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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Tuning 2D Electrochemical Properties via Heterointerface Effects

In recent years, the study of 2D materials consisting of atomically thin sheets of matter has exploded into a vibrant research area pursued by materials chemists and condensed matter physicists alike. The structures of these materials bring about many exotic properties which, in the near future, are projected to see groundbreaking applications in energy conversion and storage, as well as low-power computation. The behavior of electrons in 2D materials can be significantly altered by bringing flakes of differing chemical structures into contact. My project aims to better understand and exploit the consequences of introducing these heterointerfaces, in hopes of electrochemically inserting transition metal ions into the gap between the layers. Such a feat has proven extremely difficult, so I intend to make use of the unique properties of TMDs (transition metal dichalcogenides) and α-ruthenium chloride to produce an interface that welcomes the intercalation of such ions. Upon successful intercalation, I […]

...Read More about Rocky Hughes

Diagnosis and Treatment of Cervical Spondylotic Myelopathy

Cervical spondylotic myelopathy (CSM) is a degenerative change that occurs in the cervical spine and causes compression of the spinal cord. Patients with CSM can experience a wide range of symptoms, including weakness and numbness in the hands and arms, loss and balance and coordination, and neck pain. CSM is the most common spinal cord dysfunction in older persons and is likely to increase in incidence as the number of older persons in the United States increases. My research will focus on the diagnosis and treatment of CSM. More specifically, I will participate in data collection and analysis of CSM patients undergoing surgery at UCSF. I will also compare clinical outcomes and complications with various approaches, including anterior cervical discectomy and fusion (ACDF), posterior cervical fusion (PCF), and laminoplasty. Ultimately, the findings from this research will hopefully help reveal the correct surgical technique that ensures the optimal clinical outcome for […]

...Read More about Jaeson Kim

Identification of a Novel Antimicrobial Compound from S. sasae

  Many of the antibiotics used today are natural products of bacterial secondary metabolism. Streptomyces spp., in particular, have been found to produce many secondary metabolites, including antifungals, antibiotics, antivirals, and antitumorals. The modern age is facing a problem of rapidly increasing antibiotic resistance coupled with a lack of discovery of new antimicrobial compounds. This project seeks to identify and investigate the spectrum of action of a potentially novel antifungal compound produced by a Streptomyces sasae isolate from burned soil plots in the Blodgett Research Forest. This compound has been shown to inhibit growth of the pyrophilous fungus Pyronema omphalodes, and preliminary investigation has found that it is likely a novel compound. Through purification and identification of this antifungal compound, my project has the potential to aid in the discovery of a novel antimicrobial, as well as expand our knowledge of metabolites produced specifically in burned-soil ecosystems.

...Read More about Nicole Kim

Determining if T2 Diabetes Predicts an Increase in Cortical Porosity

It is increasingly being recognized that diabetic bone disease, associated with an increased risk of bone fractures, cannot be detected effectively using traditional detection methods for osteoporosis. This is because patients with Type 2 Diabetes (T2D), despite having normal or even high bone densities, are still prone to fractures. The Bone Quality Research Lab at UCSF has established that deficits in the cortical bone structure are associated with T2D and the increased fracture potential found in those with T2D. My research will further develop this finding by determining if T2D status, marrow, or vessel metrics predict longitudinal increase in porosity and decrease in strength. This work will contribute to further understanding of whether cortical pore content can be used as a predictor for cortical degradation, as well as furthering our understanding of how such degradation takes place and what potential targets exist for future therapeutic studies. With the number of […]

...Read More about Pranav Kolluri

Significance of Unique Rhamnolipid Production in Paraburkholderia sp.

I am interested in learning more about the unique rhamnolipid methyl esters (RMEs) produced by the pyrophilous bacterium Paraburkholderia sp. F3 and RMEs’ ecological significance. Previous endeavors in this project have uncovered the production of the unique RMEs by P. sp. F3, which first attracted attention due to its antibiotic activity against a pyrophilous fungus (Pyronema omphalodes) found in the same environment as P. sp. F3. After purification and identification of these antibiotic compounds, the RMEs were identified as analogs of the rhamnolipids produced by Pseudomonas aeruginosa, a biosurfactant with applications in agricultural, pharmaceutical, food, cosmetics, and detergent industries. The small differences in the structures of the Pseudomonas rhamnolipids and the RMEs suggest that RMEs are stronger surfactants. If this is the case, learning more about RMEs and how to produce them could play a very important role in formulating better fire recovery strategies and also developing more effective surfactants […]

...Read More about Sara Koupaei

Development of Difluorobenzyl Synthons for Cross-Coupling Chemistry

The benzylic methylene unit (Ar-CH2-R) is a common motif in drug candidates and pharmaceuticals. However, the propensity of its C-H bonds toward oxidation creates the challenge of metabolic stability. One solution is the substitution of this motif with the benzylic difluoromethylene or difluorobenzyl units (Ar-CF2-R), wherein the reactive C-H bonds are substituted with metabolically more stable C-F bonds. However, despite the potential advantage of such an approach, few pharmaceuticals containing this motif have been commercialized. This project focuses on the development of novel Ar-CF2-M synthons for C-C cross-coupling chemistry. First, the substrate scope of the difluorocarbene insertion into Au(I)-aryl bonds will be investigated. We envision that a variety of aryl and heteroaryl-Au(I) species can undergo the difluorocarbene insertion. Secondly, conditions to couple these synthons with sp2-electrophiles will be screened and optimized. Lastly, the mechanism of the formal difluorocarbene insertion and the stability of the new aryldifluoromethyl-Au(I) species will be investigated […]

...Read More about Alexander Kvitsinski

Understanding Coexistence of the Hawaiian Tetragnatha Spiders

Understanding niche differentiation is fundamental for comprehending the complicated process of adaptive radiation, a process characterized by the rapid formation of many ecologically different species from a single ancestor. However, the way in which niche differentiation is achieved during the early stage of adaptive radiation is still highly debated among evolutionary biologists. On the one hand, through the process of character displacement, natural selection could facilitate differentiation and diversification between closely related species where they co-occur with no need for prior niche differentiation at the time of secondary contact. Alternatively, enough niche differentiation between species can be achieved in isolation, before range overlap, facilitating coexistence and reducing the chance for competitive exclusion. Therefore, the goal of this project is to conduct a comparative analysis between sympatric and allopatric populations of the two species of the green ecomorphs of Hawaiian Tetragnatha spiny-leg spiders (T. waikamoi and T. brevignatha) to answer how […]

...Read More about Jennifer Lee

Bioengineering Plant NLR Immune Receptors: A Structural Approach

  Our research aim is to provide greater insights into the functions of NLR immune receptors, which are part of the second tier of the plant immune system, based on our current knowledge of their protein structure and mechanism. As we work toward this goal, we will answer basic research questions about how these highly conserved immune receptors detect pathogens and signal an immune response. More specifically, what region of the receptor recognizes the pathogen effector? Does this region also play a role in switching the receptor to the activated state? What other structural aspects may contribute to the transition to the immune signaling active state? This research will further our mechanistic understanding of how NLR immune receptors recognize pathogens and undergo structural changes to trigger the immune response. Current literature is hopeful that engineering disease resistance in crops has great potential to reduce yield loss and chemical treatments involved […]

...Read More about Lillian Litvak

Investigating Modified mRNA Stability and Translational Fidelity

mRNA has proven to be a promising novel therapeutic class due to its programmability, low barriers to synthesis, and rapid translation into protein in vivo. mRNA as a platform technology has led to the development of broad applications such as vaccines, therapeutic protein replacement, in vivo genome editing, and in vivo cellular reprogramming. Despite growing interest in mRNAs therapeutic potential, it suffers from low delivery rates due to its instability and short half-life, thereby limiting its clinical adoption. mRNA transcripts are vulnerable to various degradation mechanisms in the cell, as well as self-catalyzed cleavage. The proposed project aims to identify chemically modified nucleotides that can be incorporated into mRNA using in vitro transcription. The modified transcripts will subsequently be characterized by their stability as well as translational fidelity. Stabler versions of modified mRNA with similar or even greater translational efficiency would help alleviate bottlenecks in therapeutic delivery, thereby conferring near-term […]

...Read More about Kenneth Loi

Identifying Photoinhibitory Quenching Recovery Genes in Green Algae

  Population growth is set to exceed the capacity of modern agricultural yields, but innovations in agricultural technologies have the potential to meet global food needs. One promising area of basic research is involves improving the biology of photosynthesis so the plants themselves can grow more efficiently. At a fundamental level, it is easy to think that more sunlight equates to more photosynthesis. However, plants often receive far more sunlight than they can use, which can be damaging to the cell. Plants and algae have evolved ingenious mechanisms to dissipate excess light, albeit rather imperfectly, as dissipation competes with photosynthesis. My research project focuses on discovering key factors involved in the photosynthetic recovery of the chloroplast after sustained exposure to excess light in the model alga, Chlamydomonas reinhardtii. Specifically, I will be using a mutant deficient in its ability to repair oversaturated photosynthetic machinery, in order to identify secondary mutations […]

...Read More about Sophia Ma

The Effect of Lighting on Glucocorticoid Levels in Ctenomys sociabilis

Ambient light is essential to a wide variety of biological processes, including behavior, reproduction, and physiology. Accordingly, changes in ambient lighting may induce stress and thereby affect the health of an animal. Analysis of glucocorticoid (GC) hormones, the hormones that help mediate stress responses provides an important means of evaluating such effects. GCs increase blood glucose levels and stimulate glucose production to provide energy for the flight or fight response to stressors. My project seeks to understand how GC levels in colonial tuco-tucos (Ctenomys sociabilis) vary in response to different ambient light conditions, as well as how variation in glucose levels tracks acute stress (GC) responses. In the wild, these subterranean rodents spend the majority of their time in dark tunnels; in the lab, the animals are exposed to constant light during the daytime. By comparing GC and blood glucose levels in animals housed in clear versus red plastic caging, […]

...Read More about Jonathan Mui

Consequences of Mitochondrial Genome Loss in Cultured Human Cells

Mitochondrial DNA Depletion Syndromes (MdDSs) are a set of diseases characterized by severe pathological effects on the liver and brain. These syndromes are implicated by low/absent levels of mitochondrial genomes, circular strands of DNA housed in the mitochondria (mtDNA) that encode for proteins important for respiration. Thus, maintenance of this genome is thought to be critical for cellular health. However, the mechanism behind the tissue-specific pathologies of these syndromes remains unclear. Recent evidence suggests that the essentiality of mtDNA for cell viability and division may vary across different conditions. Recent experiments done in Dr. Samantha Lewis’s laboratory found that fibroblasts depleted of mtDNA are viable and may retain mitochondrial membrane potential. The goal of my project is to identify candidate genes that allow for the continued resilience of cells depleted of mtDNA. Data from my project will help determine the extent to which mtDNA and its expression is essential for […]

...Read More about Ryan Quan
RyanQuan

Unification and Information Paradoxes

My research asks what unification would mean in the realm of modern physics, and the nature of the current scientific paradigm. It could potentially induce discourse of a paradigm shift, a drastic change in how humans in general understand things. In addition, by viewing the information paradox from multiple lenses, we could better approach a solution and Grand unification of quantum gravity. Current research consists of solutions of the Hawking radiation paradox in the forms of mathematical corrections, firm beliefs from intuition, new theoretical scenarios, low-energy theories, and other theories about the universe. The solution to the information paradox is not yet known, and collecting all of such solutions and synthesizing/proposing a combined theory (of one or two of the aforementioned scenarios) would allow for advancements in the field in mathematical and theoretical development. There are more paradoxes that may arise from certain mathematical solutions, and I will attempt to […]

...Read More about Hong Joo Ryoo

Investigating the Role of IgM Antibodies in the Dengue Immune Response

  Recent research regarding dengue virus serotypes 1-4 (DENV 1-4) has focused on the human immune systems production of antibodies after infection by the virus. IgG antibodies after primary infection can either protect or mediate viral replication to potentially cause severe dengue disease. These pathogenic antibodies are cross-reactive, but IgG-mediated protection for one serotype of dengue virus will not necessarily protect against the other three serotypes. Most dengue research has focused on IgG antibodies, since it was previously thought that IgM antibodies have low affinity for DENV and may not play a significant role in the DENV-specific immune response. However, recent studies suggest that IgM have potent antiviral and type-specific properties in early infection against multiple arboviruses. My research goal is to understand the role of IgM antibodies in response to DENV 1-4 infection and quantify the contribution of plasma IgM to DENV neutralization in early infection. Specifically, I want […]

...Read More about Rohan Shinkre

Interplay Between Protein Stability and Catalytic Activity in Kinases

Kinases are dynamic enzymes that carry out signal transduction in the cell. Many kinases rely on chaperones to protect them from unfolding and poise them for signaling. Chaperoning of kinases by HSP90/CDC37 has been shown to be critical for cancer cell growth and survival, and blocking this interaction could represent a new avenue of treatment for cancers. However, the biophysical nature of kinase chaperoning is not well understood. For my project, I plan to study the kinase BRAF, which, when mutated, is an important driver of oncogenesis and makes the kinase dependent on HSP90/CDC37 to protect it from degradation. In human cells, I will examine how other activating mutations affect BRAF chaperoning to understand how HSP90/CDC37 regulates client kinases. This work could reveal how mutations alter kinase structure to promote interaction with chaperones and inform the development of strategies to block this interaction therapeutically.

...Read More about Odilia Sianto

Incidence of Lung Cancer in Never-Smokers Within the Health System

Lung cancer is a leading cause of cancer-related death, even in those who have never smoked cigarettes. In the United States, about 10–15 percent of lung cancers arise in never-smokers, and approximately 17,000 to 26,000 never-smokers die annually from the disease. Despite this fact, knowledge about the epidemiology of lung cancer in never-smokers remains limited. Our proposed study will be the first to elucidate the incidence rates of lung cancer in never-smokers in our integrated health system, specifically addressing differences by sex and race that are not well established in the literature. Furthermore, our study will establish whether never-smoking women have a higher incidence rate of lung cancer relative to their male counterparts. Lastly, it will address whether lung cancer incidence in never-smokers has been increasing over time, at least within our study population. The study will help clinicians to become more cognizant about the risk of developing lung cancer […]

...Read More about Angela Sun

Discovering Covalent Ligand Inhibitors for Cancer-Driving Mutations

Currently, most chemotherapy drugs used for cancer treatment target specific upregulated or dysfunctional pathways, rather than specific cancer-driving mutations. This results in adverse side effects or reduced applicability, since the drug can also affect normal pathways of healthy cells. In many tumors, cancer-driving mutations alter amino acid residues into cysteines. Due to cysteine’s unique chemical properties, these mutations are an ideal target for covalently binding molecules. This approach is especially useful in undruggable proteins lacking traditionally targeted binding pockets. In this regard, the Nomura Research Group has applied target-based screening of its cysteine-reactive compound library to identify hit compounds that covalently bind target proteins. In this project, I will express, purify, and screen human proteins with common cancer-driving mutations. Subsequently, I intend to utilize established chemoproteomic platforms to characterize hit features like proteome-wide selectivity and on-target engagement. My project ultimately intends to identify and characterize therapeutically useful chemical compounds targeting […]

...Read More about Xavier Tao

Ethnic Variations of the Double Burden of Malnutrition in Vietnam

Vietnam’s demographic transition to increased urbanization and rapid economic development have led to a nutrition transition from traditional to nontraditional, processed diets. Vietnam endures a double burden of malnutrition, the simultaneous prevalence of childhood stunting, thinness, overweight, and obesity. However, these outcomes have not been distributed evenly, particularly when comparing child growth status between different ethnicities. There is a need to explore the prevalence of child malnutrition among Vietnam’s ethnicities, examine if there are significant differences between them, and, lastly, examine potential risk and/or protective factors associated with these outcomes. My research is a secondary analysis across five rounds on 1961 Vietnamese children from the Young Lives Cohort Study from 2002 to 2017. Community, household, and individual child characteristics (using variables modeled from the ecological framework) were collected from children aged 1, 5, 8, 12, and 15. I hope my research will encourage more research focused on recognizing each ethnic […]

...Read More about Ngoc-Thanh Tieu

Characterization of the C. elegans Dauer Microbiome

Bacteria inhabit nearly every surface on Earth, from tabletops to hydrothermal vents. Thus, it is unsurprising that a diverse community of microbes, or microbiome, also inhabits the human gut. However, these residents arent simple stowaways, as gut bacteria actively modulate host development and physiology. Therefore, as different species of bacteria modulate host physiology differently, understanding the factors that determine which bacteria can and cannot colonize the gut is of increasing importance. Host genetics, diet, and geography were all shown to play important roles in determining microbiome composition. The goal of the proposed project is to examine the role of parental transmission to progeny, which, beyond its functional consequences, may have further implications for understanding the evolution of host-microbiome interactions. Last year, I characterized the ecological succession of Caenorhabditis elegans gut microbiome during larval development as part of my honors thesis project. This summer, I will explore the dauer larval stage […]

...Read More about Kenneth Trang

Engineering Novel Epialleles via Directed DNA Methylation in Plants

Epigenetic information refers to chemical modifications to DNA and histones that can be inherited independently of the genetic sequence of a gene. These modifications control the expression of the gene and can alter the organism’s phenotype. In nature, a number of epialleles (alleles with identical sequences yet different epigenetic states) have been identified and often contribute to vast phenotypic diversity among a population of organisms. It is currently poorly understood whether epialleles can be engineered within plant systems. If possible, this could expand the toolbox available to plant breeders and engineers seeking to specify the phenotypes in their crops. I propose to perform an important proof-of-concept experiment to demonstrate the feasibility of engineering epialleles, using a visually obvious marker gene in the model plant Arabidopsis thaliana. I seek to understand if DNA methylation patterns can be engineered and if this epigenetic mark is stably inherited over multiple generations once it […]

...Read More about Connor Tumelty

The Effect of Microgravity on Murine Disc Mechanics

Living on Earth, gravity constantly exerts a mechanical load on the spine, which puts pressure on the discs and causes them to gradually lose height throughout the day. However, this constant mechanical load is greatly reduced while in environments with microgravity such as on the international space station. Due to long-term mechanical unloading in the presence of microgravity, astronauts have an incidence of disc herniation 4.3 times that of the general population. Being able to better describe the physiological changes to the IVD caused by prolonged time spent in microgravity would help the medical community understand the sensitivity of disc homeostasis to mechanical loading and therefore more fully know the role of mechanical loading in disc herniations. Given that 2 percent of the worlds population has herniated discs at any given time, having a better understanding of this affliction could be used to try and create preventative care in order […]

...Read More about Joanna Veres

Uncovering Functional Domains of Dengue Virus Non-Structural Protein 1

Dengue virus (DENV) infects an estimated 105 million people every year. More than 500,000 of these cases develop into a severe form of disease characterized by leakage of plasma from the vasculature. If left untreated, these symptoms may progress to fatal outcomes such as hemorrhage, hypovolemic shock, and organ failure. Studies have suggested that DENV non-structural protein 1 (NS1) plays an important role in the pathogenesis of severe dengue through interactions with endothelial and immune cells. In addition, the Harris Lab has recently shown in vitro and in vivo that DENV NS1 activates the inflammasome, a family of cytosolic innate immune sensors, leading to a protective immune response to DENV in a murine model of DENV infection. However, the molecular mechanisms behind DENV NS1-induced inflammasome activation remain unknown. For my project, I plan to identify the functional protein domains of NS1 involved in inflammasome activation by using NS1 chimeras containing […]

...Read More about Phoebe Wang

Relationship between Bitter Gustation and Mating Status in Drosophila

My project will investigate how mating status (virgin or mated females) affects how Drosophila, commonly known as fruit flies, will intake bitter substances when mixed in solutions with sugar. Because mated females have been shown to intake more nutrients like sugars or amino acids for the purpose of egg production, I want to investigate if mated females will also tolerate more intake of bitter (aversive) compounds that are mixed with sugars. This dynamic is super interesting because fruit flies have two different mechanisms to avoid aversive compounds: one activates bitter gustatory receptors, and the other inhibits sugar consumption. Together, these two processes allow fruit flies to avoid potentially toxic compounds, even in mixed solutions with both appetitive (sugar) and aversive (bitter) compounds. Furthermore, if this is true, then I want to investigate and illustrate the genetic and molecular mechanism that allows this process to occur, which would signify that mated […]

...Read More about Joshua Wong

Simulation of BaCo2(AsO4)2 as a Kitaev Quantum Spin Liquid Candidate

My research project is simulating the layered honeycomb material BaCo2(AsO4)2 at low temperature and high applied in-plane magnetic field, since BaCo2(AsO4)2 is theorized by the Kitaev honeycomb model to exhibit Kitaev Quantum Spin Liquid (KQSL) behaviors. Currently, the Kitaev honeycomb model is still a very new theory to explain the quantum spin liquid states, and any simulations that corroborate or contradict the experimental results will be examined within the theoretical framework of this model in order to identify possible inconsistencies between the model and the experimental results. This topic will be part of my senior honors thesis project, which expands the simulation to other candidate materials of Kitaev physics. These simulations will help to provide explanations for the magnetic behaviors of BaCo2(AsO4)2 in experiments, and any discrepancy between simulation and experimental results will be examined to determine whether the discrepancy is the product of holes in the theoretical framework of […]

...Read More about Jinze Wu

Analyzing Neural Networks in the Context of Concept Learning Tasks

Neural network models have traditionally been viewed as a black box, with tremendous capabilities in a variety of domains, yet with inexplicable inner workings. Past attempts at analyzing neural networks include analyzing model results and learned weights in an effort to design explainable artificial intelligence, as well as early efforts to determine the full capabilities of neural network models. My project seeks to continue in this tradition by investigating the logic-building aspect of neural network models. More specifically, I aim to investigate whether a novel program synthesis neural network model builds internal logical structure during the course of a simple rule-learning task, and whether the model’s logic-building process shares similarities to humans, demonstrated in biases such as a preference for simplicity or brevity.

...Read More about Mellon Zhang