Disease Ecology Within the Pear Tree Phyllosphere

Microbial communities are essential for plant development, growth, productivity, and health. Aerial parts of the plant, referred to as the phyllosphere, consist of multiple habitats for microorganisms to thrive, including beneficial and pathogenic bacteria. The vast and dynamic interactions among bacteria in the phyllosphere microbiome have the potential to significantly affect the fitness of plant populations; therefore, studying these relationships serves as a strong indicator of plant health. This project seeks to identify culturable bacteria within the pear tree phyllosphere and assemble a map of interactions between different members of the community in order to gain insight into their dynamics and how these plant-microbe interactions shape plant health. In this project, I will analyze the relationship between the phyllosphere microbiome and notable phytopathogens, such as Erwinia amylovora and Pseudomonas syringae, using direct microbe-microbe interactions through culturable methods and a bioassay in pear slices. E. amylovora and P. syringae are pathogens […]

...Read More about Sydney Abelson
Rose Hills

Gas Sensors: Identifying Electrical and Chemical Degradation Mechanisms

Chemiresistive sensors detect gas concentrations based on the change in resistance of a sensing material, providing low-cost detection in applications such as environmental monitoring. SnO2 is an industry-standard material system for chemiresistive sensing. SnO2-based sensors typically have high baseline resistance and slow dynamics at room temperature, and thus require on-board heaters to improve their sensitivity and response time. Although heating greatly improves the response of SnO2-based sensors, prolonged operation at requisite temperatures (200–300°C) results in baseline drift and changes in sensitivity over time. Such degradation is observed even in commercial SnO2-based sensors and is an open problem in chemical sensing. I propose to identify and characterize the mechanisms that underlie the degradation of SnO2-based sensors. Although the general mechanisms that govern how SnO2 responds to ambient gases, such as O2 and volatile organic compounds, have been studied, a definitive analysis that links the degradation of the electrical (i.e., chemiresistive) performance […]

...Read More about Veronica Arriaga
Rose Hills

Tyrosinase-Mediated Oxidative Coupling

The purpose of this research is to identify tyrosinase enzymes that are able to carry out tyrosinase-mediated oxidative coupling. Tyrosinases have recently been identified as enzymes that are able to undergo oxidative coupling and are a much more efficient way to couple proteins, DNA, small molecule thiols, and difficult protein substrates. Previous methods produce unwanted by-products, are not site-specific in their targeting, and can result in unwanted protein degradation, which ruins the natural folding of the proteins. Tyrosinase-mediated coupling avoids such problems and allows the reaction to run in a short amount of time without complications. Specific tyrosinases are able to couple to different biomaterials and this diversity makes them integral in the development of drug therapeutics, especially antibody drug conjugates (ADCs). These can be used in cancer drug research and can allow patient-specific targeted therapeutics. The new tyrosinase species identified by this research can be used in the growing […]

...Read More about Nicole Balian
Rose Hills

NMR Optimization and Application to MOFs

In the Ajoy Lab, we use a custom nuclear magnetic resonance (NMR) apparatus that uses high-powered lasers and microwaves to hyperpolarize samples for signal enhancement. My project will work to optimize the microwave frequency, sweep rate, and bandwidth of our apparatus to increase the lifetime of a nanodiamond sample. Increasing the lifetime of the nanodiamond sample is beneficial to resolution, as it increases the amount of time we can collect data from milliseconds to minutes. This is relevant to the field as the optimization of the nanodiamond sample, and increase in the sample lifetime, improves resolution. This increased timescale is paramount in the field of NMR. While we currently work exclusively with nanodiamonds, we aspire to expand to other materials, such as pentacene-based metal organic frameworks (MOFs). MOFs are used frequently due to their ability to be easily tailored with different metals and different linkers. For this expansion, I will […]

...Read More about Samantha Breuer
Rose Hills

The Regulation of Metabolic Flexibility in Aging

Mitochondrial function and metabolic flexibility (the ability to switch back and forth between carbohydrate and lipid utilization in response to changing physiological conditions) degrade as a normal consequence of aging. Metabolic flexibility is regulated by several mechanisms that are affected by the capacity for lactate oxidation and, therefore, mitochondrial function. Previous studies have demonstrated that endurance training improves metabolic flexibility due to improvements in mitochondrial function and the capacity for lactate oxidation. The purpose of my research is to assess metabolic flexibility in older and younger, trained and untrained individuals by measuring blood lactate and substrate oxidation rates during postabsorptive rest. I will implement a resting oral glucose tolerance test (OGTT) to analyze how blood lactate concentration interplays with carbohydrate and fatty acid oxidation rates as determined by gas exchange measurements. This method deviates from current methods of metabolic flexibility assessment by proposing a simpler and less invasive approach that […]

...Read More about Jennah Brown
Rose Hills

MmpL Transporters in M. abscessus Virulence and Impermeability

Incidence and deaths due to non-tuberculous mycobacteria (NTM) have been increasing globally, in part due to their intrinsic drug resistance. Mycobacterium abscessus (Mabs) is a pathogenic and clinically challenging NTM species, causing devastating pulmonary disease and tissue infection. Drug resistance of Mabs partly results from its unique mycomembrane, which is a formidable permeability barrier. While the inner leaflet primarily consists of mycolic acids, the outer leaflet is poorly characterized. Some mycobacterial membrane protein Large (MmpL) transporters export lipid components of the mycomembrane, but the substrates and functions of most MmpLs remain unknown. The high number of MmpLs in Mabs leads to questions about each MmpL’s function as a lipid transporter or drug efflux pump, as well as its contribution to virulence and antibiotic resistance. My project will investigate each MmpL’s role in these important traits. I will create MmpL knockouts and test the mutants to evaluate each MmpL’s function in […]

...Read More about Vivian Bui
Rose Hills

Stress-Activated Transposable Elements in Mimulus guttatus

This project focuses on gaining a deeper understanding of transposable elements (TEs) within monkey flowers. Previously, TEs were thought to be virus-like, parasitic parts of genomes. With the use of supercomputers, we will compare the genomes of many monkey flower genome samples to a reference genome to identify variation that suggests adaptation. Our work will define the role of TEs more clearly, as many are associated with mutations and only arise during specific conditions, which suggests a form of adaptation.

...Read More about Victor Canta-Gallo
Rose Hills

Investigating Flavivirus NS1's Role in Facilitating Viral Dissemination

Dengue virus (DENV) is a vector-borne virus that is transmitted by Aedes mosquitoes. Typically found in tropical and sub-tropical regions in the world, DENV can cause mild disease manifestations like dengue fever; however, cases of severe dengue disease exist and are characterized by vascular leakage and shock, which is triggered by virus infection and an overactive immune response. Medically important viruses like flaviviruses (dengue, Zika, West Nile, and yellow fever viruses, etc.) must disseminate from the initial site of infection into diverse tissues throughout the body to cause disease. Therefore, my summer research project will focus on the role of dengue virus NS1-mediated leak in virus infection and dissemination in vivo.

...Read More about Bryan Castillo-Rojas
Rose Hills

Using DNA-Directed Patterning to Study EMT and MET in Breast Cancer

Invasive breast cancer affects 1 in 8 women in the US, with over 270,000 new cases diagnosed annually. With significant advancements in diagnosis and treatment, approximatey 90 percent of deaths are related to metastasis, the migration of cancer cells from the primary tumor to peripheral organs. Here, a subpopulation of tumor cells relies on phenotypic transitions to gain traits that aid in migration and invasion. This rare population of cells exists on a spectrum of phenotypes and is more resistant to treatment, highlighting the importance of increased investigation. The goal of my study is to investigate these rare intermediate phenotypes that are induced by the epithelial-to-mesenchymal transition (EMT) and reverse mesenchymal-to-epithelial transition (MET). I will pattern tumorigenic, breast epithelial cells with other tumor microenvironment (TME) cells and determine which activate EMT/MET in tumor cells. Knowing what induces EMT/MET will allow me to control breast cancer cell phenotype and study specific […]

...Read More about Zahir Chaudhry
Rose Hills

Social Modulation of Sickness Behavior in Prairie Voles

Challenges to the immune system mobilize immune resources to trigger physiological and behavioral changes in a host. Alongside fever and cytokine responses, organisms initiate “sickness behaviors” like lethargy, social withdrawal, and decreased food and water intake to facilitate recovery from illness and prevent disease transmission to conspecifics. Yet, some species mask their sickness behaviors in group contexts to take advantage of survival and reproductive benefits, a form of social modulation. Prairie voles are a unique model for human social behavior, as they form selective, enduring social preferences for opposite-sex mates and same-sex peers, unlike traditional laboratory rodents. However, little research has investigated sickness behavior in this species, particularly in its modulation by same-sex peers, who were previously shown to facilitate recovery from stressors. My research will investigate the extent to which a same-sex peer modulates sickness behavior in male and female prairie voles provide further insight into the impact of […]

...Read More about Diana Chernyak
Rose Hills

Dark Matter Blob Signal Analysis

Currently, the nature of dark matter is a fascinating question for the field of physics. One promising candidate about the nature of dark matter is axions, which is a theoretical, lightweight particle filling all of space. According to theory, these light, axion-like particles behave like a field that oscillates at particular frequencies. However, this frequency can change over space, forming regions bounded by so-called domain walls. This year, I have been working on the Global Network of Optical Magnetometers for Exotic physics (GNOME) station at Berkeley, which uses optical techniques to measure the magnetic field in a vapor cell. According to theory, when the Earth crosses one of these axion domains, an effective magnetic field coupling will be detected in the magnetometer, so the presence of axions can be determined by analyzing the signal. To reduce noise, the GNOME collaboration operates multiple, independent magnetometers across the Earth, jointly analyzing the […]

...Read More about Nicholas Cutsail
Rose Hills

The Role of the Sorghum Circadian Clock in Blue Light-Mediated Growth

Sorghum bicolor is a biofuel feedstock and staple food crop. My research focuses on understanding the role of a core circadian clock component, Sorghum bicolor Gigantea (SbGI), in modulating sorghum sensitivity to cryptochrome signaling at different times of the day. In related grasses, cryptochromes, activated by blue light, upregulate active gibberellin degradation genes to strategically cease plant elongation. Importantly, the SbGI mutant has a severe stunted-growth phenotype relative to the wild type, and preliminary protein interaction results suggest that SbGI and cryptochromes interact. These observations inform my hypothesis that SbGI is necessary for blocking cryptochrome activity to allow for active gibberellin to accumulate in a time-specific manner to drive diurnal growth. The confirmation of this mechanism would be the first documentation of a Gigantea-cryptochrome interaction and would inform us about how the circadian clock directly coordinates daily growth. If it is known when, under what conditions, and how growth is […]

...Read More about Samuel De Riseis
Rose Hills

Rates of Chlamydia (Ct) and Gonorrhea (Ng) Within the Fijian Population

This summer, I will be traveling to Suva, Fiji with a research team from UCSF led by Dr. Deborah Dean. As part of a longitudinal study started in 2018, we aim to identify Ng antibiotic susceptibility patterns and determine current rates of resistance to antibiotics. With this in mind, we are also looking to determine the association of antibiotic resistance (AR) Ng strains with clinical signs and symptoms. In addition, we are looking at current Ng-Ct co-infection rates, in order to determine the longitudinal prevalence of Ng and STIs and other vaginal co-infections in Fiji, whose total healthcare expenditure is only 4.5% of GDP. Previous research has shown high rates of asymptomatic Ng and Ct infections and no diagnostic testing, indicating a high risk for transmission. My team’s research will be crucial in helping the Fijian Ministry of Health to develop interventions and treatment to advance antibiotic stewardship, and to […]

...Read More about Madison de Vere
Rose Hills

Fluorescence Labeling Gut Commensal Bacteria of C. elegans

Our lab is working to understand the effects of host-microbe interactions in the powerful model organism C. elegans. In order to quantify the microbiome, we have previously used a single fluorescent bacterial strain that is a known gut commensal. However, only having access to this single strain limits the types of experiments we can do, as we are forced to include this strain in studies hoping to understand colonization levels in the worm gut. In order to remedy this issue, my project will attempt to introduce a fluorescent plasmid into the chromosome of other bacterial strains we are interested in studying. This will allow us to study the effects of these strains in the gut microbiota more effectively, while also clarifying the protocol for creating fluorescent bacteria in different families.

...Read More about Ethan Deller
Rose Hills

Gene Silencing with a Novel RNAi Method in the Cassiopea Jellyfish

At night, the Cassiopea jellyfish slows its activity and enters a sleep state. Because sleep research focuses on models with centralized nervous systems, the sleep behavior of this brainless, decentralized jellyfish exposes a gap in the field that my project will address. In particular, I plan to test our novel RNA interference (RNAi) technique and use it to characterize the molecular mechanisms of sleep in Cassiopea. My lab recently developed the first RNAi protocol for jellyfish, a significant feat given that standard techniques are not easily applied to this nontraditional organism. First, I aim to develop positive control RNAi constructs to provide confidence in our future knockdowns. The constructs will target genes whose knockdown can be screened by eye: sphingosine kinase and microophthalmia-associated transcription factor. Second, I aim to silence an acetylcholine receptor subunit connected to sleep and activity using our method in sleep-deprived jellyfish. I will compare the resulting […]

...Read More about Diana Francis
Rose Hills

Tipping Environment: Online Versus In-Person

If you have gone to a fast-casual restaurant within the last few years, you will be all too familiar with how the process of tipping works. After the cashier taps your order into the restaurant’s tablet device, they flip it around with tip options for you to select. The bubbles can range from percentages to dollar amounts, depending on the restaurant (e.g., 15%, 20%, 25%, $1, $2, $3, etc.). Unlike past studies on tipping, which look at situations in which the cashier leaves and returns to pick up your check, my research will focus on these new devices and their impact on the tips that customers leave. I predict that by banishing the “custom” tip amount option to the corner of the screen and having the cashier, and the line of people behind you, immediately see which option you select, customers are being pressured into choosing a higher option. Therefore, […]

...Read More about Arjun Grover
Rose Hills

How and Why Students Select Their College Majors

My URAP Project “Choosing My Major” began in Fall 2021 with the purpose of assisting undergraduates students in choosing their major, as well as understanding why college students pick their majors. One of the main goals of this project was to collect real stories from current undergraduate students on how they came about choosing their major. Another goal was to develop a pilot survey in order to collect information from students on their decision-making process. This initial pilot survey was sent out to 78 undergraduate students, and they answered 30 questions on how they came about choosing their major. As a SURF fellow, I plan on continuing this research by modifying the survey and narrowing the questions to be more specific. Once the survey is completed and re-sent to the student body, I plan to analyze the data collected and write a report regarding the information gathered. Eventually, the information […]

...Read More about Vani Gupta
Rose Hills

Accelerating Chemical Understanding

One of the difficulties in chemistry research comes from bridging the gap between the data collected by experimental chemists and the computational data analysis done by theoretical chemists. There can be a significant disparity of knowledge between the two branches of chemistry, which can hinder the progress of research and education on both sides. Furthermore, understanding the results of the chemical data can be a daunting task for newcomers to chemistry research. My intention is to bridge this gap by developing a computational framework that gives easily understandable statements on the fundamentals of materials and molecules and their corresponding X-ray spectral fingerprints. These statements will be based on the output of electronic structure and spectral calculations from Density Functional Theory (DFT) from data calculated in the Prendergast Group. The framework can then be generalized to many areas of chemistry research, particularly topics that are energy-relevant, such as catalysis, electrochemistry (e.g., […]

...Read More about Nabiha Hasan
Rose Hills

Identifying Targets and Biological Mechanisms of Gymnastatins

Proteins are essential parts of our being, but are also at the root of many health conditions when misformed. One novel approach to treating such diseases is with molecular glues: small molecules that can cause targeted protein degradation or stabilization. My project focuses on a set of potential molecular glues known as gymnastatins, which are natural products originating from the fungal strain Gymnascella dankaliensis. The Nomura Research Group has demonstrated that gymnastatins have antiproliferative effects on breast cancer cells. Dankastatin B, the most potent gymnastatin against cancer cell viability, targets the mitochondrial membrane proteins VDAC2 and VDAC3. VDAC2 and VDAC3 were verified to be related to the proteins anticancer effects, but it is currently unknown how exactly these proteins are involved in intrinsic apoptosis (cell death). We hypothesize that dankastatin B acts as a molecular glue between VDAC2 and VDAC3, aiding in the initiation of apoptosis in cancer cells. This […]

...Read More about Emily Ho
Rose Hills

Optimization of Direct Air Capture in Environments of Steady Flow

Direct air capture (DAC) is the removal of carbon dioxide (CO2) directly from the atmosphere. While DAC is essential to achieving net zero carbon emissions and preventing irreversible damage from climate change, DAC plants require extensive energy input to draw in air. Dr. Klaus Lackner at the Center for Negative Carbon Emissions at Arizona State University has developed a prototype of a MechanicalTreeTM that utilizes passive air flow to reduce required energy. Before these machines can be deployed, we need to determine the optimal configurations to place them based on local wind patterns. We want distributions that minimize surface area yet maximize the fraction of air molecules filtered. I will develop a model in MATLAB that utilizes multi-physics simulations paired with genetic algorithms (GA) to optimize the placement of DAC machines. With this model, we can make DAC feasible for implementation on a global scale to reverse the trend of […]

...Read More about Thomas Hosmer
Rose Hills