Exploring the Impact of Speckled Clonal Patterning in Skin Carcinomas

It has been shown that tumors are not simply genetically homogeneous collections of cells, but rather growths of evolving, genetically diverse populations that typically arise from a single mutant cell. As this mutant cell proliferates, its daughter cells naturally pick up more mutations due to a variety of factors, creating genetic heterogeneity. More and more studies have been published analyzing the possible interactions of these varied populations, ultimately suggesting that there may be cooperation that influences tumor growth. My lab at UCSF has developed a system using a 4-color confetti cassette to trace clonal growth of carcinogen-induced skin tumors. Using this model, there has been evidence of malignant tumors with a speckled pattern, a phenomenon in which there exists a dominant clone and scattered throughout are non-clustered cells of another minor clone. My project aims to study the impact of this pattern of heterogeneity and ultimately test my hypothesis that […]

...Read More about Zoe Adams
L&S Sciences

Investigating Magnetism in FexWSe2

Electromagnetism is a fundamental physical phenomenon, but there is still much to learn about how and why it takes shape in solids, where the interactions between many atoms can create unique and unexpected magnetic and electronic features. This summer, my SURF project will be an investigation of magnetism in FexWSe2. WSe2 is a transition metal dichalcogenide (TMD), which are often layered, quasi-2D materials which are being studied widely due to their promise in revealing foundational aspects of physics in low-dimensional systems. Intercalating a TMD with a transition metal such as iron can introduce exotic magnetic and electronic structures to the system and create features which could be useful in technological applications. I hope to spend this summer synthesizing a high-quality bulk crystal of FexWSe2 and then characterizing its magnetic features in the laboratory. Additionally, I will be learning techniques to analyze magnetization data and make predictions about interesting properties that […]

...Read More about Meera Aravinth
L&S Sciences

Active Chromatin Marks Modulate the Activity of the Crucial Epigenetic Silencer PRC2

In mammals, Polycomb Repressive Complex 2 (PRC2) plays a crucial role in maintaining the gene-expression patterns that enforce cell differentiation during embryonic development. Mutations in the core components of PRC2 or its associated cofactors result in early embryonic lethality. PRC2 represses transcription by mono-, di- and tri-methylating histone H3 at lysine 27 of nucleosomes, the smallest structural unit of chromatin. The molecular basis and mechanistic insight into the modulation of methyltransferase activity of PRC2 by the presence of other histone modifications remains poorly understood. Previous biochemical studies of PRC2 activity in the context of various histone modifications have given conflicting results. This project will carry out enzymatic assays to measure the kinetics of PRC2 activity using nucleosome substrates carrying different histone modifications. Furthermore, to investigate the underlying molecular mechanisms behind the trends we observe in our biochemical assays, we will use cryo-electron microscopy to directly visualize the interactions between PRC2 […]

...Read More about Curtis Beck
Rose Hills

Puzzling Proofs: Navigating Proof Construction and Communication in Middle School

Recent reforms in STEM education argue for students engagement in disciplinary practices, such as the construction and communication of a mathematical proof. Researchers have argued that some of the difficulties students face with proofs in particular, may stem from their limited opportunities to engage in productive disciplinary practices, such as successfully employing multiple forms of reasoning when constructing a proof (Boero, 1999; Pedemonte, 2007). In this project, my graduate student mentor and I will explore how educators can support proof construction and communication in middle school that may encourage the use of multiple forms of reasoning through non-linear explorations. Using qualitative methods, we will study young learners reasoning patterns and disciplinary practices as they participate in innovative puzzle-like proving activities. We will pay particular attention to the role of material and social configurations that may influence young students equitable opportunities for participation in productive disciplinary practices.

...Read More about Emma Bellman

Is Sharing Caring? Investigating the Role of Horizontal Gene Transfer in Insect Fitness

You may have heard the phrase You look just like your mother, but how often have you heard You look just like a bacteria? The former is an example of the type of genetic inheritance most of us are familiar with, vertical, or inheritance from parents to offspring. This project, however, involves horizontal inheritance: that is, the exchange of genes between species, otherwise known as horizontal gene transfer (HGT). The project involves investigating how and why a horizontally transferred gene was transferred from viruses to insects several million years ago.

...Read More about Ashley Elizabeth Bendl

Track-II Diplomacy in 21st Century Nuclear Non-Proliferation

The current decline of global institutions, breakdown of negotiations and treaties, and strong emergence of new nuclear energy sectors indicate major diplomatic efforts will be necessary to curb nuclear weapon proliferation. As government cooperation withdraws from these existential political crises, scientists, engineers, academic experts, and other non-state actors may increasingly fill in diplomatic roles. However, there is a lack of consensus on the future role and strategy of these civilian efforts known as track-II diplomacy. Under what conditions do track-II dialogues successfully contribute to non-proliferation success? Track-II diplomacy is championed for preventing loose nukes after the Soviet Union collapsed, but these efforts were carried out by autonomous scientists in a uni-polar world. This study evaluates track-II efforts in non-proliferation in an increasingly undemocratic and multi-polar world with declining global leadership. Past and current non-proliferation cases supplemented with participant anecdotes are analyzed to suggest policy for non-proliferation threats on the horizon.

...Read More about Anthony Benjamin
Humanities and Social Science

Symbolism and Globalism in Bronze Age Art

The world we live in today is shaped by globalism. There is more exchange of ideas, artwork, and technology than ever before. We travel, inspire each other and use symbolism to transcend language and cultural barriers. However, is this really a new phenomena? Archaeological research constantly uncovers more evidence that humanity has been doing this for millennia. The Eastern Mediterranean Basin had an extensive network for the movement of goods, people and ideas between the civilizations of the Near East since before the Bronze Age. My research investigates the affect of this rudimentary globalism on people, as expressed through art and symbolism left in the material record of the Early Bronze Age in Cyprus. Cyprus was a center of trade, and I predict that I will find evidence of differentiation between private and publicly used items which are reflective of a multicultural worldview. I will look for hints of individual […]

...Read More about Amaris Blasgen Morningstar
Humanities and Social Science

The Samoan Crisis and the Development of U.S. Imperialism

Among U.S. foreign policy historians, the Spanish-American War of 1898 marks a commonly accepted turning point for the course of U.S. expansion and the countrys status as a great power in the European-led international system. Newer scholarship, however, has reevaluated the wars centrality for American imperial ascendance, and this project seeks to contribute to these efforts by scrutinizing an earlier moment in American history. Through an analysis of a conflict which brought the Cleveland administration to the brink of war with Bismarcks Germany, I intend to examine the intellectual influences upon the evolving and centralizing American federal government. Such influences, evident in the response to the Samoan Crisis of 18871889, enabled the projection of American power overseasenabled, in other words, American imperialism. By examining the ideas circulating among legislators and government reformers at the time, this project strives to understand just how imperially-minded the U.S. was in the post-Civil War […]

...Read More about Sophia Brown-Heidenreich
Humanities and Social Science

Cumbias, Bombas y Bombas: The Intersection of Literature and Music and the Salvadoran Civil War

By examining the intersection of sound and image, this research will trace the convergence of popular music and Salvadoran literary and artistic traditions both at home and in the diaspora, with a particular focus on its engagement with images of violence. Drawing from the cultural production of the years of the Salvadoran civil war (1980-1992) and the postwar, I will track emblematic cultural objects that affront the reality of repression of the years leading up to the war, the bloodshed of the war, and the reverberations in the years that followed. From cumbia song lyrics in revolutionary poems, to musicalized poetry in folk music formats, to authoritarian party songs, these cultural objects formed a great part of the vestiges of a national identity in diasporic groups of war refugees. This investigation, then, will give insight into the formations of national identity in transborder populations, into ideas of belonging and its […]

...Read More about Bryan Chavez Castro
Humanities and Social Science

Investigating the Effects of Body Movement on Whisker Stimulus Detection in Mice

There is evidence that body motion can either improve (Gallero-Salas et al., 2020, Gilad et al., 2018 ) or inhibit (McBride et al., 2019) performance during head-fixed behavior in mice. Therefore, it is important to understand how body movements affect sensory detection performance in behavioral tasks. My research project will look closely at the effects of body movement on a mouses performance in a whisker-based sensory detection task. From previous literature, we know that body movements modulate sensory signals in cortical areas of mice. My research will involve using behavioral paradigms in which mice are head-fixed, which is necessary to keep the head stable for measurement of neural signals while the mouse is performing a sensory detection task. Specifically, I am going to design a video-based system to measure body movements in head-fixed mice performing a sensory detection task.

...Read More about Andy Chen
L&S Sciences

Holder-Brascamp-Lieb, Red-Blue Pebbling, and Communication-Optimal Algorithms

Numerical linear algebra underlies much of the modern world. It is essential to a wide variety situations, and as such, it is of great interest to analyze and optimize the underlying algorithms. In recent years, there has been an increased interest in optimizing algorithms to reduce communication, which is frequently many orders of magnitude slower than performing calculations. The Hlder-Brascamp-Lieb inequality and the Red-Blue Pebbling Game are two powerful approaches to theoretical analysis of communication, and both are used to derive communication optimal lower bounds. Once these bounds have been derived, the next challenge is to implement an algorithm that attains these minimums, and thus, is communication minimizing. Many currently implemented algorithms do not meet these bounds, and this is a matter of great importance, with large potential time and energy savings. In this way, our project has two broad goals. Our first is to implement a communication optimal algorithm […]

...Read More about Anthony Chen
L&S Sciences

Uncovering the Role of C4 Enzymes in C3 Photosynthesis under High-Stress Conditions

The vast majority of plants and crops, used both for food and fuel, utilize a type of photosynthesis in which the enzyme RuBisCO catalyzes the primary assimilation of carbon dioxide into sugar, termed C3 photosynthesis. However, certain plant lineages have evolved both biochemical and anatomical alterations, called C4 photosynthesis, that allow the enzyme PEP carboxylase to perform the primary assimilation event of CO2. C4 photosynthesizers have both higher photosynthetic efficiency and lower rates of an energy-intensive process called photorespiration relative to C3 plants, especially under high-stress conditions. As the climate continues to become more unpredictable, the benefits of the adaptations of C4 plants over C3 plants, in particular for food and fuel production, will become ever more critical. A major hole in our understanding of how C4 photosynthesis evolved rests in the fact that while all the enzymes necessary to perform C4 photosynthesis are present in all C3 plants, their […]

...Read More about Lindsey Ching
Rose Hills

Nanoconfined Phase Change Materials for Aqueous Thermal Management

Over 40% of U.S. freshwater withdrawals are used for the generation of thermoelectric power: more than the amount withdrawn for agricultural irrigation and domestic use combined. Such high water demand can largely be attributed to waters critical role as an industrial coolant. Phase change materials can greatly decrease the volume of water required to cool thermoelectric power generators. PCMs work by absorbing heat through a phase transition, and can greatly increase the heat capacity of water. Sugar alcohols, like erythritol, are ideal phase change materials because they are cheap, widely available, non-toxic, and have very high latent heats. The Urban Group has developed a novel composite phase change material that is composed of sugar alcohols contained within the pores of metal organic framework. Their confinement within the MOF has been observed to depress their phase transition temperature by ~90C, making their use in cooling waters possible. The focus of my […]

...Read More about Kelly Chou
Rose Hills

Characterization of A. thaliana Transcription Activators

The field of metabolic engineering has expanded to utilize plants as an expression host in the biotechnology industry and current research. Transcription factors (TFs) are one of the many intriguing components in the plants metabolic pathways as they regulate the expression of the enzymes involved. While TFs are integral for control of gene expression, most TFs in plant systems are not characterized regarding their upregulation (activation) or downregulation (repression) of gene expression. In unpublished work my group has screened a library of 400 transcription factors from A. thaliana with a fraction displaying trans-activating patterns stronger than VP16, a commonly used strong trans-activation domain (TAD) from the herpes simplex virus. My goal for this project is to characterize the top 20 TFs of the previous work in their ability to activate gene expression according to their TAD. 1 I plan to apply these candidate TFs into published biological systems and hosts […]

...Read More about Jasmine Cisneros
Rose Hills

European and American Literary Realism: The Fictional Construction of Nation and Self

My research project will probe how the relationship between the protagonist and their society as illustrated within the 19th century realist novel functions as a reflective allegory for idealized national identity. I posit that the consolidation of recognizable cultural markers ,including language idiosyncrasies, geographic landmarks, and social traditions, connects character and setting in a unique way which sheds light on the idea of a singular national persona in literature; further, literary realism inevitably embodies a sense of cultural consolidation through the construction of a limited fictional setting, so as to reflect a picture of the real world as the reader imagines it. Scholars have defined cultural consolidation as the process of fortifying a collective identity toward the ultimate goal of successful-state building. Therefore, we must consider how protagonists relate to their social, spatial, and material surroundings as both individuals and generic representatives of national sentiment/ideals, and this is possible due […]

...Read More about Skylar Clark
Humanities and Social Science

Moving-Image Evidence in the Turn-of-the-Century Courtroom

New technologies such as police body cameras and deepfake algorithms have recently put questions of photographys value as evidence in the spotlight. However, photographic technologies have been part of the courtroom since the mid-nineteenth century. This project turns to the emergence of photography and cinema as evidentiary tools in the courtroom in an attempt to uncover the preconditions of our current moment of mediated justice. I will assist my graduate student mentor in advancing the larger project by constructing a newspaper archive for significant early court cases involving moving-image evidence, seeking to answer the question of how film entered American courtrooms. This will involve writing summaries of cases, compiling timelines of events, and identifying significant characters. The work will initially draw from campus collections and online newspaper databases. There will also be the opportunity to undertake further research at other local institutions in the Bay Area and Sacramento.

...Read More about Jesse Clements

Can State Legislation Encourage Retirement Preparedness in Private Employees?

More so than in other developed countries, United States adults are unprepared for retirement. Stagnating wages and the gradual death of defined benefit pensions in the private sector are largely responsible, as private employees are unlikely to have a guaranteed income stream in retirement beyond Social Security. These employees, however, often have access to defined contribution pensions (like 401(k)s) that allow them to contribute their own earnings to tax-advantaged accounts that can be accessed in retirement. In my study, I analyze the impact of state legislation on private employees decisions regarding their defined contribution pensions. Based on prevailing literature that has demonstrated the effectiveness of federal legislation, I hypothesize that state policy will have a pronounced impact on the investment habits of private employees. Using IRS pension data and macroeconomic information from the Federal Reserve, I hope to demonstrate that states have an important legislative role to play in strengthening […]

...Read More about Danny Cohen
Humanities and Social Science

Perceptions of Bias Faced by Lesbian, Bisexual, Pansexual, and Queer Women

Lesbian, bisexual, pansexual, and queer (LBPQ) women are in a unique position as members of two subordinated groupswomen and sexual minorities. However, common understandings of prejudice and bias may be failing to capture the unique experiences that stem from the intersection of these two groups. Specifically, peoples understanding of homophobia focuses on the struggles of gay men and overt legal forms of bias; and peoples understanding of sexism centralizes the experiences of cisgender, heterosexual women, despite evidence to suggest that LBPQ women face more severe forms of objectification and harassment. Thus, this research aims to bridge this gap by examining: LBPQ and gay, bisexual, pansexual, and queer mens (GBPQ) personal experiences with prejudice and bias; heterosexual folks perceptions of prejudice and bias facing GBPQ and LBPQ individuals; and the cultural mechanisms that help explain the discrepancy between lived experiences and perceptions of experience. Some mechanisms that will be examined as […]

...Read More about Gabby Collins
Humanities and Social Science

The Missing Link: The Absent Foundation of Support for First Generation Students Transitioning from High Schools to Four-Year Institutions

According to the Pell Institute, in 2012, only 25% of first-generation students attended four-year institutions. For my research project, I want to examine why this rate is so low. The existing literature focuses primarily on barriers to first-generation students once they attend college. Consequently, I want to examine barriers first generation students face when choosing to attend college in the first place. My research question for this project is: what factors dissuade first-generation students from transitioning from high school to four-year universities and how can high schools support these students in navigating this transition? To answer this question I will be conducting in-depth interviews with first-generation students from high schools and four-year colleges as well as school counselors between two schools of contrasting resources. This project will help me to provide important information on what needs to change to support a cohort of underserved students who are lost in the […]

...Read More about Romeo Connors
Humanities and Social Science

The Ecology of Antibiotic Production in Interspecies Interactions

The soil microbial community is rich with bacteria that provide an abundant source of medically valuable natural antibiotics and pharmaceuticals. In particular, Streptomyces padanus possesses antimicrobial activity and produces actinomycin D, an antibiotic with antitumor properties. However, there is a lack of understanding in the field regarding the ecology of antibiotic production in S. padanus — specifically how antibiotic products contribute to antimicrobial activity during microbial interactions. Preliminary data suggests that activity of actinomycin D inhibits growth of the fungus Metarhizium anisopliae during interspecies interactions. In my research, I will adapt an engineered CRISPR/Cas9 system to delete actinomycin D activity in S. padanus, which is a novel method for this species. I will then analyze whether Metarhizium is still inhibited by mutant S. padanus during interactions. This will confirm whether actinomycin D plays a significant role in this bacterial-fungi interaction. By creating mutant strains and testing their interactions with fungi, […]

...Read More about Aimee Cortez
L&S Sciences