures (DEE) of a keystone predator, we deployed accelerometer-GPS collars on 5 free-ranging adult male wolves in Denali National Park and Preserve (DNPP) for 8 months. GPS data from 14 concurrently monitored wolves were used to assess how movement patterns and densities varied with habitat and prey heterogeneity along the northern extent of the Alaska Range. Wolves occupying habitat that supported salmon but few large ungulates (western region) had the highest average DEE (19,450 kJ/wolf), the lowest within-pack wolf densities (4.7 wolves/1000 sq km), and the smallest average pack size (2.7 wolves/pack) relative to central and eastern DNPP, which has abundant ungulate prey (4.8 wolves/1000 sq km with 6.6 wolves/pack, and 8.4 wolves/1000 sq km with 5.3 wolves/pack, respectively). On average, wolves in central DNPP traveled significantly farther each day (21 km/day) than conspecifics to the west or east (17.3 km/day each), presumably to track highly mobile caribou that seasonally migrate through this region. Wolves walked or ran approximately 10% of each day, and both movement rates and DEE in successful male breeders was the same as that of unsuccessful breeders (~17,500 kJ/wolf). Identifying such patterns represents a critical step towards evaluating how seasonality and heterogeneous prey distribution influence space use and energy allocation in large, free-ranging carnivores.

Department of Developmental Stem Cell Biology
Ph.D. Program

Lauren Byrnes

Lauren is interested in the role of the microenvironment in regulating cellular behavior. Currently, she is working on defining the microenvironment of the pancreatic beta cell niche, and understanding the role of niche cell types in the maturation and maintenance of beta cell function. Previously, Lauren completed her Master’s degree under a DAAD and Fulbright Scholarship at Heidelberg University, where she studied the interaction of the innate immune response and endoplasmic reticulum stress in bronchial epithelial cells. Outside of the lab, Lauren enjoys running, watching basketball, exploring new cities, and cooking.

Pancreatic organogenesis is a multiplex process that coordinates signaling and transcriptional networks with pancreatic epithelial lineage decisions, cell differentiation, and branching morphogenesis. Extensive previous research on pancreatic development has elucidated much of the transcriptional circuitry required to build all epithelial cell types of the pancreatic organ. However, less is understood about how the cells within the non-epithelial compartment of the pancreas, also referred to as the pancreatic niche, participate in shaping organogenesis. In this study, we perform single-cell RNA sequencing of E14.5 pancreata to first define which cell types are present at this stage of pancreatic development. In doing so, we identify known cell types within the epithelial compartment, including endocrine, acinar, and ductal cells. Within the non-epithelial compartment, we identify endothelial cells, immune cells, and erythrocytes, as expected, but also uncover distinct populations of pancreatic mesenchyme. We find a previously undefined mesenchymal cell type in the developing pancreas that harbors a gene expression profile similar to that of the mesothelium, a lining of visceral organs important for a variety of biological functions in multiple tissues. Finally, we perform a developmental time-course study in which we compile a single-cell transcriptome atlas for cells of the pancreas at E12.5, E14.5, and E17.5. These findings will inform our next steps involving ablation studies during pancreatic development and tracing lineage relationships over the course of organogenesis.

Department of Biology
Master’s Program

Alma Ceja

Alma is interested in the application of biological sciences to the emerging field of exoplanetary science and looks forward to joining the field of exobiology in characterizing exoplanets. Her current project involves agent-based ecological modeling of intertidal crab distribution. Honors include Center for Student Research Fellow at CSU-East Bay, National Institute of Health Research Initiative for Scientific Enhancement Program Scholar, Jenny Low Chang Memorial Scholar, San Francisco Bay Scholarship, and Gloria Spencer University Women’s Association Scholar. Alma has worked as a research assistant for two years and has extensive customer service and food industry experience. Her outside interests include nature and single-subject photography. Alma is of Hispanic heritage and speaks Spanish fluently as well as conversational French.

Rising temperatures resulting from anthropogenically induced climate change have caused population distribution shifts over latitudes and altitudes. These range shifts often result in interspecies competition. Petrolisthes cinctipes, a porcelain crab dwelling in congregations under rocks in the mid-upper rocky intertidal zone, overlaps in range with Petrolisthes manimaculis, a competing congener species inhabiting the mid-lower intertidal zone. We implement an integrative ecological approach in which interspecies competition is addressed in efforts to predict the distribution of the model organism, P. cinctipes, under future climatic scenarios. This mechanistic agent-based model applies predicted temperature profiles in conjunction with observed environmental (habitat temperature), physiological (Arrhenius breakpoint temperature), and behavioral (escape temperature and competition strength) data gathered from a P. cinctipes population at Fort Ross, CA. Rising temperatures correlate with a downward shift of the population to cooler microhabitats, leading to greater densities and increased interspecies competition. Modeling the heterogeneous thermal landscape of the intertidal zone resulting from elevational differences, tidal waves, and fluctuating solar radiation allows for extrapolation in predicting larger spatial scale distribution patterns. In predicting patterns of a highly variable environment, this model is applicable to similar multivariate systems with altitudinally distributed populations responding to biotic and abiotic factors.

Department of Neuroscience
Ph.D. Program

Witney Chen

Witney graduated from Brown University, magna cum laude, with a B.S. in neuroscience. At UCSF she studies neural circuits in Parkinson’s disease patients to characterize the underpinnings of various motor, affective, and cognitive symptoms. She aims to better understand these circuits in order to inform advances in therapies. The lab is currently developing closed-loop deep brain stimulation, which detects maladaptive neural signals in real time to drive therapeutic, symptoms-targeted stimulation.

Parkinson’s disease is a movement disorder, and previous research has emphasized motor-related regions of the brain. In the motor cortico-basal ganglia circuit, the degree of neural synchronization to the beta band (13-30 Hz) and the severity of hypokinetic symptoms are both decreased by therapeutic medication and basal ganglia stimulation. Whether this hypersynchronization exists in other non-motor regions, and how this is modulated by therapy, are not well characterized. Here, we study prefrontal cortico-basal ganglia involvement in the cognitive control of movement inhibition. We hypothesize that the degree of beta band hypersynchronization in prefrontal circuitry correlates with deficits in the ability to cognitively control movement inhibition. We use intraoperative, multisite, high-resolution electrophysiology to assess the role of the inferior frontal gyrus (IFG) and subthalamic nucleus (STN) in rapid movement inhibition. Both the IFG and STN have been hypothesized to communicate via a hyperdirect pathway during movement inhibition. We use short-latency evoked potentials to confirm monosynaptic connectivity between the IFG and STN. We also characterize the circuit’s role in rapid movement inhibition while patients performed a stop signal task. We find stopping-related modulation of beta power in both the IFG and STN. This work will inform therapeutic ways to alter network activity to better treat specific symptoms of movement inhibition, such as freezing of gait.

Animal Behavior Graduate Group
Ph.D. Program

Helen Chmura

Helen's passion for science began as an undergraduate at Rocky Mountain Biological Laboratory while studying marmot behavior. After graduating from Swarthmore College Phi Beta Kappa with Honors in Biology, she spent a year studying the biological and social consequences of climate change for communities in sacred mountain regions of Peru, Chile, Papua New Guinea, and Tibet as a Watson Fellow. Upon her return, Helen worked for National Wildlife Federation on climate change adaptation. Her current research studies the response of migratory songbirds to global climate change in the Arctic. Helen is also an avid hiker and flautist.

Birds breeding in the Arctic face a narrow window of time in which to breed, molt, and prepare to migrate before winter sets in. With harsh weather restricting when nesting habitat and food resources are available, the appropriate timing of nesting is critical for reproductive success. Additionally, when birds breed can have downstream consequences for adults' ability to prepare for migration. In a rapidly warming Arctic, the optimal windows for breeding and migratory preparation may be changing and this may have consequences for avian populations. I examine the connection between yearly weather variation and migration and reproduction in migratory songbirds breeding near Toolik Field Station, Alaska and evaluate findings in light of the future changes projected for arctic ecosystems.

Geology Graduate Group
Ph.D. Program

Mark DeBlois

Mark is studying the evolution of animal locomotion, specifically swimming in sauropterygians, a group of extinct marine reptiles that dominated Mesozoic oceans. They "flew" underwater, akin to penguins but with two sets of flippers working in tandem. Mark spent the summer of 2016 in China as an NSF fellow examining fossil sauropterygians, spanning their transformation from primarily terrestrial to the fully aquatic locomotion unique to this group. Mark believes a scientific community that reflects the diverse backgrounds, cultures, and ideas that make up our country is the key to the full potential of US scientific advancement.

The invasion of aquatic environments by tetrapods occurred independently several times across many different lineages resulting in the convergent evolution of hydrofoil-shaped flippers. Shape is critical to the function of hydrofoils; however part of what forms this shape is the soft tissue, which is lost during fossil preservation. Consequently, studies of flipper shape and function in fossil taxa have simply assumed that the soft tissue envelope closely surrounds the bones, even though this is not the case in the flippers of some extant taxa. To address this problem, we developed a method based on extant taxa to reconstruct the soft tissue margin from fossil bones. We used radiographs and preserved museum specimens of cetaceans, penguins, sea lions, and sea turtles. Cetacean flippers were chosen for their diverse flipper shapes while still primarily used for steering and control. The rest were chosen to cover the gamut of flipper morphology used in underwater flight. First we created a library from the limb skeletons and corresponding soft tissue margin. Then using this library, we identified common trends in the spatial relationship between the skeleton and tissue using a custom Matlab script. When compared to a convex hull around the limb skeleton, our method more accurately reconstructed the shape and area of the flippers. Moreover, we found that the soft tissue along the leading edge of the flipper is very well constrained. The tissue does not extend far from the skeleton and follows its shape very closely. In contrast, the trailing edge extends significantly farther beyond the skeleton and varies with flipper function, (i.e. predominantly for steering and control as in cetaceans versus predominantly for propulsion as in underwater flyers like penguins, sea lions, and sea turtles). The soft tissue beyond the trailing edge is more constrained within functional groups than with all groups combined, emphasizing the need for identifying and specific functional analogs when reconstructing anatomy and function in extinct taxa. This project presents a quantitative method to reconstruct the soft tissue envelope around the limb skeleton of extinct marine taxa such as plesiosaurs and ichthyosaurs for the first time, opening the door to more rigorous hydrodynamic studies on these and other extinct marine taxa.

Department of Biology
Master’s Program

Dwayne Evans

An MBRS-RISE (Research Initiative for Scientific Enhancement) and Genentech Dissertation Scholar, Dwayne's research interests include the evolution of drug resistance in the Human Immunodeficiency Virus type-1 when exposed to Pre Exposure Prophylaxis (PrEP). At SFSU, his research is focused on determining whether PrEP increases the number of patients with drug resistance. Dwayne plans on pursuing a Ph.D. in bioinformatics and continuing to study the relationship between HIV drug resistance and patient infection rates. Aside from research, Dwayne enjoys mentoring undergraduates, learning R programming language and teaching locking choreography in dance classes.

HIV-1’s rapid mutation rate allows it to be efficient at producing a diverse viral genome. The diversity of HIV-1’s genome confers the virus drug resistance by allowing it to evade drug treatments. PrEP is used as a preventative against HIV-1 infection instead of a treatment for individuals already infected with the virus. PrEP is a relatively new drug prophylaxis that has not been extensively studied as an effective preventive strategy against HIV. Thus, the extent to which resistance to PrEP develops in HIV-1 infected individuals is not yet known. My research plans to evaluate the effectiveness of PrEP across multiple different studies. Some of these studies include the iPrEX, FEM-PREP, TDF2, and Partner’s PrEP Trials. In addition, I wish to examine how many individuals in the PrEP vs. placebo arm develop PrEP resistance. Ultimately, I want to determine how costly are the drug resistance mutations (DRMs).

Pharmacology & Toxicology Graduate Group
Ph.D. Program

Samantha Francis Stuart

Samantha is researching the roles of aging and chronic inflammation following heart attack, focusing primarily on modulation of inflammation as a strategy to attenuate tissue remodeling and prevent eventual heart failure. Samantha has received a pre-doctoral fellowship from the NIH-funded Pharmacology Training Program at UC Davis, and she has experience teaching general nutrition and basics of pharmacology and toxicology. Outside of the lab, Samantha's interests include yoga, cycling, and Spurs basketball.

Introduction: Cardiac function is fine-tuned by the autonomic nervous system and autonomic input is critical for the ability to respond to changes in demands – such as increased cardiac output during exercise. The physiological process of aging has been shown to result in changes in autonomic control of the heart, namely decreased vagal input and increased sympathetic activity. Aging is also associated with increased deposition of fibrosis throughout the heart. Together, these changes in sympathetic activity and fibrosis may increase the risk for arrhythmias.

Objective: To determine how aging affects the response to sympathetic stimulation in intact mouse hearts.

Methods: Young adult (3 – 4 months old) and aged adult (20 – 24 months old) C57Bl6 male mice were studied. Optical mapping was performed using an innervated heart approach. Briefly, hearts were excised with the spinal cord and thoracic cavity intact and cannulated through the descending aorta. Hearts were perfused with voltage-sensitive (Vm, Rh237) and calcium-sensitive (Ca2+, Rhod2-AM) indicators. Two stimulation electrodes were used – one situated at the apex of the heart for ventricular pacing and one inserted into the spinal canal for sympathetic nerve stimulation (SNS). For each animal, SNS thresholds were determined as the lowest stimulation frequency able to elicit a 20% increase in heart rate (HR); the high SNS stimulation frequency was set at 5 Hz more than the low threshold. After SNS hearts were perfused with isoproterenol (1μM, ISO) to assess the function of beta-adrenergic response.

Results: The low threshold for SNS stimulation was increased in aged mice (aged: 5.1±0.19 Hz vs. young: 4.0±0.47 Hz, p<0.05). Aged animals had a lower baseline HR (aged: 186±12 bpm vs. young: 280±13 bpm, p=0.025). In aged animals HR increased to 270±17 bpm with low SNS stimulation (45% increase, p=0.040) and to 447±9 bpm (140% increase, p=0.001) from baseline. Likewise, in young animals HR increased to 363±36 bpm with low SNS stimulation (30% increase, p=0.28) and to 482±11 bpm (72% increase, p=0.002) from baseline. Despite an increased susceptibility to pacing-induced arrhythmias in the aged group, there were no significant differences between action potential and calcium transient duration in the aged or young groups.

Conclusions: In this study, we showed that aging increases the stimulation threshold for SNS-induced changes in HR. However, when stimulated with supra-threshold frequencies or with ISO, HR, action potential and calcium transient responses were similar in aged and young hearts. These data suggest that altered nerve function and not necessarily β-adrenergic signaling is responsible for these differences. Thus, future studies will focus on quantifying changes in sympathetic nerve density and/or neurotransmitter content.

Department of Chemistry & Biochemistry
Master’s Program

Trevor Gokey

Trevor recently earned an MS in computer science at SFSU and plans to utilize his double MS in Chemistry and Biochemistry to research at the Ph.D. level. He enjoys leveraging aspects of computer hardware, operating systems, and programming to investigate biochemical problems, and particularly enjoys writing computational software. Trevor has already published four papers in the area of computational biochemistry, primarily using simulation techniques to study the structure and function of various macromolecules. Outside of research, Trevor's interests revolve around the science of cooking, coffee, optimization, and automation. He hopes to live long enough to witness an atomic-scale simulation of a synapse.

GLUT5 is a member of the GLUT sugar transporter family and is unique in that it passes fructose but not glucose into cells. Breast cancer cells, but not normal breast cells, highly upregulate GLUT5 in order to sustain their high metabolic demands, making GLUT5 a potential target for anti-tumor therapeutics. Other GLUT transporters are known to switch between two states during glucose passage, however recent crystallographic data suggests GLUT5 utilizes four states during fructose passage. The mechanisms which account for fructose specificity and drive GLUT5 between the four conformational states are unclear. To address this, we utilized non-equilibrium molecular dynamics techniques to model fructose permeation through GLUT5. The methods shown here revealed several energy barriers that fructose must overcome to pass through GLUT5 and these barriers identified key residues which account for GLUT5 substrate specificity.

Department of Plant Biology
Ph.D. Program

Brianna Haining

Brianna began her studies at New York University Abu Dhabi (NYU’s “World’s Honors College”) as a part of the school’s inaugural class. Now, she is a rising second year graduate student at UC Berkeley. As a joint student in the Hake and Blackman labs, she is pursuing research that lies at the interface of adaptation and development. Specifically, Brianna is investigating variation in the iron uptake properties of Setaria italica, or foxtail millet, which is a crop important in many regions of the developing world. While she is not at lab, Brianna enjoys knitting and SCUBA.

Iron deficiency is the most common deficiency, affecting over two billion people including many women of childbearing age and children. The associated costs are immense in terms of both human life and economic output. Different cereal cultivars vary in their uptake and allocation of heavy metals, including iron. It is possible that these differences in iron uptake are due to differences in the soil at the cultivar’s origin. To test this hypothesis in the staple crop Setaria italica, 15 different cultivars were selected based on diversity of soil type at origin. Then, a hydroponic system was developed in order to test the iron uptake properties of these S. italica lines. Plants were exposed to excess (1 mM), sufficient (0.15 mM), and insufficient (0.06 mM) concentrations of Fe-EDTA for the duration of their life cycle. The flag leaves from all individuals were harvested and subjected to MS analysis. Plants exposed to extreme iron conditions produced lower weight panicles and were on average shorter than their counterparts grown in iron sufficient media. Cultivar type also influenced final flag leaf iron content. Future work will investigate the genetic basis of this variation.

Department of Neuroscience
Ph.D. Program

Stephanie Holden

Stephanie is investigating how maladaptive neural circuit plasticity after traumatic brain injury may lead to the development of seizures. She hopes her research will contribute to the identification of new neural targets for preventing or treating post-traumatic epilepsy. In a separate project, she is exploring whether cell transplants into the brain can reduce cortical circuit excitability after stroke. Stephanie is pursuing her interest in science outreach through programs such as the Science & Health Education Partnership and NeuWrite San Francisco. Outside of science, she enjoys baking, planning social events, and partaking in outdoor activities such as hiking, running, kayaking, and soccer.

Post-traumatic epilepsy (PTE) is a type of epilepsy that results from traumatic brain injury (TBI). While we need treatments that prevent PTE, we do not know how TBI leads to epilepsy. The thalamus, a deep brain structure that is important for sleep, sensation, and attention, generates abnormal neuronal activity in some types of epilepsies and may also be affected by TBI. I hypothesize that injury changes the excitatory and inhibitory connections between neurons in the thalamus, and that manipulating the activity of the thalamus could interrupt epileptic seizures that develop after injury. To test these hypotheses, I am studying changes in neuronal connections in a rodent model of TBI, and I will try to stop seizures by controlling the activity of thalamus. My results will reveal how TBI causes the formation of abnormal connections in the brain that may lead to epileptic seizures, and could also reveal a novel target for preventing or curing PTE.

Animal Behavior Graduate Group
Ph.D. Program

Allison Injaian

Allison’s research interests lie at the intersection of animal behavior, conservation biology, and urban ecology. She has completed research demonstrating noise pollution impacts across multiple levels of biological organization in a native bird, the Tree Swallow. These results are currently being written up for publication. Future projects include noise pollution impacts on telomere attrition, stress levels, oxidative damage, and return rate to breeding grounds. Allison also truly enjoys teaching and received the UC Davis 2015 Outstanding Graduate Student Teaching Award.

Traffic noise travels far beyond roads, impacting animals that live in both urban and natural environments. Non-urban animals, such as tree swallows, may suffer great consequences of noise exposure, as they are not adapted to deal with this stressor. Here, I experimentally investigate traffic noise impacts on tree swallows during the breeding period, specifically looking at changes at the behavioral and physiological levels. I will use the results of my PhD research to help inform conservation efforts of native birds.

Department of Biology
Master’s Program

Monet Jimenez

Despite the various challenges she faced as a first-generation college student, Monet was awarded the Research Initiative for Scientific Enhancement (RISE) fellowship during her first year and selected to continue her second year as an MS Dissertation Genentech Scholar. Her current research investigates how histone proteins influence the biology of chromatin and their contribution to male infertility in C. elegans. Additionally, as the co-founder and Vice President of SFSU SACNAS, she strives to create a community where her colleagues are connected to opportunities in science, and youth are empowered to pursue advanced degrees in science. In the future she intends to apply to MD/Ph.D. programs where she can study the impact of health disparities on a molecular level. She is determined to be a compassionate leader in both medicine and science.

During spermatogenesis, it is imperative that the right genes are accessible at a precise time and place; therefore, the regulation of DNA accessibility is a highly complex process. DNA is organized into nucleosomes composed of the core histones H2A, H2B, H3, and H4, which are then further compacted into chromatin. Histones are central components of chromatin that influence how tightly, or loosely, DNA is packaged. Helping to diversify how chromatin compaction is regulated, core histones are replaced with respective histone variants. Histone variants have been key contributors to a multitude of cellular processes gone wrong, including cancer. Though their incorporation is conserved, it is not fully understood how they alter DNA accessibility. In C.elegans, there are two key H2A variants: the evolutionarily conserved HTZ-1 and sperm-specific HTAS-1. With unique incorporation during spermatogenesis, and since mutants lacking their expression results in sterility and sub-fertility, respectively; we are interested in understanding how these histone variants function distinctly during spermatogenesis. Upon comparison, these histone variants differ the most in their N- and C- terminal domains, thus I hypothesize that these variable domains correlate to their unique incorporation and differential influences on DNA accessibility. To test this, I will be using Fluorescent-In-Situ-Hybridization to visualize if HTZ-1 and HTAS-1 preferentially localize to “active” DNA and/or “repressed” DNA. I will also be using the CRISPR/Cas-9 genome editing system to engineer independent expression of the differing domains to identify important regions that are required for successful spermatogenesis. I expect that the N-term and C-term domains of HTZ-1 and HTAS-1 will be key, since these regions are most accessible to cell-type specific players involved in regulating chromatin. By assessing each domain on an independent basis and whether these variants are turning genes “on” or “off,” we provide insight about how histone variants work together to sustain cell-type diversity. This will not only bridge gaps in knowledge about the understudied spermatogenesis, but will provide insight about the way cells regulate DNA accessibility in a tissue-dependent manner.

School of Veterinary Medicine/Integrative Pathobiology
Ph.D. Program

Steven Kubiski

A DVM and board-certified anatomic pathologist, Steve completed a joint veterinary pathology residency through UC Davis and the San Diego Zoo, following a year as a post-DVM research associate and diagnostician. He has sustained a primary interest in the pathophysiology of infectious diseases, especially mechanisms by which viruses evolve to infect different target cells as well as new host species. His current research is focused on characterizing the seroprevalence, genetic diversity, and pathogenic potential of a circovirus recently discovered in dogs.

Dr. Kubiski’s research focus is aimed at complementing advanced techniques in viral discovery with investigation of the pathogenic potential of novel or newly emergent viruses and their potential impact on animal health. In 2012, our laboratory discovered a novel canine circovirus in a dog that presented at necropsy to Dr. Kubiski with a progressive, systemic, and fatal illness as well as pathologic changes in the tissues suspect for a viral etiology. Circoviral RNA and capsid protein was identified in the tissues and lesions of this dog, as well as four other diseased dogs in a limited retrospective analysis of post-mortem cases. Over the past year, Dr. Kubiski has collected sets of tissues from pathologists and clinicians throughout the U.S. as well as cases from Germany and Canada, documenting the tissue distribution and lesions associated with the presence of circovirus. Interestingly, this virus can also be detected in the feces of healthy dogs. In order to determine the significance of this virus in the dog population with respect to the apparent disparate outcome of infection, Dr. Kubiski’s objectives are as follows: 1) Determine how common exposure is to the virus by conducting a multi-institutional serosurvey using an ELISA that was developed, optimized, and validated by Dr. Kubiski. 2) Sequence and analyze the genomes of circoviruses detected in dogs with diarrhea, and compare this to genomes of virus detected in healthy dogs to determine if degree of genetic variation or specific variants might account for differences in pathogenicity. To date, the clinical scenario, pathologic changes, and genetic information of sequenced canine circoviruses appears to closely resemble the situation with one of the only other mammalian circovirus, porcine circovirus (PCV). In pigs, non-pathogenic isolates of PCV are remarkably stable whereas those associated with severe, worldwide morbidity exhibit a significant amount of genetic variation. 3) Isolate different variants from the aforementioned dogs using peripheral blood mononuclear cells, to serve as pilot work for future studies on co-infections and in-vitro pathogenesis.

Department of Bioengineering
Ph.D. Program

Amanda Miguel

Amanda's graduate work focuses on understanding the shape and growth of bacteria under stressful environments, using a combination of high-throughput genetic assays, biochemical analysis of bacterial structure, and single cell level microscopy. Her research interests also include structural analysis of protein-drug relationships through computational modeling, with a specific interest in bacteria-targeting antibiotics. Outside of her research, Amanda pursues her passion for mentoring and teaching as a co-coordinator for the Bioengineering TA mentorship program, and also volunteers her time for educational outreach to nearby middle schools. Her hobbies include biking, playing guitar, and scrapbooking.

The Rcs Phosphorelay is a stress response pathway that responds to perturbations in the cell envelope and controls the expression of a variety of genes involved in capsule formation, motility and virulence. Induction of the Rcs system via cell envelope stress critically relies on non-essential outer membrane lipoprotein RcsF, and it has been shown that the level of this protein in the envelope is key to the induction of the Rcs system. Here we examine the effects on cell morphology upon activation of the system using an inducible RcsF system. In both batch culture and single cell experiments, we observe that induction of the system causes a corresponding decrease in cell size over time. Through microfluidic experiments we characterize the length, growth rate and division time of single cells transitioning to a shorter length after induction, giving insight into the molecular mechanism by which single cells change shape via Rcs activation.

Department of Developmental Stem Cell Biology
Ph.D. Program

Andrew Norman
Roche/ARCS Foundation Scholar

Andrew is interested in the evolution of sperm development among primates. In other developmental systems, evolution of non-coding genomic regions (gene enhancers) has been shown to underlie the evolution of phenotypes. However, classical enhancer screening systems are typically used to discover embryonic enhancer activity and are impractical for the discovery of enhancer activity in adult developmental systems, such as sperm formation. To overcome this, he has recently developed a novel, in vitro method of screening potential sperm development enhancers, and is using it to screen enhancer candidates that cannot be otherwise verified. This knowledge could lead to therapeutic interventions in sperm formation. In his spare time, Andrew is an avid gardener, hiker and all-around naturalist. He is continually inspired by the great works of science fiction literature, both new and classic. Andrew’s goal is to lead his own research group or entrepreneurial effort, either in academia or the private sector.

Human sperm are phenotypically distinct from those of other primates. Since gene enhancers underlie the evolution of traits in many organisms, we undertook a high-throughput screen of human-evolved sequences to identify candidate enhancers in an in vitro sperm cell model. One candidate is near the transcription factor Gli2, a critical downstream effector of the Sonic Hedgehog pathway, which has been implicated in sperm development. Chromatin interaction data suggests that this enhancer interacts with the Gli2 gene, supporting a role in driving Gli2 expression. We are generating mouse models in which this enhancer has been modified in order to demonstrate its requirement for normal Gli2 expression, normal mouse embryonic development and normal adult sperm formation.

Population Biology Graduate Group
Ph.D. Program

Moria Robinson

For her dissertation research, Moria is studying how variation in soil resources alters the structure of food webs between plants, caterpillars, and their natural enemies. Her work focuses on a diverse, yet understudied fauna of moth caterpillars in California chaparral vegetation, contributing life history data and images to online identification resources and upcoming field guides. Her research emphasizes undergraduate mentorship in the lab and field, and has led to independent student research that examines effects of wildfire on insect densities and growth.

Soils in California are highly diverse, and this variation can have remarkable effects on biodiversity. Serpentine soils in Northern California are known for being poor in nutrients and high in heavy metals, making them very harsh environments for plant growth. These effects on plants can, in turn, alter the herbivore communities they support. For my dissertation, I am studying how soil type alters plant characteristics, and how these changes cause herbivore communities to be more or less diverse. I have found that harsh serpentine soils support less diverse, but more specialized assemblages of butterfly and moth caterpillar. These findings help us understand how variation in soils can impact diversity throughout the food web.

Neuroscience Graduate Group
Ph.D. Program

Amber Schedlbauer

Amber has been working on a project that will use direct electrical stimulation of the human brain to improve memory performance in individuals. Her published work in Scientific Reports employed neuroimaging and graph theory techniques to construct whole-brain networks that are linked to the underlying biological process of memory retrieval. Amber’s interests involve using more integrative approaches to discover the underlying mechanisms of memory retrieval that can eventually be applied to other cognitive domains, such as Alzheimer’s Disease and normal aging. Outside of her research, she enjoys climbing and hiking in the beautiful California outdoors.

The ability to successfully navigate our complex internal and external environments relies on access to records of stored information, or memories. A subset of this information is referred to as episodic memory, where specific details of a past event can be remembered. Modern theories of the neural basis of episodic memory retrieval posit a critical role for network interactions among different regions throughout the brain. While performing a memory task, direct brain recordings in a unique patient population were obtained using a technique called intracranial electroencephalography. Based on this recorded activity, individual functional networks were constructed and used to identify regions of importance when people correctly remembered information. Those regions were then directly electrically stimulated to try to modulate memory. When undergoing stimulation, the memory performance of the participants suggested that electrical stimulation can have targeted effects on retrieval of information. This study has enhanced our understanding of episodic memory processes, an outcome that could ultimately benefit those with memory problems, like Alzheimer’s patients.

Department of Biology
Ph.D. Program

Leah Schwiesow

Leah graduated from Gonzaga University in 2009 with a BS in Chemistry. After a couple of years of working in the biotech industry, she discovered her love for microbes. In the lab, she is interested in determining how a transcription factor, lscR, works to sense changing environmental conditions within the host to optimize expression of the virulence factors in the enteric pathogen Yersinia pseudotuberculosis. After graduation, Leah hopes to continue research in microbial pathogenesis and work to discover novel targets for antimicrobial therapies. In her spare time, she enjoys exploring the world with her friends and family.

To be able to understand how to treat infectious diseases, we must understand the processes that allow pathogens to survive and thrive in the host. The human pathogen Yersinia pseudotuberculosis enters the mammalian host through the oral route of infection, often through contaminated food or water. Upon entering the small intestine, the bacteria are able to transverse the gut barrier and travel to the mesenteric lymph nodes. From there, Y. pseudotuberculosis can enter the bloodstream to disseminate to deeper tissues such as the liver and the spleen. Throughout this infection route, Y. pseudotuberculosis experiences changes in oxygen tension, oxidative stress, and iron availability and must respond accordingly to survive. We previously demonstrated that Y. pseudotuberculosis requires the iron-sulfur cluster-containing global transcriptional regulator IscR to cause disease in the host. We hypothesize that IscR senses changes in the host environment to optimize expression of genes important for Y. pseudotuberculosis pathogenesis. Here, we demonstrate that a ΔiscR mutant has a survival defect in whole blood. To understand the basis for this survival defect, we performed transcriptomics analysis comparing a ΔiscR strain and a WT strain of Y. pseudotuberculosis grown in whole blood or regular lab media to (1) determine factors that are important for Y. pseudotuberculosis blood survival and (2) determine which of these factors are controlled directly or indirectly by IscR. We determined a set of 78 genes that were differentially expressed between the WT and the ΔiscR mutant in whole blood, but not regular lab media. Currently, we are analyzing these hits to determine their role in IscR-mediated Y. pseudotuberculosis pathogenesis.

Department of Genetics
Ph.D. Program

Charles Seller

Charles is studying the developmental regulation of DNA replication in the Drosophila embryo. His project is focused on understanding how the protein Rif1 is deployed by the fly embryo to delay the replication of heterochromatin at the mid-blastula transition. Charles enjoys running and reading when not in the lab.

The length of S phase (the amount of time it takes to replicate the genome) changes by over 200 fold during an animal's life. Very little is known about how these developmental changes occur, and although many molecular pathways controlling features of replication time have been identified, their actual contributions to S phase length have been difficult to resolve. In the embryos of diverse animal species, development begins with a series of rapid cell divisions that slow down dramatically over embryogenesis. In the embryo of the fruit fly, Drosophila melanogaster, this deceleration occurs through the abrupt prolongation of S phase duration. Here we describe a new developmental function for the conserved DNA replication regulator Rif1 in controlling the lengthening of S phase in the embryo. Using high-resolution live imaging on developing embryos we provide new insight into the regulation of Rif1 during the cell cycle. Our work generates a new model of a developmental program controlling the duration of S phase.

Department of Biomedical Sciences
Ph.D. Program

Lucas Smith

During his time in San Francisco, Lucas has had the opportunity to work in both industry and academia and to contribute to a number of publications. Lucas is interested in cancer and aging, and he is currently working on a project aimed at identifying rejuvenating factors that mitigate the age-related decline in learning and memory seen in mice and humans. He is specifically interested in uncovering the sources of the “pro-aging” factors found in old blood, such that we can mitigate their production and hopefully slow the aging process. Outside of science, he enjoys hiking, biking, and cooking.

Aging drives cognitive and regenerative impairments in the adult brain, increasing susceptibility to neurodegenerative disorders in healthy individuals. Experiments using heterochronic parabiosis, in which the circulatory systems of young and old animals are joined, indicate that circulating pro-aging factors in old blood drive aging phenotypes in the brain. Here we identify β2-microglobulin (B2M), a component of major histocompatibility complex class 1 (MHC I) molecules, as a circulating factor that negatively regulates cognitive and regenerative function in the adult hippocampus in an age-dependent manner. B2M is elevated in the blood of aging humans and mice, and it is increased within the hippocampus of aged mice and young heterochronic parabionts. Exogenous B2M injected systemically, or locally in the hippocampus, impairs hippocampal-dependent cognitive function and neurogenesis in young mice. The negative effects of B2M and heterochronic parabiosis are, in part, mitigated in the hippocampus of young transporter associated with antigen processing 1 (Tap1)-deficient mice with reduced cell surface expression of MHC I. The absence of endogenous B2M expression abrogates age-related cognitive decline and enhances neurogenesis in aged mice. Our data indicate that systemic B2M accumulation in aging blood promotes age-related cognitive dysfunction and impairs neurogenesis, in part via MHC I, suggesting that B2M may be targeted therapeutically in old age.

Population Biology Graduate Group
Ph.D. Program

Michelle Stitzer

Michelle’s work in Plant Sciences focuses on the evolutionary genetics of transposable elements in com and its wild relative teosinte. While most genes are reliably transmitted from one generation to the next, static in their position in the genome, transposable elements can move across and between chromosomes. Michelle is broadly interested in linking molecular changes generated by the movement of transposable elements to evolutionary innovation, genetic load, and adaptation. Outside of the lab, she enjoys exploring the California flora.

Transposable elements were discovered in maize in the 1940’s as unstable loci, apparent when certain genetic crosses yielded kernels with unexpected purple speckles. Today, we know these “jumping genes” are present across the tree of life, and generate mutations that change the genome of plants, animals, and fungi. Inside the genome of every cell, there is a tumultuous ecosystem of transposable elements struggling for control of the genomic landscape, sometimes cooperating with related transposable elements to do so. The host genome endeavors to restrain these mobile elements, as their movement generates mutations that can be harmful to the function of the host genome. In most genomes, this selfish activity is restrained by the host, and transposable element DNA makes up a minority of the genome. The maize genome presents a paradox - over 85% of the maize genome is made up of transposable elements, yet the plant survives with seemingly little ill consequence. The actual fitness consequence of different transposable element copy number has not yet been tested in maize, so it is unknown whether plants with a handful of copies of transposable elements survive and reproduce better than plants with thousands of copies. My analysis of existing data shows no correlation between copy number and fitness, a result not seen in other plants like rice that naturally have fewer transposable elements. This suggests that the maize genome has specific mechanisms to restrain damage from transposable elements, but my result is confounded by the hundreds of thousands of single nucleotide differences that exist between various genotypes of maize. To disentangle these data, this spring I will plant populations of maize that have different numbers of “Mutator” and “Dotted” transposable elements in their genome, but have otherwise identical genetic backgrounds. I will grow these plants in a controlled environment, so the only difference between plants is the copy number of transposable elements. This will allow me to attribute differences in plant growth and survival to copy number of different types of transposable elements. This quantitative understanding of the fitness costs of transposable element movement will provide novel data for understanding and predicting the response of different maize genotypes to agriculturally stressful environments.

Department of Biomedical Sciences
Ph.D. Program

Adrienne Stormo

Adrienne developed an interest in basic scientific research as a child, when she would spend weekends and summers working in her mother’s genetics lab. She became curious about what genetics and cell biology can tell us about human health and disease. Currently, she is studying the function of LRRK2 (leucine-rich repeat kinase 2), a large kinase that plays a role in both familial and sporadic forms of Parkinson’s Disease. Outside of the lab, Adrienne has a passion for teaching and mentoring. Since high school, she has been tutoring students and volunteering at local public schools in hopes of encouraging kids to pursue science in college and beyond.

Mutations in the gene that encodes leucine-rich repeat kinase 2 (LRRK2) are the most common known cause of Parkinson's Disease (PD), but we have very little knowledge about what the LRRK2 protein does in healthy cells and how mutations lead to PD. We recently identified a novel LRRK2-interacting protein that alters LRRK2 localization and regulates protein turnover. Defining LRRK2’s regulatory network will result in new understanding of LRRK2 biology, and potentially uncover new targets for therapeutic intervention in PD.

Department of Microbiology & Environmental Toxicology
Ph.D. Program

Jennifer Teschler

The goal of Jennifer’s project is to elucidate the molecular mechanisms underlying virulence and environmental survival in the human pathogen Vibrio cholerae. During its residence in the aquatic environment and the human host, V. cholerae encounters a number of shifting environmental factors. V. cholerae utilizes two-component signal transduction systems (TCSs) to monitor and respond to these changing conditions, as TCSs are the primary signaling mechanism in most bacteria. Jennifer’s research group has identified a novel TCS, VxrAB, that regulates both intestinal colonization and biofilm formation, a process that is critical for environmental survival and transmission to human hosts. Further study of this TCS may lead to the identification of new targets for the inhibition and treatment of gastroenteric pathogens, as TCSs are absent in mammals and represent an attractive target for future antimicrobial agents.

Two-component signal transduction systems (TCSs) play an important role in the ability of pathogenic bacteria to sense fluctuating environmental conditions and elicit the appropriate biological responses. The facultative human pathogen [Vibrio cholerae]i utilizes TCSs to sense and activate responses to the variety of environmental factors inside and outside of the host. This includes the regulation of biofilm formation, an important growth mode during both the intestinal and transmission stages of [V. cholerae's]i life cycle. In this work, we demonstrate that the recently characterized TCS VxrAB is a novel regulator of [V. cholerae]i biofilm formation and is required for efficient biofilm formation.

School of Veterinary Medicine/Integrative Pathobiology
Ph.D. Program

Eric Velasquez

In 2011, Eric became the first person in his family to complete college when he graduated with a BS in Biochemistry and Molecular Biology from UC Davis. He stayed to pursue the combined DVM-Ph.D. program and has earned numerous scholarships to fund all stages of his education. Eric studies how the gut microbiota protects us against diarrheal pathogens and intestinal inflammation. In addition to research, he manages a laboratory animal colony and mentors younger scientists. After biking home from school each day, Eric learns how to be a parent.

It is well established that the host genome determines susceptibility of laboratory mice to disease. We show that a second factor, natural variation in the composition of the gut microbiota, influences susceptibility to Salmonella infection. Interestingly, endogenous Enterobacteriaceae, a low abundance taxon that is not readily detected by microbiome sequencing, was identified as a driver of increased resistance. Our data suggest that natural variation in the gut microbiota composition can influence experimental results and the reproducibility of in vivo mammalian models. Furthermore, our results have ramifications for understanding the variability between individuals in their susceptibility to human infectious diseases.

Department of Plant Biology
Ph.D. Program

Ouwei Wang

Ouwei’s project investigates the regulation of perchlorate reduction enzymes in response to alternative electron acceptors. Perchlorate is a widespread toxic compound in drinking water, but it’s also used as an electron acceptor in a metabolism initiated by perchlorate reductase in some bacteria. The transcription of perchlorate reductase is inhibited by the presence of oxygen and nitrate, which are common alternative electron acceptors used by most perchlorate reducing bacteria. Ouwei’s work is focused on understanding the molecular mechanism and identifying the regulatory factors involved in perchlorate reductase regulation. This work has applied value, as both in situ and ex situ stimulation of perchlorate reduction must contend with the inhibitory presence of nitrate and oxygen. After coming to America as a teenager with little knowledge of the English language, Ouwei has worked very hard to pursue his dream of becoming a scientist. With a Ph.D. degree, he hopes to inspire other members of the immigrant community to pursue their higher education goals.

Microbial contaminations in industrial fermentation processes constitute one of the most devastating threats to the productivity and operational costs of biotechnology facilities. Although bleach derivatives can be added to process waters to prevent infection, these disinfectants are also biocidal against the process organism. We focus on engineering a process E. coli strain to grow in high concentrations oxychlorine disinfectants allowing for chemostat culturing with low risk of contamination.

PHYSICAL SCIENCES

  • Da Rong "Daren" Cheng
    ARCS Foundation Scholar
    Stanford - Mathematics
    PI:Richard Schoen

    “Min-max Construction of Minimal Submanifolds via Phase Transitions”

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  • Christopher Davis
    Kimball Foundation Scholar
    Stanford - Physics
    PI:Aaron Roodman

    “Improving Measurements of Cosmic Acceleration”

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  • Samantha Dixon
    Peggy Huntington, JBH Foundation,
    Debbie Wreyford & Ken Winans Scholar
    UC Berkeley - Physics
    PI:Saul Perlmutter

    “Unraveling the Mysteries of Dark Energy with Type Ia Supernovae”

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  • Luke Evans
    ARCS Foundation Scholar
    SF State University - Mathematics
    PI: n-Kit Lai

    “Mathematical Phase Retrieval and Some Generalizations”

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  • Joshua Greenfield
    ARCS Foundation Scholar
    UC Davis - Chemistry
    PI:Kirill Kovnir

    “Development of a Low-Temperature Solvothermal Route to a Variety of Novel Iron Chalcogenides”

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  • Neil Griffis
    Clark Mitchel Scholar
    UC Davis - Earth & Planetary Sciences
    PI:Isabel Montanez

    “High-Resolution CA-TIMS Dating of the Carboniferous—Permian Succession, Paraná Basin, Brazil”

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  • Zach Jennings
    ARCS Foundation Scholar
    UC Santa Cruz - Astronomy & Astrophysics
    PI:Jean Brodie

    “A Wide-Field Survey of 25 Extragalactic Globular Cluster Systems”

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  • Patrick L. Kramer
    ARCS Foundation Scholar
    Stanford - Chemistry
    PI:Michael Fayer

    “Watching Water's Ultrafast Motions in Ionic Liquids and Gels”

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  • Mark Levin
    Arlene Inch Scholar
    UC Berkeley - Chemistry
    PI:F. Dean Toste

    “An Au(III) Platform for [18F]-Trifluoromethylation”

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  • Jeremy Maurer
    ARCS Foundation Scholar
    Stanford - Geophysics
    PI: Paul Segall

    “Using geodetic data to constrain the interseismic moment deficit rates (IMDR) is currently an under-utilized but potentially powerful method for understanding the seismic hazard presented by crustal faults.”

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  • Danquynh Nguyen
    ARCS Foundation Scholar
    UC Santa Cruz - Mathematics
    PI:Chongying Dong

    “On the Modular Vertex Operator Algebras”

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  • Kevin Raines
    William K. Bowes, Jr. Foundation Scholar
    Stanford - Applied Physics
    PI:Sebastian Doniach

    “Inverse Diffraction as Inference”

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  • Alex Rider
    ARCS Stanford Graduate Fellow
    Stanford - Physics
    PI:Giorgio Gratta

    “Search for Millicharged Particles Using Optically Levitated Microspheres”

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  • Anna Rosen
    Linda Dyer Millard Scholar
    UC Santa Cruz - Astronomy & Astrophysics
    PI:Enrico Ramirez-Ruiz

    “An Unstable Truth: How Massive Stars get their Mass”

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  • Shervin Sahba
    Devlin Family Endowment Fund Scholar
    SF State University - Physics & Astronomy
    PI:Weining Man

    “Experiment and Simulation in Photonic Structures: Bandgap Formation in Disordered Media”

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  • Anna Maria Schindler
    Robert Lansdon Trust Scholar
    SF State University - Mathematics
    PI:Federico Ardila

    “The Equivariant Ehrhart Theory of the Permutahedron”

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  • Harrison Jesse Smith
    ARCS Foundation Scholar
    UC Davis - Computer Science
    PI:Michael Neff

    “Understanding The Impact of Animated Gesture Performance on Personality Perception”

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  • Laurel Stephenson Haskins
    Jack Lund Endowment Fund Scholar
    UC Santa Cruz - Physics
    PI:Michael Dine

    “Perturbation Theory in Supersymmetry Quantum Electrodynamics”

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Department of Mathematics
Ph.D. Program

Daren Cheng
ARCS Foundation Scholar

Daren’s research focuses mainly on the analytical properties of harmonic maps and minimal surfaces, two of the most fundamental objects in geometric analysis. In the past he has worked on the partial regularity of energy-minimizing harmonic maps with rough domain metric. Currently he is looking into stable minimal surfaces of higher codimension. The goal is to prove local estimates and to analyze the limit of a sequence of stable minimal surfaces. After obtaining his degree, Daren plans to pursue an academic career and continue his research in geometric analysis. Aside from mathematics, he has a deep interest in Chinese history and literature. In fact, it is his belief that good historical writings have a lot in common with good mathematical expositions.

A fundamental question in geometry is whether within every ambient space there exists a minimal surface, i.e. a stationary point of the function that assigns to each surface its area. Much work has been devoted to answering this question since the turn of the 20th century, and a wide range of different methods have been developed. Here we present yet another, and perhaps simpler, approach to finding minimal surfaces based on the mathematical theory of phase transitions.

Department of Physics
Ph.D. Program

Christopher Davis

Chris thesis project deals with improving measurements of the accelerating expansion of the universe: by measuring the location and shape of three hundred million galaxies we can test General Relativity on cosmological scales. Chris is developing a novel method to infer the distances of galaxies by correlating their positions with the cosmic web of dark matter, and is also improving gravitational lensing measurements by modeling the distortions to galaxy shapes that arise from the complex optical system of the 4-meter Victor Blanco Telescope and the Dark Energy Camera. In his spare time, Chris plays jazz bass throughout the Bay Area.

By using the locations and shapes of three hundred million galaxies, the Dark Energy Survey will test General Relativity to unprecedented precision. Galaxy surveys like the Dark Energy Survey will be limited not by the number of galaxies or the volume of space probed, but instead by our understanding of systematic errors in measuring our galaxies. I work on new methods for improving these measurements, in particular using measurements of the cosmic web to infer the distribution of galaxy samples..

Department of Physics
Ph.D. Program

Samantha Dixon

As an undergraduate, Samantha conducted research in a lab on an experiment to detect ultra-high energy cosmic rays, and wrote an honor's thesis for her work on an experiment searching for dark matter. She spent one summer as an intern at NASA's Goddard Space Flight Center studying the Cosmic Microwave Background. At UC Berkeley her research uses data from Type Ia supernovae, a special class of exploding stars, to probe the expansion history of the Universe. This expansion history provides us with an important piece of the puzzle for uncovering the nature of dark energy. In the future, Samantha plans to continue research in astrophysics and cosmology.

Measurements of type Ia supernovae, a special class of exploding stars, were essential to the discovery of the accelerating expansion of the Universe. They continue to serve as one of the best tools available for tracking our cosmic history. This poster presents an overview of the observations and analyses being performed by the Supernova Cosmology Project and the Nearby Supernova Factory collaborations as well as the implications of these results on our current understanding of the "dark energy" that drives the accelerating expansion.

Department of Mathematics
Master’s Program

Luke Evans

Luke is currently pursuing research involving phase retrieval in regard to frames in Hilbert spaces. In general, his research interests are in harmonic, functional and applied analysis. In addition to academic research, Luke has worked as a student intern at Lawrence Livermore National Laboratory developing hydrodynamics discretization schemes. Outside of academics, Luke enjoys running, exploring San Francisco neighborhoods, and reading.

Phase retrieval is the recovery of unknown signals from measurements with noisy or lost phase. Recovery from loss of phase occurs in a wide range of applications such as x-ray crystallography, speech processing and quantum information theory. In a finite-dimensional vector space, the measurements are inner products with respect to a given spanning set of measurement vectors, and one can consider the minimal number of measurement vectors required for phaseless reconstruction of a signal as well as any other necessary and sufficient conditions on the measurement vectors for successful reconstruction.

In finite dimensions, we develop theory for two generalizations of phase retrieval. We introduce the concept of ``conjugate phase retrieval'' in complex vector spaces and give results towards characterizing the sets of vectors with this property. Further characterizations of vectors allowing norm retrieval are also shown. In the infinite dimensional case, we investigate phase retrieval in spaces of band-limited functions. In particular, results and examples are given suggesting a possible characterization of phase retrievable sampling sequences in Paley-Wiener spaces.

Department of Chemistry
Ph.D. Program

Joshua Greenfield

Joshua's research is focused on the development of a solvothermal synthetic route to novel iron-based superconductors and low-dimensional hybrid-inorganic materials with exotic magnetic properties. He has presented his work at multiple national conferences and has authored five publications. In addition to performing his own research and mentoring undergraduate and high school students in the lab, Joshua is also active in educational outreach, performing chemistry demonstrations for local elementary schools and the public, including the annual Picnic Day Chemistry Shows.

The discovery of superconductivity in the tetragonal forms of iron selenide and sulfide has spurred considerable interest in the field of layered iron chalcogenides, and a great deal of research is currently being conducted on related compounds with alkali metals and/or organic molecules intercalated between the iron chalcogenide layers in an effort to find new superconductors with ever higher critical temperatures. The usual synthetic route to these metastable compounds involves high-temperature solid-state reactions to form a binary precursor (FeSe or FeS), followed by post-synthetic intercalation of the desired spacer layer. This multi-step process generally results in the formation of fine powders with very poor crystallinity, such that structural and other characterization methods are difficult and oftentimes inconclusive; while a number of compounds with improved superconducting properties have been produced, the lack of single-crystal diffraction experiments leaves most of the details of their crystal structures unknown.

We have developed a solvothermal synthetic route in which elemental precursors are heated in alcohol- and amine-based solvents at low temperatures (100-200 °C) to produce a wide variety of iron chalcogenides. In addition to the binary parent phases, this technique can produce high-quality single crystals of novel compounds with reduced dimensionality, intercalated spacer layers, and even unprecedented topologies by simply adjusting the solvent, stoichiometry, and reaction temperature. Presented here are the details of the development of this solvothermal technique, as well as the structures and properties of a number of novel compounds that we have discovered along the way.

Geology Graduate Group
Ph.D. Program

Neil Patrick Griffis

After receiving his M.Sc. in Geology, Neil was hired as a Sedimentary Geologist for Schlumberger in Salt Lake City, Utah and in Calgary, Alberta, Canada. His current research focuses on reconstructing the timing and magnitude of Earth's penultimate icehouse. This project involves extensive fieldwork in Patagonia and Southern Brazil where he analyzes glacial deposits. In addition, Neil is gaining expertise in high-precision U-Pb geochemistry and radiogenic isotopic analysis of Earth materials. Outside of school he is an avid skier, whitewater kayaker and backpacker.

The late Paleozoic Ice Age (LPIA) is Earth’s only record of a CO2-forced climatic transition from an icehouse to greenhouse state in a vegetated world and in the presence of metazoan life. Despite a refined framework of Gondwanan ice distribution, questions remain about the timing, volume, and synchronicity of high-latitude continental ice and the subsequent deglaciation, ultimately precluding our understanding of linkages between ice volume, sea level, and high- and low-latitude climate. Poor constraints on the timing and synchronicity of glacial and interglacial transitions reflect a lack of accurate high-resolution radioisotopic dates from high-latitude ice-proximal Carboniferous-Permian successions. In turn, the dearth of dates inhibits robust intra-Gondwana correlations and their correlation to lower latitude proxy records. The Rio Bonitio Fm in southern Brazil hosts the oldest non-glaciogenic Carboniferous-Permian deposits of the Paraná Basin, recording the icehouse-to-greenhouse transition. Despite a widespread effort over the last two decades to constrain these deposits in time by means of U-Pb zircon geochronology, discrepancies in published data sets of the Candiota and Faxinal coals of the Rio Bonito Fm and range from syndeposition of coals to upwards of 30 Ma between deposits. These discrepancies have hindered the correlation of the Candiota and Faxinal sediments and the underlying glacial deposits within the larger Gondwanan framework and may in part be due to post-eruptive open system behavior of zircon and cryptic analytical artifacts. Here we present the first U-Pb ages on closed system single crystal zircons using CA-TIMS techniques on Carboniferous-Permian ash deposits of the Paraná Basin. Our results indicate two major and distinct coal-forming periods that are separated by ca 12 Ma. Our results and conclusions are not in agreement with multi-crystal U-Pb TIMS ages as well as SIMS ages that suggest coeval deposition of these coals. In addition preliminary results from a new ash fall ash obtained from core in the North of the Basin are in agreement with the age of the Candiota section in the South and suggest deglaciation was near synchronous across the Paraná Basin and occurring near the Carboniferous-Permian boundary.

Department of Astronomy & Astrophysics
Ph.D. Program

Zachary Jennings

Zach’s primary research focus is the study of extragalactic globular cluster systems. He is also very interested in modern machine learning and statistical techniques, and has taken supplemental coursework to add a formal "Emphasis in Statistics" to his Ph.D. His dissertation work will include one of the largest globular cluster catalogs ever published and will be the first such catalog to employ modern statistical techniques in the process of globular cluster selection, greatly increasing the quality of the catalog. This dissertation will complete his graduate school career, which already includes four published papers.

Globular clusters, or GCs, are incredibly dense clusters of stars bound together by gravity. These clusters contain hundreds of thousands of stars packed into a spherical ball just a few light years in radius. Such clusters are also extremely old; most GCs were formed over ten billion years ago, in the early universe. GCs are mostly located in the distant outskirts of galaxies. Because GCs are so old and dense, the GC systems of galaxies survive through the multitudes of merger events that galaxies undergo in their lifetimes. A GC system is thus an aggregate history of a galaxy’s assembly: each merger event deposits the GCs of the smaller galaxy into the system of the larger galaxy. I present a study of the GC systems of 25 nearby elliptical galaxies in deep, wide-field images taken from cutting-edge telescopes on the summit of Mauna Kea in Hawaii. This dataset allow us to study the GC systems of these 25 galaxies to unprecedented scale and depth. I also present novel statistical methodology for distinguishing these GC systems from non-GC contaminants that are easily confused in our imaging dataset. The combination of our wide-field images and statistical methodology offers an unprecedentedly deep look into the GC systems of these galaxies and, by extension, a unique picture of the way these galaxies have assembled over their cosmic histories.

Department of Chemistry
Ph.D. Program

Patrick Kramer

Patrick’s concentration is in Chemical Physics, studying the ultrafast vibrational dynamics of small hydrogen-bonding molecules (such as water and alcohols) in complex condensed-phase environments using two-­dimensional infrared (2D IR) spectroscopy. Patrick has contributed to the development of a theory allowing analysis and separation of the various structural and rotational contributions and applied it to his measurements on the experimental system of methanol in a room-temperature ionic liquid - a solvent system of great interest for new advances in chemical processing and batteries, for example. After graduation, Patrick would like to proceed to an academic career developing new methodologies for extracting ultrafast dynamical information from chemical systems. Outside of the lab, he enjoys travel, hiking, and Scotch whiskey.

Ultrafast infrared spectroscopy is used to examine the femtosecond to picosecond timescale interactions of water and similar hydrogen bonding solutes (such as alcohols) within complex environments that differ greatly from simple bulk solvents, such as room temperature ionic liquids, hydrogels, and biomolecule-ionic liquid systems. The time- and polarization-resolved pulsed laser experiments reveal a hierarchy of relaxation timescales, ranging from librational motion around an intact hydrogen bond to complete randomization of the solute local environment due to large-scale fluctuations of solvent molecules. Solute rotational motion and the changing interactions with local liquid structure are often found to be closely related and coupled using newly developed methodology.

Department of Chemistry
Ph.D. Program

Mark Levin

Mark is working on the development of new transition metal catalyzed reactions. Synthetic catalytic reactions make up the toolbox by which virtually all new molecules are made - from pharmaceuticals, to plastics, to OLED light bulbs, to paints and fertilizers. As more sophisticated reactions are invented, the potential chemical space accessible to researchers in all fields is expanded, and the efficiency of existing production is increased. Mark's research is particularly focused on developing new concepts for catalytic reactions, focusing on the Au(l)/(111) and Pt(ll)/Pt(IV) redox couples as platforms for proof-of-concept reaction development. Recently, Mark began a collaboration with the Lawrence Berkeley National Lab Radiopharmaceutical division to employ new methodologies for the synthesis of PET tracers. In his spare time, he plays guitar and writes Wikipedia articles about organic chemistry.

The synthesis of radiofluoride containing probe compounds is central to the practice or Positron Emission Tomography - development of new probe molecules allows for new avenues in diagnostic medicine and in the understanding of pharmacological mechanism of action. However, the short lifetime of the radionuclide imposes exceptional constraints on the chemistry used for their synthesis. As such, the technology for many classes of important structural motifs falls short of demand. In this work, a protocol based on organometallic complexes of gold that allows access to a previously unavailable class of PET probes is demonstrated. This work will enable exciting new avenues in drug development and diagnostic medicine.

Department of Geophysics
Ph.D. Program

Jeremy Maurer

Jeremy’s research focues on crustal deformation modeling and earthquake hazards. He is currently investigating overall seismic hazard in Southern California and magnitudes of earthquakes induced by disposal of wastewater deep underground, using theoretical studies, statistics, and modeling to try to quantify seismic hazard and reduce it when possible. Jeremy plans to pursue a career path in research and teaching. When he is not busy running models or looking at data, Jeremy enjoys spending time with his wife and two children, and playing sports with friends.

Using geodetic data to constrain the interseismic moment deficit rates (IMDR) is currently an under-utilized but potentially powerful method for understanding the seismic hazard presented by crustal faults. One class of methods historically used to estimate the IMDR is known as Kostrov-type summation, which integrate surface strain rates (Ward, 1994; Savage & Simpson, 1997). This method gives an approximate estimate of the minimum scalar MDR. Strain-rate can be estimated by triangulating velocities to find line-length changes (e.g. Savage & Simpson, 1997), estimating strains analytically using basis functions (e.g., Tape, et al., 2009), or interpolating geodetic velocities onto a regular grid followed by numerical differentiation (e.g., Haines & Holt, 1993; Kato et al., 1998; Shen et al., 2015; Wu et al., 2011). There is an inherent trade-off in these methods between misfit and smoothness.

I adopt a geostatistical approach that estimates the surface velocity field using parameters estimated from the data itself, and generate many random realizations of the velocity field true to the data that that are smooth and fit the data within errors everywhere. Numerically differentiating these gives strain and moment deficit rates with uncertainties. I apply this method to Southern California and compare my results to other strain rate estimates and moment accumulation rates for Southern California. I also briefly introduce a new method for estimating IMDR using traditional finite fault models and compare the results obtained using an elastic block model developed by Johnson (2013) for Southern California to that obtained by integrating surface strain. I use estimate how much of the surface strain can be explained by backslip on faults. Understanding the MDR with its uncertainty provides valuable information for understanding earthquake hazards in this geologically complex region.

Department of Geophysics
Ph.D. Program

Danquynh Nguyen

Danquynh’s primary research interests lie in Vertex Operator Algebra theory, a mathematical framework whose importance reaches well outside of mathematics. It is prevalent in theoretical physics, in particular, as well as in conformal field theory and string theory, which attempts to provide a unified description of all the forces of nature. She currently studies integral forms and was recently awarded an NSF Fellowship to go to China to do research on the topic. As her path to being a graduate student was a rather non-traditional one, she tries to give back as much as possible. Danquynh believes in leaving a legacy; and she wants hers to be that of a mathematician whose contributions expanded scientific knowledge and a teacher who inspired generations of students, especially women.

The rationality of a vertex operator algebra (VOA) and the classification of its irreducible modules are among the most important problems in the theory of VOAs and have been studied extensively over the field of complex numbers. By studying the singular vectors of the Verma modules, we hope to extend these results to fields of certain characteristics.

Department of Applied Physics
Ph.D. Program

Kevin Scott Raines

Kevin's research occurs at the intersection of biophysics and machine learning. In biophysics, his interests range from the atomic structure of proteins, to the epigenetic profile of kidney cancer, to correlations at the social scale between health and economics. Within each of these areas, he develops and applies computational techniques to extract patterns from copious data. Currently, he is working on a project to incorporate neural networks into phase retrieval algorithms in order to solve protein structures from limited and noisy measurements. In his spare time, he enjoys cooking, exercise, drawing, traveling, and learning new (and old) languages.

Diffraction has been used for over two centuries to probe the structure of matter on a variety of time and spatial scales. In optics, statistical approaches to both modeling and data processing have long enjoyed an important place along side the basic physics that gives rise to the measurements. We take a similar approach, formulating structure problems from diffraction measurements as a problem in inference. We use tools from information theory to analyze diffraction problems from limited measurements, enabling us to quantify the importance of background knowledge in the analysis of experimental data. We expect that these tools will enable us to overcome physical limitations imposed on measurements to solve structures from limited and noisy data.

Department of Physics
Ph.D. Program

Alexander Rider
ARCS Stanford Graduate Fellow

An Eagle Scout, Alex is interested in experiments that test the fundamental way nature works. Currently, he is building an experiment to see how gravity works when objects are separated by distances much less than the thickness of a human hair. He has published work looking for new particles and on radiation detectors. When not in the lab, Alex enjoys outdoor activities like bicycling, hiking, and camping.

We report results from a search for stable particles with charge > 10^−5 e in bulk matter using levitated dielectric microspheres in high vacuum. No evidence for such particles was found in a total sample of 1.4 ng, providing an upper limit on the abundance per nucleon of 2.5 x 10^−14 at the 95% confidence level for the material tested. These results provide the first direct search for single particles with charge < 0.1 e bound in macroscopic quantities of matter and demonstrate the ability to perform sensitive force measurements using optically levitated microspheres in vacuum.

Department of Astronomy & Astrophysics
Ph.D. Program

Anna Rosen

Through the use of analytical and numerical methods, Anna’s research focuses on the formation of massive stars as well as how stellar feedback - the injection of energy and momentum by stars into their surroundings - affects their formation and environment. The computational tools that she has developed have taken star formation simulations to the next level in complexity while also increasing our understanding of how the most massive stars form and how their formation affects their environment. Anna is also active in outreach and mentoring to increase both diversity and retention in the field of Astrophysics.

Massive stars play an essential role in the Universe. They are rare, yet the energy and momentum they inject into the interstellar medium with their intense radiation fields dwarfs the contribution by their vastly more numerous low-mass cousins. Previous studies have concluded that the feedback associated with massive stars' radiation fields is an important mechanism regulating their formation. Therefore detailed simulation of the formation of massive stars requires an accurate treatment of radiation. For this purpose, we have developed a new, highly accurate radiation algorithm that properly treats the absorption of the direct radiation field from stars and the re-emission and processing by interstellar dust. We use our new tool to perform three-dimensional radiation-hydrodynamic simulations of the collapse of massive pre-stellar cores with laminar and turbulent initial conditions and properly resolve regions where we expect instabilities to grow. We find that mass is channeled to the stellar system via gravitational and Rayleigh-Taylor (RT) instabilities. For laminar initial conditions, proper treatment of the direct radiation field produces later onset of instability, but does not suppress it entirely provided the edges of radiation-dominated bubbles are adequately resolved. Instabilities arise immediately for turbulent pre-stellar cores because the initial turbulence seeds the instabilities. Our results suggest that RT features are significant and should be present around accreting massive stars throughout their formation.

Department of Physics & Astronomy
Master’s Program

AShervin Sahba

Shervin felt his calling to science after years working as a private tutor in San Francisco. Still active in education, he is now researching photonic materials, investigating the flow of light in media. His work seeks to design devices that can reinforce and ultimately supplant today’s electronic signal systems. Now in his second year as an ARCS Scholar, Shervin is interested in computational science that allows large scale exploration of physics, leading to his internship with the Blue Waters Petascale Institute on supercomputing. In his free time, he partakes in recreational mathematics, hiking, and cycling.

Analogous to semiconductor band gaps in silicon electronics, frequency band gaps in photonic crystals allow the manipulation of light. The promise of creating logical circuitry through photonics compels us to investigate the physical fundamentals that permit bandgap formation. In this work, we experimentally explore anisotropic structures, pitting disorder against self-uniformity to investigate the precursors that lead to photonic band gap geometries. Next, via computational techniques, we simulate novel devices that can lead to signal processing technologies.

Department of Mathematics
Master’s Program

Anna Maria Schindler

Anna took an indirect route to mathematics, majoring in the humanities as an undergraduate at Wesleyan University and working as a restaurant cook for two years after graduating. It was tutoring that first drove Anna to return to the study of mathematics, and teaching continues to be one of her greatest passions. Anna’s research interests are in algebra and combinatorics. In particular, she is studying spectral graph theory and equivariant Ehrhart theory. She hopes to attend a Ph.D. program after graduating from SFSU, ultimately aspiring to continue a life of exploring, contributing to, and spreading mathematical knowledge.

Equivariant Ehrhart theory can be thought of as a way to measure the symmetry of a polytope. Building on classical Ehrhart theory, which enumerates the lattice points of polytopes, this equivariant extension introduces group actions. My research investigates the permutahedron under the action of the symmetric group, studying the parts of the permutahedron that are fixed by different reflections and rotations. In particular, I enumerate these fixed points using polynomials and quasipolynomials, as well as their generating functions.

Department of Computer Science
Ph.D. Program

Harrison Jesse Smith

Jesse is fortunate to have found a research area at the intersection of two of his passions: theater and computer science. His current work focuses on understanding how motion capture data can be procedurally modified to influence an audience's perceptions of performer personality and emotionality. These insights could be applied to create more effective teaching simulations, more believable virtual companions, and more immersive video games and virtual reality experiences. When not in front of a computer screen, Jesse enjoys backpacking, cooking, soap making, and rock climbing.

Applications such as virtual tutors, games, and natural interfaces increasingly require animated characters to take on social roles while interacting with humans. The effectiveness of these applications depends on our ability to control the social presence of characters, including their personality. Understanding how movement influences the perception of personality allows us to generate characters more capable of fulfilling social roles. This work focuses on gesture as a key component of social communication and examines how variations in gesture style can predictably influence personality perception. The results reveal a parsimonious set of procedural adjustments capable of varying personality perceptions along two dimensions.

Department of Physics
Ph.D. Program

Laurel Stephenson-Haskins

Laurel is conducting research on problems in theoretical particle physics and cosmology. She has three publications to her credit and two in progress. Her work has the potential to alter current paradigms for building models of inflation, and to resolve fundamental issues in quantum field theory and the theory of the strong interactions. Laurel is also an outstanding teacher and has sought opportunities to develop her skills in a variety of settings.

We study some aspects of perturbation theory in supersymmetric gauge theories with massive charged matter. In general gauges, infrared (IR) divergences and nonlocal behavior arise in 1PI diagrams, associated with a 1/k^4 term in the propagator for the vector superfield. We examine this structure in supersymmetric QED. The IR divergences are gauge-dependent and must cancel in physical quantities like the electron pole mass. We demonstrate that cancellation takes place in a non- trivial way, amounting to a reorganization of the perturbative series from powers of e^2 to powers of e. We also show how these complications are avoided in cases where a Wilsonian effective action can be defined.

ENGINEERING

  • Jeremy Bancroft Brown
    ARCS Foundation Scholar
    UC San Francisco - Bioengineering
    PI:John Kurhanewicz

    “RF Microcoil-Bioreactor System for Development of Novel Therapeutics and Metabolic Imaging Probes in Microsamples of Living Human Prostate Tissue”

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  • Gaby Baylon
    Leslie & George Hume Scholar
    Shelagh & Tom Rohlen Scholar
    Stanford - Mechanical Engineering
    PI:Marc Levenston

    “The Effect of Sulfated Glycosaminoglycan Concentration on the Transient Osmotic Swelling of Articular Cartilage and Meniscus Fibrocartilage in Confined Compression”

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  • Orianna DeMasi
    ARCS Foundation Scholar
    UC Berkeley - Computer Science
    PI:Jim Demmel & Benjamin Recht

    “Using Data and Computing to Aid Mental Healthcare”

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  • Audrey Ford
    Bailey & Chris Meyer Scholar
    Janet & Alan Stanford Scholar
    UC Berkeley - Mechanical Engineering
    PI:Lisa Pruitt

    “Plastic Fatigue in Orthopedic Implants: Crack Growth in Polycarbonate Urethane”

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  • Emily Hollenbeck
    Chris & Bruce Brent Scholar
    Jane Fuller Gillespie Memorial Scholar
    Stanford - Chemical Engineering
    PI:Gerald Fuller & Lynette Cegelski

    “Measuring Adhesion Between Uropathogenic E. coli and Bladder-Epithelial Cells ”

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  • Jean Kim
    Venetta & John Rohal Scholar
    Mr. & Mrs. William H. Moorhouse Jr. Scholar
    UC San Francisco - Bioengineering
    PI:Tejal Desai

    “Long-Term Intraocular Pressure Reduction with Polycaprolactone Drug Delivery Implants for Glaucoma”

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  • Molly Nicholas
    Nordstrom Stores Scholar
    UC Berkeley - EECS
    PI:Eric Paulos

    “Physical Buffering Icon: Using Simple Robotic Gestures to Communicate Processing Time”

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  • Trenton Otto
    ARCS Foundation Scholar
    UC Berkeley - Chemical & Biomolecular Engineering
    PI:Enrique Iglesia

    “Challenges and Strategies in the Encapsulation and Stabilization of Monodisperse Au Clusters within Zeolites”

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  • Willie Mae Reese
    Lucille M. Jewett Scholar
    UC Berkeley - Materials Science & Engineering
    PI:Kevin Healy

    “A Novel Polyphenol Coating for Organ on a Chip Applications”

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  • Alex Reinking
    LShirley Freund Memorial Scholar
    UC Berkeley - EECS
    PI:Koushik Sen

    “A Type-Directed Approach to Program Repair”

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  • Gennifer Smith
    Nancy S. Mueller Scholar
    Stanford - Electrical Engineering
    PI:Audrey Bowden

    “Robust Dipstick Urinalysis Using a Low-Cost, Micro-Volume Slipping Manifold”

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  • Lily Ann Tomkovic
    Georgiana Ducas Endowment Fund Scholar
    UC Davis - Civil & Environmental Engineering
    PI:Fabian Bombardelli

    “A Hydrodynamic Model of the Yolo Bypass using HEC-RAS 1D/2D”

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  • Miklos Zoller
    ARCS Foundation Scholar
    UC Berkeley - Civil & Environmental Engineering
    PI:Sanjay Govindjee

    “Microsphere Modeling for Nonlinear Inelastic Materials”

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Department of Bioengineering
Ph.D. Program

Jeremy Bancroft Brown

Jeremy is an MD/Ph.D. student in Bioengineering at UCSF and UC Berkeley. His research is focused on engineering a radiofrequency microcoil-bioreactor system for MRI-based microarchitecture and metabolism studies of individual living human prostate biopsies. A working prototype of the system has been constructed and tested in living prostate cancer cells. These techniques may be able to noninvasively predict the aggressiveness of a prostate tumor or predict individualized responses to therapy. Jeremy has contributed to publications in Radiology, Medical Physics, the Journal of Digital Imaging, and the Canadian Journal of Physics. In his spare time, Jeremy relaxes with his family and runs on the alternately foggy and sunny trails of Golden Gate Park.

There is a pressing clinical need to differentiate indolent and aggressive prostate cancer and to monitor therapeutic responses; consequently, our long-term goal is to discover novel MRI biomarkers of prostate cancer aggressiveness that can be used to guide treatment decisions. To this end, we are developing a laboratory device that acquires structural and metabolic MRI data from individual living biopsies of prostate cancer patients, which enables early-stage testing of novel molecular imaging agents that are derived from naturally occurring metabolites (such as hyperpolarized 1-13C pyruvate) without exposing patients to risk. Using this device, we hope to identify promising MRI biomarkers for ultimate validation in clinical MRI studies of prostate cancer patients; additionally, in the future, we hope to develop the use of this device for improved clinical diagnosis of prostate tissue specimens.

Department of Mechanical Engineering
Ph.D. Program

Eva (“Gaby”) Baylon

Gaby is interested in the structure-function relation of fibrocartilage tissue in the knee joint, in particular, the role osmotic swelling plays in its mechanical behavior. Her Ph.D. project focuses on the creation of a finite element model to be validated using an experimental swelling model as well as establishing a relationship between osmotic swelling and non-invasive, quantitative MRI-based parameters for diagnostic purposes. Gaby has served as president of the Latino/a Engineering Graduate Organization at Stanford and is a member of several diversity advocacy committees. Upon completion of her Ph.D., Gaby will pursue an engineering faculty position at the university level.

The osmotic swelling stress that results from the interaction between the negatively charged sulfated glycosaminoglycans (sGAGs) and the ionic interstitial fluid in the knee joint is important to the load bearing capabilities of articular cartilage and meniscal fibrocartilage. Changes in the sGAG content, such as those that occur as a result of degenerative joint disease (i.e. Osteoarthritis), alter the osmotic swelling stress and thus, the ability of both tissues to sustain compressive loading. Previous studies have examined effects of osmotic interactions on the compression and shear moduli of cartilage and meniscus in unconfined and confined compression, but the influence of concentrations of sGAG in the tissues have not been explored. This study compared the effect of altered osmotic environments on the swelling stress of normal and degenerated articular cartilage as well as adult and immature meniscus fibrocartilage, tissue groups selected to span overlapping ranges of sGAG concentration.

Department of Computer Science
Ph.D. Program

Orianna DeMasi

Orianna is interested in applications of machine learning for high performance computing, specifically auto-tuning. Her research project involves how to efficiently find parameter values to make a code run quickly. It has been established that codes must be tuned to each machine, but it is not known how to do this quickly, without trying all parameter values. This interest was developed while she was working in the Complex Systems Group at Lawrence Berkeley National Laboratory (LBNL). When she isn’t on a computer, she can be found digging in her garden, keeping her cats out of her garden, and collecting butterflies. After obtaining her Ph.D., Orianna plans to pursue a staff scientist position at a DOE lab.

Orianna is interested in the way that novel data sources and computing technologies can help mental health care. Novel data sources have emerged, such as smartphones and wearable activity trackers that collect large amounts of behavioral data on individuals. This information about individuals’ behavior can shape the way mental health treatments are designed and the way care providers interact with patients. For example, using behavioral data, it is possible to better target interventions to times when individuals are in need, evaluate whether treatments are helping individuals get better, and help care providers better understand how individuals have been doing.

Department of Mechanical Engineering
Ph.D. Program

Audrey Ford

Audrey’s research interests are in the biomechanics of soft tissue. She is interested in cartilage mechanics and repair strategies, with a focus on developing cartilage tissue engineering techniques to repair or replace damaged articular cartilage (i.e., in knees and hips). A polyethylene plastic bearing surface is used in the successful design of many hip, knee, and shoulder replacements. Polycarbonate urethane has been introduced as an alternative plastic for orthopedic implants due to its more elastomeric and cartilage-like properties. However, without 20 years of clinical data with this new material, it is difficult to predict the effects of repetitive loading over several decades. To try to predict the performance of polycarbonate urethane, Audrey is using fatigue analysis to understand how it can fail under cyclic loading and is also working to understand how the micro-level structure of the material influences its resistance to crack growth and fracture. A greater understanding of the fatigue properties of polycarbonate urethane will help to inform and improve the design of future orthopedic implants. Outside of her work as a graduate student, Audrey also trains and races with the UC Berkeley triathlon team.

A polyethylene plastic is currently used as a cushioning surface in the successful design of many hip, knee, and shoulder replacements. Polycarbonate urethane has been introduced as an alternative plastic for orthopedic implants because of its elastic impact strength and cartilage-like properties. However, without 20 years of clinical data with this new material, it is difficult to predict the effects of millions of cycles of loading over several decades of use in a patient. I use fatigue analysis to understand how this plastic can fail under cyclic loading to predict the long-term performance of polycarbonate urethane. I also work to understand how the micro-level structure of the material influences its resistance to crack growth and fracture so that we can more fully understand the device-level properties. A greater understanding of the fatigue properties of polycarbonate urethane will help to inform and improve the design of future longer-lasting orthopedic implants.

Department of Chemical Engineering
Ph.D. Program

Emily Hollenbeck

Emily's research centeres on understanding different strategies used by microorganisms during the infection process from a biophysical perspective. This ranges from studying the initial adhesion of pathogens to host tissue to the formation of microbial communities that are difficult to eradicate with traditional antibiotics. During her time at Stanford, Emily has been a fellow in the Center for Molecular Analysis and Design, a program that fosters and supports interdisciplinary research. Upon graduating, Emily plans to pursue a career in human health, potentially developing novel therapies to treat bacterial infection.

Bacterial adhesion to host cells is often a first step in the infection process. For example, uropathogenic Escherichia coli, the major causative agent of urinary tract infection, bind to host bladder-epithelial cells and initiate cell invasion. This triggers a subsequent pathogenic cascade characterized by recurrent infection. There is currently growing interest in developing new antimicrobials that, instead of targeting bacterial survival and placing high selective pressure for drug-resistant mutations, target mechanisms promoting infection such as binding to host cells. This new therapeutic strategy requires a detailed understanding of bacterial adhesion. To address this issue, we used in vitro methods to examine the factors that contribute to the adhesion of E. coli to the bladder epithelium, including both traditional tissue-culture based assays and novel mechanical measurements. Specifically, we used an adapted live-cell rheometer to make direct physical measurements of bacterial adhesion to a monolayer of bladder epithelial cells. This method allowed us to quantify the extent to which extracellular bacterial components affect adhesion. Our results indicate that an extracellular amyloid fiber commonly produced by uropathogenic strains of E. coli, termed curli, increase adhesion to bladder epithelial cells and may therefore play a role in the infection process. In the future, we plan to use these techniques to assess the effectiveness of various small molecules in blocking bacterial binding to host cells.

Department of Bioengineering
Ph.D. Program

Jean Kim

Jean’s research focuses on development and preclinical evaluation of polycaprolactone implants for glaucoma. By developing intracameral implants that achieve zero-order release of therapeutics over six months, she aims to provide better therapy for glaucoma patients. This year, Jean received the Mary Anne Koda-Kimble Seed Award for Innovation to pursue one of her projects in glaucoma therapy. In addition, Jean dedicated time to mentor a graduate rotation student and a high school summer intern in the lab. She has also worked as a peer advisor for junior graduate students since she joined the program in 2012.

Long-term intraocular pressure reduction with polycaprolactone drug delivery implants for glaucoma.

Department of Computer Science
Ph.D. Program

Molly Nicholas

Bangladesh to Berkeley. Clown Conservatory to Qualcomm. These have been some of the stops on Molly’s journey so far. Her research goals are exploring how theatrical techniques and methods may influence the fields of electrical engineering and computer science, and vice versa. Her work as a performer developed Molly’s intuition about how to engage an audience. The time she spent in Bangladesh gave her a broader sense of the world, and helped her develop a more nuanced understanding of tough problems like poverty. The Qbadge she created at Qualcomm was a tantalizing taste for the work she is eager to do. Now Molly wants to be on the cutting edge of research at the University level, and solve problems that don't even exist yet.

As interactive objects that move, robots offer a unique opportunity for highly expressive interfaces. Simple gestures, designed and implemented by an expert puppeteer, may influence the way humans perceive a robot performing a task. Gathering data from novice users after they watched several videos showed some trends in shifting vocabulary, and emotional affect. Specifically, users seemed to feel more confused by the static robots than by the robots that added extraneous movement, and more curious about the moving robots. Further work is needed to explore the movement vocabulary available to robots.

Department of Chemical Engineering
Ph.D. Program

Trenton Otto

Trenton came to UC Berkeley because of the university’s excellent catalysis research and its close collaborations with industry. His project concerns the encapsulation of catalytically active metal species within zeolites. In particular, he aims to develop synthetic strategies for the encapsulation of metal clusters -- such as gold nano-particles -- that have been found to have potential but are precluded from commercial use due to their poor stability or selectivity, or their propensity to adsorb poisons. Over the long-term, Trenton would like to work in Research & Development in the chemical industry or in a national laboratory on catalysis projects.

Gold particles smaller than 5 nm in diameter exhibit unprecedented catalytic activity in a variety of important reactions including carbon monoxide oxidation, alcohol oxidation, and alkene epoxidation. The use of these particles in practice, however, is limited by their strong tendency to sinter and form large, inactive agglomerates. In this work, we propose a technique to addresses this inherent instability by embedding gold nanoparticles into microporous zeolite crystals, which restrict the mobility of the gold clusters and prevent agglomeration while also allowing reactant species to access the active gold surfaces.

Department of Materials Science & Engineering
Ph.D. Program

Willie Mae Reese Lucille M. Jewett Scholar

Originally from Carlsbad, NM, Willie completed her BS in Materials Science and Engineering at MIT. After graduating she joined Teach for America, a non-profit organization that aims to increase awareness about educational inequality in urban and low income communities. In 2011, she began a co-op at Intel Corporation, successfully completing a short-term project to reduce operational costs on metrology equipment and the long-term project of developing tools to help track costs in other areas. In her current research project, she is using focused ion beam (FIB) lithography and electron-beam lithography to pattern surfaces with submicron pores or pits to create microenvironments for cells. She is studying two effects of the nano-pores and pits to specifically understand how these surfaces can be applied to better direct wound healing.

Organ-on-a-chip devices or microphysiological systems (MPSs) can be used to combine genetically relevant cell lines in micro-environments that recapitulate not only organ specific structure, but also organ system relationships to access on and off-target toxicities and efficacies. Most MPSs are easily manufactured via lithography techniques using poly-dimethylsiloxane (PDMS), which has shown to be biologically compatible and amenable to many standard cell culture techniques due to it’s high transparency, high oxygen permeability, and low auto-fluorescence. Devices can be produced inexpensively with highly precise reproducible structures. Although PDMS has several positive attributes, many have shown that due to its hydrophobicity, small molecules can be absorbed into the PDMS creating unpredictable drug concentrations in MPSs.

To address this limitation, we designed and developed a novel macrocyclic polyphenol, which is able to reduce the absorbance of the model drug compounds rhodamine B and C1-BODIPYC12 into PDMS up to 90 and 95 percent, respectively. This outperforms established polyphenol coatings such as polydopamine or pyrogallol. Initial experiments have shown low cytotoxicity allowing for the culture of iPSC-derived cardiomyocytes for at least one month. Preliminary experiments also show good coating stability not only on PDMS but also on other biologically relevant polymeric materials such as tissue culture polystyrene, polycarbonate, and Teflon.This coating is also advantageous over other solutions of drug absorption such as Sol-Gel methods or other glass like coatings, due to it’s ease of use, low cost, and high oxygen permeability.

Department of Computer Science
Ph.D. Program

Alexander Reinking

Alexander’s research focus is in software synthesis, with the goal of designing algorithms that generate program source code from simpler specifications. His paper, "A Type-Directed Approach to Program Repair", was published at Computer Aided Verification in 2015 and won second place in the Programming Languages Design and Implementation Student Research Competition. Alexander also spent two summers as a software engineering intern for Microsoft, where he worked on lntune, a cloud-based, enterprise, device management product.

Developing enterprise software often requires composing several libraries together with a large body of in-house code. Large APIs introduce a steep learning curve for new developers as a result of their complex object-oriented underpinnings. While the written code in general reflects a programmer’s intent, due to evolutions in an API, code can often become ill typed, yet still syntactically correct. Such code fragments will no longer compile, and will need to be updated. We describe an algorithm that automatically repairs such errors, and discuss its application to common problems in software engineering.

Department of Electrical Engineering
Ph.D. Program

Gennifer Smith

Gennifer's main research interest is low-cost medical diagnostics. As an undergraduate she was an intern at Sandia National Laboratories and helped develop a point-of-care device for diagnosing tuberculosis and assessing antibiotic resistance. She is currently working on a low-cost device for urinalysis, which will include antibiotic susceptibility testing. Gennifer has also been involved in several other projects including image quantitation and phantom fabrication for optical coherence tomography. Gennifer has mentored several undergraduate students performing research at Stanford and hopes to continue a career in academics. Outside of the lab, Gennifer enjoys playing board games and Minecraft with her son.

Urinalysis dipsticks were designed to revolutionize urine-based medical diagnosis. They are cheap, extremely portable, and have multiple assays patterned on a single platform. They were also meant to be incredibly easy to use. Unfortunately, there are many aspects in both the preparation and the analysis of the dipsticks that are plagued by user error. This high error is one reason that dipsticks have failed to flourish in both the at-home market and in low-resource settings. Sources of error include: inaccurate volume deposition, varying lighting conditions, inconsistent timing measurements, and misinterpreted color comparisons. We introduce novel manifold and companion software for dipstick urinalysis that eliminates the aforementioned error sources. A micro-volume slipping manifold ensures precise sample delivery, an opaque acrylic box guarantees consistent lighting conditions, a simple sticker-based timing mechanism maintains accurate timing, and custom software that processes video data captured by a mobile phone ensures proper color comparisons. We show that the results obtained with the proposed device are as accurate and consistent as a properly executed dip-and-wipe method, the industry gold-standard, suggesting the potential for this strategy to enable confident urinalysis testing. Furthermore, the proposed all-acrylic slipping manifold is reusable and low in cost, making it a potential solution for at-home users and low-resource settings.

Department of Civil & Environmental Engineering
Ph.D. Program

Lily Ann Tomkovic

During the course of her graduate career, Lily has been developing hydrodynamic models of natural systems. She is now applying this expertise in numerical modeling to an inter-tidal restoration project, exploring the linkage between hydrodynamics and ecologic function. As a graduate student, she has held an internship with the U.S. Army Corps' Davis office, the Hydrologic Engineering Center (HEC), and continues to maintain that relationship, bridging the resources of both UC Davis and HEC. She is an active member of the Society of Women Engineers, mentoring and engaging with young women interested in STEM fields. To complement her modeling work on the Yolo Bypass, she does volunteer work for the Yolo Basin Foundation. In addition, she is active in environmental stewardship through rock climbing, whitewater kayaking, and snowboarding.

In particular, the Yolo Bypass is a critical component of a plan by the state of California (California Eco Restore) in order to implement habitat restoration actions in the Sacramento-San Joaquin Delta. I have been working on simulating the flow in the Bypass in order to understand the interaction of hydrodynamics and primary productivity and habitat creation. This model will be provided to the public as a tool for interested parties to further explore the dynamics of the floodplain.

Department of Civil & Environmental Engineering
Ph.D. Program

Miklos Zoller

Miklos’s research focuses on material modeling, as new materials are being discovered and created annually but constitutive relationships for their mechanical behavior have not yet been determined. He has been working on a micro-mechanics model for large deformation elastic and viscoelastic materials. The model approximates the complicated microstructure of polymer chains by a sphere, which is described by a few variables relating to the kinematics of the deformation. He has completed the work for the time-independent response for the large deformation case. He's now working on the time-dependent/viscoelastic response and getting closer to determining the best algorithm for the homogenization procedure.

Microsphere material modeling typically involves the development of fully three-dimensional constitutive equations from well known one-dimensional micromechanical models. The microsphere framework has been previously applied to a wide variety of phenomena, but its application has always involved relaxation for quasi-incompressible mechanical motions and affine with respect to all other phenomena. My research is an extension of this method by lifting these restrictions to allow for fully relaxed constitutive relations at the continuum level based on well-known one-dimensional micromechanical models in the presence of other internal evolutionary phenomena.

ENVIRONMENTAL SCIENCES

  • Sarah Fakhreddine
    Rhoda Goldman Memorial Scholar
    Stanford - Earth System Science
    PI:Scott Fendorf

    “Geochemical Triggers of Arsenic Mobilization During Managed Aquifer Recharge”

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  • Zeka Kuspau
    Orange County Community Foundation Scholar
    UC Santa Cruz - Microbiology & Environmental Toxicology
    PI:Myra Finkelstein & Donald Smith

    “Assessment of the Glucocorticoid Stress Response in the Critically Endangered California Condor (Gymnogyps californianus) at Multiple Time Scales”

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  • Claire Masteller
    Nordstrom Stores Scholar
    UC Santa Cruz - Earth & Planetary Sciences
    PI:Noah Finnegan

    “How Rivers Remember: The Impacts of Prior Stress History on Grain Scale Topography and Bedload Transport”

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  • Matt Whalen
    ARCS Foundation Scholar
    UC Davis - Ecology
    PI:John Stachowicz

    “Detecting Ecologically-Relevant Scales of Topography for the Development of Rocky Shore Communities”

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Department of Earth System Sciences
Ph.D. Program

Sarah Fakhreddine

Sarah’s research focuses on understanding the geochemical processes that control the fate and transport of groundwater contaminants. Through the use of laboratory experiments and computational modeling, her work examines how artificial groundwater recharge can alter the native geochemistry of an aquifer and subsequently degrade the groundwater quality. She is particularly interested in applying a geochemical understanding of these processes to provide water managers with recommendations for methods to minimize the mobilization of groundwater contaminants. After completing her Ph.D., she plans to pursue a career in research either at the university level or in a national laboratory. Outside the lab, she enjoys exploring the area around Stanford, hiking, biking and scuba diving.

Managed Aquifer Recharge (MAR) is an increasingly popular method to augment local groundwater supplies and store water for later usage. However, MAR sites can alternative aquifer geochemistry and result in the mobilization of naturally-occurring metal contaminants, including arsenic and other toxic metals, as has been observed at numerous MAR sites. Additionally, MAR projects can utilize various recharge water chemistries many of which have not previously been tested and can potentially have adverse interactions with aquifer sediments. Here, we investigate the shifts in groundwater quality which occur as a result of MAR of highly purified recycled water (< 0.01 M electrolyte concentrations) in two distinct recharge environments: (1) shallow infiltration basins and (2) direct, deep (>150m) injection wells. We conduct a series of column experiments using sediments collected near infiltration basins and a pilot injection site within the Orange County Groundwater Basin. We evaluate the effect of varying Ca++ and Mg++ concentration and varying levels of residual disinfectants including hydrogen peroxide and chloramines. Results suggest that arsenic mobilization within the infiltration area is controlled by adsorption of As(V) oxyanions on negatively-charge phyllosilicate clay minerals. Within the deep, injection-area sediments, our results suggest that continuous injection of aerobic recharge water will not mobilize appreciable concentrations of As due to the repartitioning of As(V) oxyanions onto newly precipitated Fe (hydr)oxides. However, shifts in groundwater pH during injection can threaten the stability of adsorbed As and should be closely monitored. In both systems, higher concentrations of Ca++ can promote As retention within the aquifer sediments and decrease As release to the surrounding pore water.

Department of Microbiology & Environmental Toxicology
Ph.D. Program

Zeka Kuspa

Zeka believes science is not useful unless it is shared, and that science should be translatable and have measurable impact. Her research on the effects of lead exposure on the endangered California condor is novel and necessary, with a primary goal to fill important knowledge gaps on the sublethal effects of lead exposure in condors and other impacted avian species world-wide. Achieving this goal will require compelling and effective science communication; this, along with quality science, is a main focus of her graduate effort. Zeka has sought opportunities to share her work on condors and her passion for conservation at every turn, be it authoring peer-reviewed journal articles, teaching Girl Scouts about wildlife toxicology, or organizing educational nature walks. Her hope is that these efforts will inform effective decision making from the level of individuals to policy makers.

Vertebrates respond to stressful stimuli with the secretion of glucocorticoid (GC) hormones and measurements of these hormones in wild species can provide insight into physiological responses to environmental and human-induced stressors. California condors are a critically endangered and intensively managed avian species for which no GC studies have been performed. The availability of commercial immunoassay kits, especially those that do not require radioactive materials, has increased the accessibility of hormone measurements for researchers and field biologists. However, few of these kits have been validated for non-plasma sample types, and measuring a baseline stress level from blood sampling can be challenging if not logistically infeasible in wild animals. Indirect measures of plasma GC (e.g., GC levels in saliva, feces, urine, hair, feathers) allow for less-invasive sampling procedures and also allow for assessment of baseline GC levels in field settings because there is a time-lag between GC elevation in circulation and elevation in those peripheral samples. Here we evaluated two commercially available corticosterone immunoassay kits, a competitive corticosterone enzyme-linked immunosorbent assay (ELISA) and a corticosterone I125 double antibody radioimmunoassay (RIA) kit, for use with California condor plasma, urates, and feather samples. We found the RIA kit to be reliable for GC and metabolite (GC(m)) measurement in all three sample types. Notably, GC(m) values were not comparable between the two kits for any sample type, highlighting the need for caution when comparing immunoassay results across methods. RIA measurements of total GC in condor plasma collected from 33 condors within 15 minutes of a handling stressor were highly variable (range: 13 – 189 ng/mL, median: 71 ng/mL, n=42) suggesting notable individual differences in stress response, but within range of GC measurements in other avian species. In response to acute stress caused by capture and handling, we measured a 1.6 – 35-fold increase in urate GC(m) concentrations within 2 hours post-stressor, providing a biological validation for our measurement method. Feather GC(m) concentrations were within expected ranges for bird feathers (range=5.7-33.5 ng/g, median= 9.3 ng/g), but additional work is needed to interpret changes in GC(m) concentrations between and within condor feathers. In light of the value of GC(m) measurements to environmental research, we emphasize the need for extensive validation of commercial immunoassay kits before use with novel species and non-plasma sample types.

Department of Earth & Planetary Sciences
Ph.D. Program

Claire Masteller

Claire is interested in the physical conditions under which sediment begins to move and the processes that affect its mobility. She uses a combination of computer modeling, field observations, and novel physical experiments in miniature rivers to study sediment transport. The application of physics to problems grounded in the landscape that we interact with every day fuels her passion for research. In 2015, Claire cofounded a UCSC student-led group focusing on diversity in geoscience.

Memory is preserved in rivers through the sorting and arrangement of grains on their beds, which reflect previous flow conditions. Manifestations of this phenomenon include observed hysteresis in bedload rating curves (e.g., Moog and Whiting, 1998; Reid et al., 1985) and correlations between the stage at the start of a transport event and the stage at the end of transport during a previous event (Turowski et al., 2011). This observed history dependence represents a key difficulty in the accurate prediction of bedload transport rates. To begin to systematically explore these memory effects on fluvial bedload transport, we experimentally examined how a gravel bed river responds to variations in prior stress history.

Specifically, we compare the response of the grain-scale topography of a gravel river bed to both below and above threshold flow conditions. We find that under low flow, when no sediment transport occurs, the bed compacts as the highest protruding grains pivot into low elevation pockets. This reorganization appears to occur logarithmically with low flow duration, making it analogous to compaction observed in dry granular flows subjected to agitation. The amount of prior compaction affects bedload transport rates at the onset of above threshold flow, with more compact beds yielding less bedload flux. In contrast, we find that under sediment-transporting flows, the bed dilates because grains are re-deposited in relatively precarious positions. During the same applied transport flow, we observe that the most pronounced dilation occurs when the initial bed is the most compact, suggesting that that the potential for dilation is related to the degree of previous compaction.

These observations highlight that a gravel bed experiences two different behaviors, compaction under low shear stresses, and dilation under high, sediment transporting, shear stresses. This observation is consistent with previous studies on the compaction and dilation of granular media, as well as flume experiments conducted using glass beads. Further, this study highlights the varying response of grain-scale topography and bedload transport rates to prior flow and bed conditions, implying history dependence in fluvial systems.

Ecology Graduate Group
Ph.D. Program

Matthew Whalen

Matt is interested in the causes and consequences of biological diversity in the sea. His dissertation research explores how environmental variation across space and time mediates species coexistence and, in turn, ecological functions like primary production and water filtration. Matt has been very successful in supporting his research, having secured funds from UC Davis, Bodega Marine Laboratory, and the Environmental Protection Agency. He has experience working in natural and aquaculture settings, from the water’s edge to the deep sea, on questions ranging from basic ecological theory to global conservation concerns. He is a strong independent researcher and also a valued collaborator. Outside of his research, Matt enjoys hiking, cooking, and brewing beer with his wife, Sarah, a park ranger at Pt. Reyes National Seashore.

Many of the best questions in ecology are difficult to answer because of the hierarchical nature of living systems, which scale from cellular process to organisms interacting in communities to global elemental cycles. In order to predict how gradients in environmental conditions set the pace of productivity in ecosystems, or how ecosystems respond to disturbances, we need to understand how ecological patterns at one scale emerge from processes operating at another scale. Furthermore, we may genuinely be interested in understanding how variation in the environment affects ecosystems at individual, community, and global scales because we now experience the world at all of these scales. Data syntheses in ecology are often criticized because the extent to which key ecosystem properties change across scales remains unclear for many systems. I have recently looked to marine rocky shores as a model system for testing how different scales of environmental variation affect biodiversity. Rocky shore landscapes contain steep gradients in environmental conditions over small spatial scales that lead to zonation patterns that we can often see around tide pools. Despite the intense wave energy experienced on exposed rocky coasts, we often observe high diversity in rocky shore communities, both across and within zones. I hypothesize that topographic variation at different scales helps maintain diversity on rocky shores, and that covariance between the traits of organisms and environmental conditions holds a key for understanding scale-dependence in nature more generally. I will present my recent work from Bodega Marine Reserve in which I identify scales of landscape variation on a rocky shore from millimeters to meters, and relate this variation to the diversity and distributions of organisms living where land meets the sea.

SCIENCE COMMUNICATIONS

  • Emma Hiolski
    Barbara & John Glynn Scholar
    UC Santa Cruz - Science Communications
    PI:Robert Irion

    “Method to the Madness: Science Communication as a Structured Endeavor”

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  • Aylin Woodward
    ARCS Foundation Scholar
    UC Santa Cruz - Science Communications
    PI:Robert Irion

    “Method to the Madness: Science Communication as a Structured Endeavor”

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Department of Science Communication
Graduate Certificate

Emma Hiolski

As a Ph.D. student in Environmental Toxicology, Emma always enjoyed explaining her projects and lab adventures to family and friends, but something was missing. Her passion for science communication was kindled when she took a science writing course through her department and discovered that she could combine her enthusiasm for both science and writing into an exciting and fulfilling career. Emma is especially eager to learn more about new multi-media approaches to sharing science in accessible and engaging ways. Ultimately, her goal is to help increase science literacy and ensure that she reaches as diverse an audience as possible.

Telling a scientific story requires more planning and strategy than one might think. Science communication and journalism involves using a distinct narrative structure to tell a story with the greatest impact. Writers leverage catchy openers and resonating kickers to leave the reader thinking about the story long after have they've minimized the webpage or thrown out the newspaper, combining the history with personal anecdotes and relevant social context.

Department of Science Communication
Graduate Certificate

Aylin Woodward

Throughout her undergraduate career, Aylin studied fossil foot bones and the evolution of bipedalism. And yet, the common theme that emerged was that she loved to write and could do it rather well. Ultimately she determined that her future belongs in the world of teaching, particularly in the world of melding science and communication. Having a background as both a woman in science and a previous varsity athlete with ties throughout the professional, collegiate and youth alpine skiing worlds, she is well positioned to disseminate her work to others via athletic training clinics and education of coaches working day-to-day, on the ground, in the sport. Often the assumed gap between a field of study like biological anthropology and its relevance to today's world serves as a barrier to empowering and impassioning burgeoning interests and future engagement with the subject. Aylin hopes that her science writing will serve to break down such barriers and encourage others to engage with paleoanthropology in a meaningful, intellectual manner.

Telling a scientific story requires more planning and strategy than one might think. Science communication and journalism involves using a distinct narrative structure to tell a story with the greatest impact. Writers leverage catchy openers and resonating kickers to leave the reader thinking about the story long after have they've minimized the webpage or thrown out the newspaper, combining the history with personal anecdotes and relevant social context.