Detecting natural selection with ancient and modern DNA data

I’m interested in developing computational methods to quantitatively describe the impact of natural selection on various traits and genes expressed in modern human populations. Detecting and inferring natural selection is central to understanding how populations of individuals have evolved over time. Advances in next-generation genomic sequencing technologies have made it possible to extract high-quality DNA data from ancient relics such as fossils. Specifically, I want to understand how this ancient DNA data can help us detect selection, and I’ll also be testing methods that I develop with real ancient DNA data from Europe. Combining both modern and ancient DNA samples into an analysis will allow me to paint a clear picture of how our genome has evolved in response to various environmental factors over the past ten thousand years. I’ll be developing scalable methods that can use both ancient and modern DNA data to accurately detect selection across hundreds of […]

...Read More about Zaid Ahmad
L&S Sciences

Timing is Everything: Bird-brained Ideas About the Importance of Melatonin for Reproduction

We will use wild-caught European starlings to explore where melatonin may be produced in the bird brain (outside of the pineal gland) by detection of enzymes involved in its synthesis. Generally, organisms strategically allocate energy among physiological processes, and these processes are highly sensitive to the environment. Species that reproduce seasonally utilize environmental cues to coordinate physiology at the proper time. These cues are translated into signals through neuroendocrine signals, leading to the production of melatonin in the pineal gland; however, the pineal gland has never been found to regulate reproduction in any seasonally reproducing bird species. How, and where, melatonin may be exerting a physiological effect on the reproductive physiology and timing of birds is wholly unknown but we hypothesize that the hypothalamus – a major part of the HPG axis – may produce it de novo.

...Read More about Genevieve Akponye
SURF SMART

Quantum Machine Learning for High Energy Physics

The question I aim to answer this summer is whether quantum machine learning can provide an advantage over classical machine learning techniques for certain high energy physics applications. Analyzing data from particle collider experiments involves distinguishing signal events, which correspond to the particle physics of interest, from background events. Currently, classical machine learning techniques are used to tackle many of these classification problems. However, these techniques often require large amounts of data to classify with a high degree of certainty. In the growing area of anomaly-detection searches, datasets may be small. This can lead to poor classification performance of classical machine learning models. Several recent results have shown that quantum machine learning can provide an advantage for data-limited classification problems. However, these works have applied quantum machine learning to situations where classical machine learning techniques are already sufficient. Over this summer, I plan to directly test the possibility for a […]

...Read More about Sulaiman Alvi
L&S Sciences

Using paleomagnetism and geochronology to test a bifurcating mantle plume hypothesis

1.1 billion years ago, Laurentia, the Craton which makes up majority of modern North America’s landmass, was rifting apart in the Lake Superior region and growing in the American Southwest. Both of these processes produce magma. As magma cools, the magnetic minerals within align with Earth’s magnetic field and these alignments can be used to determine the age of a rock (paleomagnetism). Similarly, small crystals formed within the magma can also indicate a rocks age (geochronology). There is a likely connection between the locations due to similar timing of emplacement and geochemical signals. Recent, high-quality data collected for Lake Superior indicate a high volume, short duration magmatic event 1096 million years ago, which is inconsistent with a typical rift (long duration, low volume). It is hypothesized that an upwelling magma plume encountered topography at the base of the crust, bifurcating it, sending some magma into the rift, with the rest […]

...Read More about Nicolas Anderson
L&S Sciences

How Much Black Wealth is “Acceptable” in America Today

We are embarking on the 100th anniversary of the decimation of the thriving African American community in Tulsa, Oklahoman, also known as “Black Wall Street (BWS).” Evidence suggests the destruction of BWS and its aftermath was meant to physically, psychologically, and economically impede African American prosperity (Messer, Shriver, and Adams, 2018). A psychological mechanism that has never been studied is: how much black wealth is “too much” in white and black Americans? Today, 100 years after BWS’s destruction, black wealth continues to suffer at the individual and generational level (Conley, 1999; Oliver & Shapiro, 1995). Putting aside systemic racism, red-lining, lending discrepancies, and other forms of black American suppression, looking at business ownership, control, and profitability alone tells a bleak story. My research seeks to explore the wealth threshold for Blacks / African Americans that leads to a perceived threat or bias in both black and white perceivers. My study aims to […]

...Read More about Ockemia Bean
Humanities and Social Science

Synthesis and Characterization of Cu3N for the Electrochemical Reduction of CO2

With abundant greenhouse gas emissions negatively affecting environmental and human health, it is extremely important that research is conducted on semiconductor materials that can both produce energy renewably and reduce existing pools of atmospheric carbon dioxide. In accordance with this pressing task, I will be working on a project to synthesize and develop a transition metal nitride (Cu3N) with the ultimate aim of demonstrating its ability to reduce carbon dioxide both selectively and efficiently into liquid and gaseous fuels, using solar energy. While copper nitride has a high absorption coefficient, a narrow band gap, and other properties that would enable it to perform favorably in photovoltaic and photoelectrochemical cells, little research has been done on its potential within the context of CO2 reduction reactions due to difficulties encountered in its synthesis. I will thus be building off of the Cooper Lab’s work at Lawrence Berkeley National Laboratory to effectively synthesize […]

...Read More about Noah Bussell
Rose Hills

Indulgences and the Common People in Late Medieval England: A Tool of Devotional and Communal Solidarity?

An Indulgence, a remission of temporal punishment of sin whose guilt has been already forgiven through the sacrament of confession, has played a major devotional role in the lives of all social classes in Late Medieval England. Although the Early Modern historiography and the negative portrayal in popular culture (Canterbury Tales by Chaucer) diminished the overall credibility of indulgences, I will try to discern the extent of Indulgence’s devotional and communal effects on the common English lives and people. By exploring their primary communal and religious context, I want to examine Indulgences not only as a religious insurance of temporal punishment but as a tool reinforcing communal solidarity through the use of secondary sources, and Indulgences in the National Archives, The British Library, Bodleian Library, and Borthwick Institute for Archives.

...Read More about Viktoriya Carpio
Humanities and Social Science

Can Preschoolers Learn from Metaphors?

Can preschoolers learn from metaphors? While many studies have shown that adults use metaphors to guide their thinking and reasoning, the question of whether young children can do the same remains unexplored. We use metaphors in our everyday lives (e.g. “Tourists flooded the popular beach town over break” or “A second wave of the virus is expected to hit after the holidays due to travel”), and they help us reason about abstract concepts (e.g. “I was surprised when she attacked my claim but I regrouped and defended my idea with even stronger evidence”). Over the course of this summer, my mentor Rebecca and I will collect data from young preschool-age children to investigate their understanding and use of metaphorical language. Though previous metaphor research has primarily focused on adult subjects, we hope to extend this research to younger ages, and discover whether preschoolers can also use metaphors to learn.

...Read More about Zoe Carwin
SURF SMART

Her Vision of the Sea: Reframing Sylvia Plath through Ecopoetry

While Sylvia Plath has not customarily been considered an ecopoet, many of her poems describe exchanges between the individual and the natural world. Scott Knickerbocker demonstrates how Plath’s work “expresses the wildness and vitality she craved in nature through language itself,” focusing on what he terms “sensuous poesis”, which “enact[s] through formal devices such as sound effects the speaker’s experience of the complexity, mystery, and beauty of nature.” My research continues in this vein, focusing specifically on how Plath herself related to the natural world, and the role she saw for herself within that greater world. Given her remarkable ability to perceive the smallest details of both the human and non-human world around her, the persistent critical interpretation of Plath’s poetry as written by a mentally ill author seems limited. It is more compelling to examine Plath, both biographically and poetically, not as pathologically self-absorbed, but instead as possessed of […]

...Read More about Andrew Chan
Humanities and Social Science

Contested Memory and the Racialization of Monuments in the United States

The status of monuments depicting white colonialism has been highly debated for years, with some historians stating that they should remain while others ask for their removal. Although these monuments have been contested since their creation, the Black Lives Matter movement has become an avenue for immediate change. In response, artists put up contemporary monuments that highlight racial injustice throughout the world. However, within the Black Lives Matter movement, both these contested statues as well as the newly placed, contemporary pieces of art are toppled or destroyed. This research project will look into the context of both these old and contemporary Bay Area monuments/murals, which includes the reason for their placement and the reception upon their placement. Then, it will look into their destruction, and the sentiments tied to these actions. By doing so, this research will find where the United States stands when it comes to racial injustice in […]

...Read More about Ivan Chavez
Humanities and Social Science

Comparison of Glacier Vertical Thinning and Horizontal Retreat in Yosemite During the Last Glacial Maximum

Glaciers are important freshwater sources around the world. They are especially significant during climate change because they serve as nature’s drought buffer to balance years with less rain. Understanding previous global glacier melting events will help us understand how glaciers today will respond to global warming. Many mountain glaciers are not well constrained. The goal of my study is to provide more insights into the unsolved Tioga glacier melting patterns in Yosemite National Park, located in the Sierra Nevada range in California, after the Last Glacial Maximum, the most recent global glacial maximum event. The main question I aim to answer is whether the glacier melted uniformly in a short period or altered between retreating and advancing during a longer melt period. Geochemical dating methods will aid in addressing questions related to the timing, rates, and patterns of Tioga glacier’s glacial retreat and glacial thinning. I will conduct fieldwork and […]

...Read More about Yueyi Che
L&S Sciences

Machine-Guided Directed Evolution of MAAP to Promote AAV Secretion

Gene therapy has been a rapidly emerging field of experimental therapeutics, wherein nucleic acids are delivered into cells via viral vectors in the effort to treat diseases associated with genetic defects. An increasing number of clinical trials have shown that the recombinant adeno-associated virus (rAAV) is an efficient vehicle for gene therapy. However, the low production capacity of rAAV has been a major bottleneck that decelerates AAV gene therapy development. To overcome this, the present project aims to target membrane-associated accessory protein (MAAP), which is known to serve a critical role in promoting secretion of AAV virion. Initial rounds of direct evolution of MAAP will be conducted to enrich functional variants in the construction of an AAV library. This library will further undergo next generation sequencing to recover functionally improved variants in comparison with wild type MAAP. The resulting sequence-function dataset will further train machine learning algorithms in predicting optimally […]

...Read More about Aleysha Chen
Rose Hills

Developing a High-throughput Method of Generating Pooled CRISPR-induced Deletions in Drosophila

The CRISPR-Cas9 system has opened doors to our understanding of genome editing, genetic disease, and targeted therapies. This technology has been applied in fruit flies, Drosophila, to generate targeted germline deletions to study genes and chromosome organization. These experiments are currently limited by extensively long procedures, where generating a pool of Drosophila with unique CRISPR deletions requires separate cycles of plasmid cloning of guide RNA, embryo injection, and sequence analysis for each locus. This imposes a restricting upper limit on the number of deletions that can be induced and analyzed at once. My project seeks to develop a high-throughput method for generating precise deletions in flies by modifying this procedure and collapsing these cycles into a multiplexed, four-step approach. This technology will ideally enable systemic generation of a pool of Drosophila mutants, pushing this upper limit to potential ten times the original efficiency or more. This would open possibilities to […]

...Read More about Anne Chen
Rose Hills

The influence of spontaneous neural activity on the development of intrinsically photosensitive retinal ganglion cells

The retina is the neural tissue lining the back of the eye that senses incoming light and relays this information to the brain, allowing for vision to occur. During development, “waves” of neural activity propagate across the retina, and to areas of the brain that receive retinal input. Retinal waves play an important role in establishing the organization of retinal inputs to the brain, but there is only limited evidence that they play a role in the development of the retina itself. I am exploring the role of waves in the development of a class of output neurons of the retina called intrinsically photosensitive Retinal Ganglion Cells (ipRGCs), which express the light-sensitive protein Melanopsin. These ipRGCs themselves participate in retinal waves during a period of development in which they undergo a significant amount of cell death. By comparing the densities and connectivity of ipRGCs in wild type mice and mice […]

...Read More about Andy Chen
Rose Hills

Beyond the Screen: Examining Spatial Structure in Hypertext Fiction

The home page of tthe website entitled The Unknown begins with the text, “The Unknown: The Original Great American Hypertext Novel.” The Unknown is a piece of electronic literature—literature that exploits the capabilities of the computer—in the genre of hypertext fiction. Hypertext fiction itself is literature that links pages through hypertext to create new kinds of narratives. As a genre in a field of writing that has only emerged with the rise of computers, these narrative possibilities are just beginning to be explored and discussed. I propose that graph theory, a field of mathematics dedicated to studying vertices (comparable to pages on the web) and the edges that connect them (comparable to the links between pages) can expand discussion on hypertext fiction in an entirely new dimension. More specifically, I plan to analyze The Unknown as a graph and then compare the spatiality that this visualization affords to The Unknown’s […]

...Read More about Mallen Clifton
Humanities and Social Science

Economic Recoveries for Doubled-Up Households from the Great Recession

In the twenty years I have spent living in different types of dwellings, including households that support more than one family, I have noticed that these doubled-up households seem to take longer to recover from an economic crisis. Is this a pattern? This study seeks to investigate and measure if living in doubled-up households lengthens economic recovery. We will look at doubled-up households and how economic circumstances and other possible shocks might impact these types of dwellings by analyzing household income recoveries post 2008 recession, comparing traditional households with comparable doubled-up households. The economic recovery in the United States from the Great Recession saw real median household income return to the 2007 peak by 2016 and continued to climb, but in that timespan there was an increase in the number and share of doubled-up households. This influx of doubled-up households created a false signal of macroeconomic wellbeing; it demonstrated a […]

...Read More about Rhammses Del Rio
Humanities and Social Science

Tracking Changes in Neural Activity from Novel Brain Stimulation

Non-invasive brain stimulation (NIBS) safely manipulates neural excitability in the brain, offering neuroscientists a powerful tool to study the human brain and clinicians a potential treatment for psychiatric and neurological disorders. NIBS methods influence the brain’s electrical activity by generating an electric field over a targeted region of the scalp. For example, directing stimulation over the motor cortex can elicit movement in a muscle of interest. The intensity of movement may reflect the integrity of the nervous system’s motor pathway but measuring electrical changes in the brain proves vital to understanding how the brain responds to stimulation. A new magnetic NIBS device developed at Berkeley requires an investigation of these electrophysiological changes. I will study our device’s effect on neural activity using electroencephalography (EEG), a non-invasive method of monitoring electrical signals in the brain. Using EEG, we hope to understand how the device modulates neural excitability and endogenous neural oscillations.

...Read More about Owen Doyle
Rose Hills

Perception of /d/ by Spanish-English Bilinguals

The consonant /d/ in English and Spanish differs in its place of articulation: English has alveolar [d] while Spanish has dental [d̪]. Previous research has reported that Spanish-English bilinguals are able to produce both constrictions, resembling two monolinguals. Thus, this research will focus on two main questions: a) How do Spanish-English bilinguals acquire this distinction? and b) how late can they acquire this distinction? We will collect data through a series of tasks in which Spanish-English bilingual subjects will discriminate between manipulated /d/ stimuli, allowing us to identify which acoustic cues they are more sensitive to. Furthermore, by comparing different ages of acquisition of a second language, we will analyze which age groups are most sensitive to this acoustic distinction and when sensitivity starts to decrease. This research will also allow us to better understand how age affects language acquisition, and if there is an age limit after which subjects […]

...Read More about Jesus Duarte
SURF SMART

Greenfield Village and the Pedagogy of Urban Scale Models

My project explores the pedagogy of urban scale models as they are disseminated from scholarly fieldwork. As my central ‘text’ I will use Detroit’s Greenfield Village — the nation’s first living history museum, created by the automobile baron Henry Ford — and trace the user experience of the park, exploring the discourse of good design it sought to construct. Greenfield Village is an essential document of the early 20th-century ‘field study,’ a method of sociological investigation which held that by systematically carving up and analyzing the city, one could reform it. In this way, field trips to Greenfield Village by students and tourists alike became a practical application of the field study, where everyday individuals could inhabit the role of the planner-on-high. Such renderings of cities began to pop up across the country — from Philadelphia to New York — all of which can be traced back to this academic […]

...Read More about Isaac Engelberg
Humanities and Social Science

Tracking the Expression of Sleep-related Genes in the Cassiopea Jellyfish

Sleep behavior in Cassiopea, the upside-down jellyfish, challenges the common association between sleep and brain function. In lieu of a brain and centralized nervous system (CNS), Cassiopea has a decentralized net of ganglia that initiate pulsing activity at a slower rate during the night. My project seeks to understand how an animal that lacks a CNS undergoes a whole-body behavioral state change. More specifically, I will examine how this behavior affects the expression of several genes connected to sleep and activity using in situ hybridization and quantitative PCR. These genes encode an acetylcholine receptor subunit, choline acetyltransferase, a GABAergic receptor, a sodium-calcium exchanger, and a glutathione S-transferase. Characterizing the expression of these genes will help illustrate the connection between ganglion usage and sleep behavior. I will silence one gene of interest, the acetylcholine receptor subunit, using RNA interference, and compare the gene expression of sleep-deprived jellyfish to those of jellyfish […]

...Read More about Diana Francis
Rose Hills

The Roots of Menstrual Capitalism: How Menstruation Became Commodified

Before the invention of disposable pads and tampons during the late 1920s and early 1930s, period products were homespun creations. Period products were made by women for women out of leftover pieces of cotton and other fabrics that were often washed and reused. Those who could afford to, however, would dispose the pieces of soiled cloth. The ease of disposing menstrual cloths then resulted in the creation of products that were meant to be thrown away. Disposable menstrual pads and later tampons, unlike their more rustic forefathers, were branded and their advertisements associated these products with a new kind of modern “delicate” woman. While material culture, or the objects that surround individuals, are typically used to establish status and identity, menstruation’s material culture produces identity and status in more nuanced ways because period products are meant to be invisible. This invisibility, or menstruation suppression, paired with the commodification of period […]

...Read More about Karah Giesecke
Humanities and Social Science

Using Disorder to Control Topology in MnBi2Te4

Topological insulators, electronic materials that behave like insulators in their interior but can conduct current on their edges or surfaces, hold a lot of potential for improving the function and energy efficiency of various devices. These materials have unique electrical properties resulting from their conducting edge and surface states. Specifically, these states can transport charge with very low resistivity, leading to efficient conduction. Topological insulator materials are heavily influenced by the symmetry of their crystal structure─the pattern in which their atoms are arranged. For this reason, my project will investigate the effects of structural disorder─which breaks spatial symmetries─on the properties of a relatively new topological insulator with the chemical formula MnBi2Te4 (Manganese, Bismuth, and Tellurium) through computational quantum mechanical modeling methods such as Density Functional Theory. Namely, I will look at the effect of slightly distorting the crystal structure on the magnetism, electronic structure, and other properties of the material.

...Read More about Amoolya Grandhi
Rose Hills

Understanding the necessity of visual cortex task learning

We have seen that acute inactivation or intermittent optogenetic silencing of the visual cortex of the brain results in behavioral deficits. On the other hand, permanent lesioning or chronic silencing results in mice recovering their ability to perform the detection task. In this paradigm, the mice have been habituated to the task over a certain period of time and thus have learnt it. To put it simply, in spite of deactivating the visual cortex required for task performance, mice are capable of recovering and using other processes to conduct the task. My question is whether this chronic deactivation would allow the mice to learn the task in the first place, i.e. during habituation. If the mice are able to learn the detection task without the visual cortex, it would suggest that there is some other pathway that comes to play upon the deactivation of the visual cortex. By comparing the […]

...Read More about Anushree Shirish Gupte
L&S Sciences

Function and structure of human iPSC-derived liver organoids self-assembled in microgravity

Liver transplantation is currently the only treatment for end-stage liver disease, but engraftment of liver organoids holds promise as a viable approach to resolve the shortage of donor livers. While traditional organoid cultures take place atop two-dimensional (2D) plates, rotating wall vessel bioreactors (RWVs) can be used to culture three-dimensional spheroid organoids, augmenting cell-cell interactions through the low shear stress, low turbulence environment provided by RWVs. The use of human induced pluripotent stem cells (iPSCs) in organoids can further advance clinical translation, because using a transplant recipient’s own iPSCs may eliminate the need for life-long immunosuppression post-transplant. However, the precise functional qualities of RWV-grown, iPSC-derived organoids are not completely understood. Our lab’s preliminary data suggest that two genes, albumin and CYP1A1, are upregulated in RWV-cultured organoids compared to 2D cultures. My project aims to characterize the functionalities of RWV-generated, iPSC-derived organoids by investigating patterns of localization and expression for albumin […]

...Read More about Simon Han
L&S Sciences

Feminization of Labor in the U.S. Prison-Industrial Complex

My project follows two trends that have developed since the 1970s and appear to converge on the site of the imprisoned female body. The first trend is the globalized “feminization of labor,” where large numbers of women join the workforce. The second is the increasing number of females incarcerated within the United States. Specifically, I want to examine the rhetoric of records and documents concerning the female prison laborer. I am interested to see how the language that dictates the subjectivity of women in prison has shifted, as its population has increased over time, and in comparison to their male counterparts. I will examine public records from government agencies and corporations, contracts for prison labor, news coverage and political messaging. I will look for patterns and trends in language that describe these women, their labor and their imprisonment.

...Read More about Eva Hannan
Humanities and Social Science

Understanding Circadian Control of the Luteinizing Hormone Surge with Inhibitory DREADDs

All steps of female reproduction—including ovulation, fertilization, and pregnancy—rely on timed secretion of reproductive hormones, which are synchronized to external time by exposure to sunlight during daytime and darkness at night. Circadian disruption (ex. irregular work/sleep schedules) can lead to reproductive issues; thus, understanding how the circadian system controls reproductive hormones is critical for identifying potential therapeutic targets for treating infertility and other gynecological disorders, and could help develop safer and more effective contraceptives. The “master clock” of the body’s circadian system is the brain’s suprachiasmatic nucleus (SCN), which releases a variety of neurochemicals (e.g., VIP, AVP) to coordinate a surge in luteinizing hormone (LH) which triggers ovulation. Two neuronal cell types that mediate this pathway are kisspeptin and gonadotropin-inhibitory hormone (GnIH). To examine the role of AVP and VIP neurons in coordinating the LH surge necessary for ovulation, I will inhibit their communication to kisspeptin and GnIH cells using […]

...Read More about Stacy Hu
L&S Sciences

Mixed-Race People in the French Empire: Memoir and Colonial Administration

In 1918, French officials reported a population of French-Indochinese mixed-race children living in the Saint-Médard region of France. These métis were the children of Indochinese workers and French women. Alarmed at the presence of interracial couples but resigned to their inevitability, the government allowed them to marry, expressing hope that the French women would exert their “assimilatory” power on their foreign husbands and children. These were a few among many métis in the French empire: throughout the 20th century, thousands of mixed-race children from Vietnam, Laos, and Cambodia passed through government institutions meant to “Frenchify” them. During the same period, the French government propagated a nationwide colonial culture. Made pervasive through popular media such as literature and colonial exhibitions, this culture announced France’s intentions to simultaneously assimilate foreign subjects and assert their exoticism. To this administration, métis were an uncomfortable complication. Drawing from archival sources, published memoirs by métis, and […]

...Read More about Miranda Jiang
Humanities and Social Science

Comparative Primate Cognition: Lemurs and Old World Monkeys

In the realms of primatology and animal science, it is generally considered that Old World monkeys possess greater cognitive powers than lemurs. I will be investigating this assumption through the observational analysis and testing of these animals’ cognitive abilities. This will include comparing skills such as memory and problem solving between populations of these primates at the Oakland Zoo, a leader in animal welfare and conservation. Species included will be red-tailed monkeys (Cercopithecus Ascanius), crowned lemurs (Eulemur coronatus), and ring-tailed lemurs (Lemur catta). Through the presenting of different types and shapes of containers filled with high-value food items, and periods of absence from this stimulus, I plan to discover the amount of time it takes for the animals to figure out the problem at each phase of the study. This research will not only help to better understand variation in primate cognitions, but will also aid in conservation efforts by […]

...Read More about Emmaline Jones
Humanities and Social Science

Investigating the role of dengue virus nonstructural protein 1-induced NLRP3 inflammasome activation in dengue pathogenesis

With an estimated 105 million infections globally, dengue virus (DENV), the causative agent of dengue fever, places a severe burden upon global public health. Severe manifestations of dengue fever are characterized by leak of plasma from the vascular system; these symptoms can develop into hypovolemic shock and organ failure if left untreated. The Harris laboratory and others have discovered that DENV non-structural protein 1 (NS1) is critical to dengue pathogenesis and can directly trigger vascular leak. The exact mechanism of NS1-induced vascular leak is still unknown, but recent work has shown that the DENV NS1 can activate inflammasomes, an innate immune sensor within cells. Inflammasome activation causes the release of inflammatory mediators which can lead to the disruption of the endothelium. However, it is currently unknown how NS1 activates the inflammasome. My project will focus on investigating this mechanism and its importance in causing vascular leak. Thus, I aim to […]

...Read More about Evan Juan
Rose Hills

Korean Women’s Perceptions of Korean Abortion Policy Changes and U.S. Abortion Debate

In the United States, abortion has been legal since the Supreme Court decision in Roe v. Wade (1973), but abortion restrictions have been gradually increasing since then. In contrast, the Republic of Korea overturned its anti-abortion legislation on January 1, 2021. This project uses in-depth interviewing to study Korean women’s perceptions on abortion, opinions on the future state of abortion policies in Korea, and interpretations of the U.S. abortion debate. This study will examine how a forthcoming abortion legislation will reflect women’s opinions of abortion, speculate on how the policy changes may actually impact the lives of women, and explore whether Korea may follow a similar political history as the U.S., wherein abortion is becoming more difficult to obtain.

...Read More about Da Eun Jung
Humanities and Social Science

Remote Sensing of the Impact of Mega-fires on Snow

Mountain snow is a virtual reservoir that stores water during the winter and releases it when it is most needed at the beginning of the agricultural growing season. Snowpack water storage, measured as snow water equivalent (SWE), is therefore important to track and predict. Most numerical models that try to predict snow use maps of forests from previous years, but major disturbances, such those caused by fire, make these older versions unreliable for the future. This project aims to improve our ability to observe and predict SWE in areas where there has recently been a major wildfire. This summer I will work with high-resolution maps of trees and snow created from Light Detection and Ranging (Lidar) cameras on specialized aircraft to research on questions around Lidar snow depth observations and density modeling. Specifically, I will try to explore the spreading patterns of fire on the snow cover and how this […]

...Read More about Jovian Kan
SURF SMART

CFD Data Compression on High-Order Unstructured Meshes

As processing power available to high performance computers has increased, the overall performance has bottlenecked due to the limits of data transfer and storage. For small and medium sized computational fluid dynamics (CFD) researchers, the size of generated data is becoming problematic. In particular, CFD data faces a large resistance to general compression algorithms such as Lempel-Ziv encoding found in .zip files. Applications in CFD including wind-turbine design and aeronautics demand accurate capture of fluid dynamics phenomena on complex geometries such as turbine blades or airplane wings. For these complex geometries, grid-like straight-edged meshes prove ineffective. Instead meshes which are both curved (referred to as “high-order”) and non-gridlike (referred to as “unstructured”) are gaining popularity. As such, research into a novel compression algorithm of CFD data on high-order unstructured meshes will help small scale CFD researchers efficiently store their data.

...Read More about Aaron Kavaler
L&S Sciences

Analysis of Gene Flow Between Neighboring Poison Frog Species in Ecuador

In Ecuador, the Epipedobates clade of poison frogs (Dendrobatidae) have speciated in different climate zones (Tarvin et al., 2017). Poison frogs are aposematic; they possess colorations and markings that serve to warn predators of their toxic defenses. Determining poison frog species can be difficult due to aposematism, as possessing different color and marking patterns does not necessarily indicate a separate species (Tarvin et al., 2017). Thus, genomic level studies are necessary to understand ongoing gene flow, i.e., the introduction of genetic material from one species to another through interbreeding. Advances in next-generation sequencing (NGS) has allowed increased research on how climate change affects biodiversity and gene flow between species. Gene flow studies are important in evolution as they help us to understand the speciation process. The goal of this project is to understand how climate differences affect gene flow among neighboring poison frog species using genomic information. To do this, […]

...Read More about Novia Kayfetz-Vuong
L&S Sciences

Role of Brown Fat-secreted Factors in Cardiomyocyte Proliferation and Regeneration

Heart disease continues to be a defining illness of our generation, as the poor regenerative potential of the human heart renders fatal the loss of millions of heart muscle cells that follow heart attacks. Yet, there seems to exist a striking heterogeneity across species in this regenerative potential. Neonatal mice, for example, exhibit a much more robust ability to regenerate these heart cells (also called cardiomyocytes), but lose this ability in adulthood. Why? A recent key evolutionary intuition came in the inverse correlation between organisms’ metabolic rate and cardiac regenerative capacity. Thus, a secretory organ vital to regulating neonatal thermogenesis, brown fat, may be key. Several brown fat-secreted factors have been shown to improve cardiac function. In addition, our preliminary data unveils molecular communications between brown fat and the heart in triggering the loss of neonatal cardiomyocyte proliferative and regenerative capacity. Thus, we are looking to investigate the effects of […]

...Read More about Allen Khudaverdyan
Rose Hills

Characterization of the Vaginal Microbiome Following Treatment for Chlamydia among Fijian Women

Chlamydia trachomatis (Ct) is the leading bacterial cause of sexually transmitted infections (STIs) worldwide with over 130 million people newly infected each year. Among Fijian women, Ct is hyperendemic—17.85% are infected whereas the global prevalence is 4.2%. There is growing concern that antibiotic treatment for Ct may contribute to an imbalance in the vaginal microbial composition which increases the risk of STIs like Neisseria gonorrhoeae (Ng), herpes simplex virus type 2 (HSV-2), human Papillomavirus (HPV), HIV-13 and possibly reinfection with Ct. My research will elucidate the effects of Azithromycin treatment on the vaginal microbiota among Fijian women with Ct at baseline who clear or do not clear their infection at follow-up compared to age-matched women who are uninfected and who either remain uninfected or develop Ct infection. This will help reveal the role antibiotic treatment plays in the vaginal microbial diversity, imbalance, and disease pathogenesis and the beneficial microbiota that […]

...Read More about Reshma Kodimerla
L&S Sciences

Historicizing the Personal Belief Exemption to Vaccination in American History

Current U.S. state laws permit vaccine mandate exemptions based on medical contraindications, religious beliefs, or personal beliefs. In recent years, outbreaks of measles attributed to subpar vaccination rates have caused the personal belief exemption to come under close scrutiny from lawmakers, medical officials, and the public. Current scholarly literature, however, lacks a clear history of the personal belief exemption, in part because that history varies by state. In this project, I will visualize and narrate the story of the personal belief exemption in American history. Through an interactive essay grounded in original historical research, I will explore how the exemption’s changing language, geographical spread, uneven application, and legal context reflect and inform America’s ever-shifting notions of conscience, liberty, and morality. In doing so, I aim to create a resource about the history of the personal belief exemption accessible to members of the public, policymakers, and public health experts, that I […]

...Read More about Jonathan Kuo
Humanities and Social Science

Understanding Fatigue Behavior in UH polyethylene for Total Joint Replacements

TJRs are commonplace in the U.S. with over one million first-time knee and hip implant surgeries performed per year. Approximately 12% of those TJRs will require revision surgery, and a leading cause of revision surgeries is fatigue-induced wear of the plastic UH TJR component. This research aims to determine how various microstructural and chemical properties of clinically relevant formulations of UH effect initiation and propagation of cracks. Understanding structure/property/processing relationships in clinical formulations of UH can further inform designs to better suit patient needs, ultimately resulting in better patient outcomes. I will perform experiments to determine the effect of radiation dose on fatigue properties in a specific clinical formulation of UH called GUR 1020. Specifically, I will learn to prepare UH samples for mechanical property testing, operate optical and scanning electron microscopes to observe crack growth and fracture surfaces, and perform standard mechanical property tests on a load frame.

...Read More about Samantha Kwan
SURF SMART

Acoustic Bandgaps for Improved Quantum Memory Coherence

Quantum computing is a new paradigm that could revolutionize how we process information. For these applications, it is critical that the systems can maintain quantum coherence for long periods of time. In this project, we will investigate new acoustic designs to extend quantum coherence in superconducting quantum qubits and nanomechanical resonators. At low temperatures where quantum devices operate, the dominant energy loss in acoustic and superconducting resonators occurs due to coupling to two-level-system defects. The goal of our research will be to engineer a platform that can be used to study these defects. Because proper shielding is critical to keep a quantum system isolated from its environment, a challenge will be to design a shielding system with a bandgap that blocks acoustic waves from escaping into the environment at our frequencies of interest. We will use an acoustic metamaterial-based design, which will be a periodic arrangement of unit cells engineered […]

...Read More about Eric Li
Rose Hills

Learning from an Ancient Process: Using Gametogenesis Pathways to Rejuvenate Aging Cells

Cellular aging is a nearly universal trait of all organisms and is a risk factor for a variety of human diseases. Cellular rejuvenation occurs in every human body during gametogenesis, the process by which we form gametes, also known as sperm and egg. In yeast, overexpression of a gametogenesis-specific transcription factor, Ndt80, has been shown to extend lifespan and rejuvenate the nucleolus in aging cells. Using genome-wide screening of gametogenesis genes, the Ünal lab has identified 86 rejuvenation candidates that can extend yeast lifespan. My research will focus on characterizing a subset of these candidates and identifying those that can counteract age-associated expansion of the nucleolus, a common biomarker of cellular age. Using fluorescence microscopy, I will determine how aging affects different nucleolar proteins in a wild-type context and then determine which rejuvenation candidates can reverse these age-related nucleolar phenotypes. My research will give insight into how aging affects the […]

...Read More about Tina Li
Rose Hills

Not Your Campus’s Movement: UC Berkeley and the Politics of Solidarity in the post-Civil Rights and Power Movement Era

With recent cases of violence against the Asian-American community in mind, it is now more relevant than ever to examine Asian-American history, and efforts that have been made for greater rights and representation. This summer, I will be working with my mentor researching materials that characterize the Asian-American Movement of the 1960’s. The research will be focused around the 2010 novel I Hotel by Karen Tei Yamashita, and specifically her exploration of the historical parallel between Japanese-American Internment and Native-American incarceration on Tule Lake. I will conduct archival research with the Bancroft Library, looking at collections relating to the legal defense for the Tule Lake internees, the International Hotel Eviction, and the Third World Liberation Front with the objective of finding intersections between the aims of the Asian-American Movement and American-Indian sovereignty. I will also use this opportunity to research minority allyship between the Black Panther Party and the Red […]

...Read More about Sydney Liang
SURF SMART

CRISPR-Cas9-mediated genome editing to reduce levels of cyanide in cassava

In tropical regions around the world, the cassava plant’s starchy tuberous roots are relied on as a staple source of calories. The crop is naturally drought tolerant and can be stored underground for extended periods of time – preventing the need for immediate harvesting and storage. However, prior to consumption, cassava requires significant processing due to the cyanogenic glucosides that it naturally produces. The cyanogenic glucosides linamarin and lotaustralin are synthesized in the leaves of the cassava plant and transported basipetal in the plant to the tuberous roots. The cassava genes CYP79D1 and CYP79D2 encode the enzyme responsible for the first step of the cyanogenic glucoside biosynthetic pathway. Downregulation of these genes should lead to a reduction in cyanide content in cassava leaves and tuberous roots. Therefore: the goal of this project is to use CRISPR-Cas9 gene editing technology to engineer non-toxic varieties of cassava by causing knockouts in the […]

...Read More about Samantha Lieberman
Rose Hills

Design and Biomechanics of a Tissue Micro-stretcher

The human body experiences various mechanical loads which cells respond to correspondingly to maintain homeostasis. However, drastic stimuli changes might lead to various diseases and degeneration. To enable regenerative medical strategies, we must first understand the connection between cell and organ mechanics. With this motivation, my mentor is developing a deformable microfluidic chip that can apply these mechanical loads to a single layer of cells. Currently, the chip is tailored for loads in the annulus fibrosus of the spine, but other systems with similar loading could be considered. The current design is limited to testing one tissue sample and one stretching condition per cycle. We will create a new design that improves the chip’s ability to produce data by testing multiple stretching conditions and samples simultaneously. Specifically, I will employ finite element modeling and create a genetic algorithm to manipulate and optimize the chip design to match physiologically relevant, experimental […]

...Read More about Jianhua Lim
SURF SMART

Identifying and Characterizing a Genetic Modifier for Cataracts

The cataract, or clouding of the lens of the eye, is the leading cause of blindness worldwide. Currently, the only effective treatment to remove cataracts is surgery, which costs $6.8 billion annually in the United States. Understanding the underlying mechanisms that cause cataracts may lead to new therapeutic strategies to prevent or delay the progression of cataracts, thereby alleviating the need for surgical intervention and possibly saving billions of dollars. Gap junctions are membrane channels that connect adjacent cells, allowing the transfer of metabolites, ions, and other small molecules for maintaining normal transparency of the lens. Previous research from the Gong Lab has shown that the deletion of alpha3 connexin, a primary component of lens gap junctions, results in severe cataracts in the 129SvJae (129) mouse strain but displays mild cataracts in the C57BL/6J (B6) mouse strain. My research project seeks to identify and characterize a novel genetic modifier on […]

...Read More about William Lin
L&S Sciences

The Inferred Reader: Natural Language Processing for Narrative Understanding

Understanding literary narratives requires a strong grasp of the underlying language; unlike text drawn from Wikipedia, social media, or the news, literary prose is ripe with embellished descriptions and figurative language. Plot points are revealed in the form of nuanced events rather than explicit recollections: we read about a character’s ‘final breath’ rather than their death. The success of attention-based neural networks on an assortment of semantic inference and interpretation tasks suggests that they provide an effective model of human language, but a noticeable drop in performance when applied to literary data has inspired a call for domain-specific systems. This work draws on equal parts natural language processing research and literary theory to develop such ‘born-literary’ NLP models, designed specifically for the task of narrative understanding. If successful in predicting plot outcomes, the representations learned by these models may capture some of the latent narrative structures that encode storytelling devices […]

...Read More about Max Litster
L&S Sciences

Establishing The Mechanisms of AGS MANF in Neuroprotection and Regulated Cell Death Using CRISPR-Engineered AGS and Mouse Neural Cells

My goal is to identify the mechanisms of innate metabolic resilience and discover targets with translational potential for neuroprotection by characterizing the function of protein variants that make Arctic ground squirrels (AGS) resistant to cerebral ischemia. Studies show that cellular resistance to metabolic stressors is an intrinsic property of neural cells generated from AGS. Through functional genomic screens and computational analysis, they identified novel cytoprotective protein variants with amino acid substitutions that are unique to AGS but otherwise conserved in mammals. Among the identified proteins with the most striking metabolic resilience phenotypes, mesencephalic astrocyte-derived neurotrophic factor (MANF) demonstrates enhanced cytoprotective effects specific to the AGS variant. I hypothesize that this key AGS MANF variant promotes ischemia resilience and neuronal survival by enhancing sulfatide binding, ER stress response, and mitochondrial function while reducing cell death under metabolic stress conditions. I will characterize the neuroprotective potential of this AGS cytoprotective variant, which […]

...Read More about Ted Daniel Llera
L&S Sciences

Marguerite Dice and Anti-communist Clubwomen

Women’s clubs are often exclusively remembered as advocating for progressive causes—education, suffrage, conservation—but little attention has been paid to the way that some of them gave rise to nationalist, anti-communist clubs for women. My interest in this topic builds on my research on a little-known clubwoman named Marguerite Dice. Born in 1884 to a Republican Union Army veteran father and politically connected mother, she dedicated her life to progressive women’s clubs, but spent at least 30 years advocating for conservative, anti-communist causes. Her life neatly tracks with the evolution of the Republican Party over the same period—she was born into the party of Lincoln, and died a fervent supporter of the hyper-conservative party of Goldwater and Nixon—making her an interesting case study in the evolution of not only women’s conservatism, but American conservatism generally. This project will utilize archival materials from women’s clubs to explore the social circles, intellectual interests, […]

...Read More about Annabelle Long
Humanities and Social Science

Catullus, Gender-fluidity, and Trans*lation

In the past few decades, discussion of gender-fluidity in poetry has become more prevalent, but it is often limited to contemporary literature and the realm of modern queer theory. My research investigates poetic portrayals of gender-fluidity in the work of the ancient Roman poet Gaius Valerius Catullus. I am focusing in particular on the original poetry of Catullus alongside Romantic, Victorian and contemporary translations/adaptations in English in order to track how these portrayals have changed over time. The approach is grounded by the conception of poetry in translation as valuable in its own right and by the parallel conception that artistic performance of gender is its own sort of ‘translation’. This project also discusses and explores the portrayal and sociolinguistic creation of gender in Catullus’ poetry in the context of poem form and content. With this work I hope to present a novel perspective on these poems that provides insight […]

...Read More about Phee Marcial
Humanities and Social Science

Unplanned Pregnancies in Women with Histories of ADHD: The Role of Executive Functioning

Recent investigations reveal that women with childhood histories of Attention-Deficit/ Hyperactivity Disorder (ADHD) continue to experience major impairments even after symptoms have abated. One such important outcome is increased rates of unplanned pregnancy by adulthood. Existing literature has identified academic underachievement and risky sexual behavior during early-to-mid-adolescence as mediators of the childhood ADHD-unplanned pregnancy link. However, executive functioning (EF) may be an underlying mechanism that better explains this relation and is potentially more amenable to possible health education interventions. Thus, this study aims to elucidate the relation between childhood ADHD and unplanned pregnancy by investigating the potential mediating role of adolescent executive functioning (EF). A better understanding of this outcome is crucial because unplanned pregnancies can significantly alter the course of a woman’s life, health, and finances, as well as the life of her child.

...Read More about Elizabeth “Libby” McBride
Humanities and Social Science

Settler Colonialism and American Political Development: A Congressional Analysis

What are the legacies of settler colonialism on American political development? Scholars understand settler colonialism as a “structure, not an event,” yet little attention has been devoted to understanding how settler colonialism has impacted the formation of the American state. To this end, this SURF-SMART project seeks to answer the question: How much legislative activity has been devoted to territory governance in the United States and how has this changed over time? To investigate this question, my graduate mentor and I will be constructing an original dataset tracking congressional activity from 1789 to 1947 using data from legislative journal indices. Afterwards, I will analyze this data by visualizing it as a stacked area chart that can make visible the changing proportion of legislative topics–such as westward expansion, public lands management, and “Indian removal”–over time. This analysis will provide the baseline, descriptive information needed to characterize the extent to which early […]

...Read More about Audrey J McClish
SURF SMART

Wavelength Dependence of the ‘Imaka Ground Layer Adaptive Optics Experiment

The twinkling of stars and other astronomical targets due to the Earth’s atmosphere is a long-standing disadvantage that ground-based telescopes face compared to their space-based peers. Large observatories have used adaptive optics (AO) to correct for atmospheric blurring, producing nearly diffraction-limited images. Ground layer AO (GLAO) seeks to apply corrections to a wider field of view than traditional AO by selectively targeting lower atmospheric layers. My SURF project will look at the last three years of data from the ‘imaka GLAO experiment to characterize the instrument’s correction over a variety of conditions and over multiple wavelengths. Better corrections over larger fields and shorter wavelengths enables observations of extended targets in multiple spectrums. The results from this work will inform GLAO systems in the next generation of ground based telescopes.

...Read More about Eden McEwen
Rose Hills

Trans Visual Archives and the Pop-Up Museum

In recent decades, pop-up museums have been the site of both radical trans critique and the emergence of a highly commodified “selfie museum.” What is it about the pop-up— an ephemeral, shape-shifting installation of objects and artworks— that allows it to be harnessed by both trans activists/archivists and for-profit corporate sponsors? Why do these queered reimaginings occur in a historical moment saturated with neoliberal museum policies and increasing state surveillance of bodies? To examine these questions, I will utilise three key case studies of trans-led pop-ups from various colonial contexts, engage debates around gender and decolonization, and pose an anti-capitalist critique of the culture industry. SURF will allow me to develop a robust theoretical framework for a senior thesis by working through a reading list in three major phases: museology and the pop-up, contemporary trans studies, and trans-led pop-up museums in the US and Perú. Additionally, I will immerse myself […]

...Read More about Sam McGinnis
Humanities and Social Science

The impact of subcortical lesions on motor adaptation to different error sizes

Motor adaptation comprises the essential processes which allow us to adapt to new environmental demands. Recent work has shown that motor adaptation includes both an explicit and implicit learning component. Explicit learning is strategic and utilizes performance errors, while implicit learning is unconscious and driven by motor execution errors. The cerebellum is central to generating these error signals, as has been shown extensively through the impaired adaptation of patients with cerebellar degeneration when completing visuomotor perturbation tasks. However, findings regarding the function of the cerebellum in implicit adaptation to varying error sizes remains unclear, as paradigms using larger error sizes are often confounded with explicit strategy. The role of the basal ganglia is further ambiguous, as a consensus has not yet been reached regarding its involvement in implicit adaptation. Through the use of the “clamped feedback” method, my project will isolate implicit adaptation, such that I will be able to […]

...Read More about Tara Najafi
L&S Sciences

Investigating the role of transposable elements in fungal plant pathogen genome evolution

Fungal plant pathogens pose a significant threat to biodiversity and food security worldwide. This threat is aggravated by their quickly evolving genomes that adapt to evade host plant defenses––even newly deployed resistant crops are often only effective for a few years in the field. Among these pathogens is Magnaporthe oryzae, which infects rice and many other grasses, resulting in significant crop losses each year. Transposable elements (TEs) are DNA sequences that can change their position within the genome and are thought to generate genomic diversity; thus, they are hypothesized to be involved in the evolution of M. oryzae. However, much is still poorly understood about how these elements shape the M. oryzae genome. My research will ask how TEs play a role in M. oryzae’s adaptation to host plant defenses and expansion of host range by investigating the differences in TE content between various host-specific lineages of M. oryzae. The […]

...Read More about Anne Nakamoto
L&S Sciences

Atomic-scale Imaging of Ion Dynamics for the Development of Memristors

A memristor is a device with the property that its electrical resistance depends on the history of applied voltage, and changes with the amount of current that passes through it. This atypical property of history-dependent resistance is analogous to how memory functions. As a result, memristors have been used in applications ranging from non-volatile analog memory to synaptic analogs and neuromorphic computing. However, there is a lack of in-depth understanding of the atomic-scale behavior that causes this property. My project aims to understand how the dominant dynamics, electromigration and ion transport, result in the unique behavior of the resistance. This understanding is a necessary precursor to solving the two main challenges in the current field of memristors: large parameter variability and cycling endurance degradation. I will study the relationship between dynamical defect structures and 2D device behavior by using Scanning Tunneling Microscopy (STM) to directly image ion dynamics and measure […]

...Read More about Rastko Nastic
Rose Hills

Investigating the Mechanisms Governing Kisspeptin Cell Activity in Reproduction

Fertility in women and across mammalian species requires a series of temporally coordinated neuroendocrine events by the circadian system in the brain. Disruptions to circadian timing across mammalian species from stress or environmental factors result in irregularities in the estrous/menstrual cycles, reduced fertility, and increased miscarriage rates. The proposed studies examine the role of neuroendocrine signaling events and circadian timekeeping in ovulation. Across mammalian species, ovulation requires timed neuroendocrine events organized by the master circadian pacemaker in the suprachiasmatic nucleus (SCN). Evidence points to E2-sensitive kisspeptin (Kp) neurons, potent stimulators of the reproductive axis that maintain their own circadian timekeeping, as the locus for estradiol (E2) and neuroendocrine signal integration. The preovulatory luteinizing hormone (LH) surge, the hormone signaling cascade required for ovulation, is triggered by timed neuroendocrine signals from the SCN to kisspeptin (Kp) neurons. Alterations in neuroendocrine signals to Kp neurons results in disrupted fertility. Findings from the […]

...Read More about Justin Nelson
L&S Sciences

Characterization of 3D Rat-Reaching Kinematics

Behavior is the output of complex neural computations in the brain; however, our understanding of how the motor cortex controls movement is not yet fully understood. This project investigates the key gap of knowledge in this field by demonstrating through quantification general principles of motor learning and coordination in a systems-neuroscience paradigm. To achieve this goal, I will analyze the variability of high-dimensional behavioral data during a novel 3D rat-reaching task. No motor behavior, such as a reach for a glass of water, is ever the same. There is always variability. I hypothesize the variability of representative kinematics is structured, with variability increasing in the direction of the dimension of the task. Since animals behave in 3D, leveraging tools for better quantification of complex reaching behavior like 3D rat kinematics is important. This project seeks to provide a basis for understanding the link between neural systems and behavior.

...Read More about Emily Nguyen
Rose Hills

Time Series Analysis of Groundwater in the Sierra Nevada

Groundwater is essential to ecosystems in Sierra Nevada meadows. Flora and fauna depend on groundwater cycles for a reliable source of water. Climate change is expected to disrupt groundwater supply, so understanding precisely how groundwater responds to temperature change, and how groundwater affects surrounding flora is an integral part of protecting meadow ecosystems in the face of climate change. This summer, I will develop a mathematical model to analyze time series of meadow groundwater, in order to study the relationship between groundwater and the ecosystems it fuels. I will study what local factors influence how groundwater levels respond to temperature, and how vegetation responds to varying groundwater. I have the support of a graduate student, Jen Natalie, who collected this groundwater and greenness data, as well as Professor Albert Ruhi, who taught me all I know about time series analysis. As a mathematics major who is passionate about climate change, […]

...Read More about Julia Nicholson
L&S Sciences

How do hyaluronic hydrogels stimulate immune response and muscle cell differentiation?

Muscle injuries from accidents, blast trauma, surgical situations, and sports can lead to acute muscle tissue loss and severe permanent damage to the body. Therefore, it is essential to develop methods to enhance the wound healing and regeneration process. This project aims to promote muscle regeneration through stem cell transplantation. However, a major challenge is that immediately after transplantation into damaged tissue, donor cells encounter a harsh environment with substantial death-promoting stimuli. This project aims to provide a hyaluronic acid environment that helps stimulate mechanisms of cell engraftment within the host tissues during muscle regeneration. Hyaluronic acid is an especially attractive material due to it being a natural component of the cell extracellular matrix and playing a large role in biological processes. This project aims to implant muscle stem cells, along with common immune cells known as macrophages, in order to observe their interplay and how the gel can be […]

...Read More about Derek Ning
Rose Hills

Compactification of Anomalies in Six-Dimensional Interacting Quantum Field Theory

Quantum field theory (QFT) — a theory describing subatomic particles as excitations of fundamental ‘fields’ — has long been established as the de facto framework for modern particle physics, yet it remains a topic riddled with open problems. Interacting QFTs in higher dimensions, particularly 6D, is one such problem, motivated by string theory, a highly theoretical mathematical model attempting to describe all of nature. These interacting QFTs have Lagrangians (precursors to ‘equations of motion’) that can probe M5-branes, which are objects of fundamental interest in string theory. However, the Lagrangians for these theories are susceptible to quantum anomalies, which are red flags indicating that a symmetry of classical physics is incompatible with quantum mechanics. Analysis of the behavior of these anomalies, and the quantum interactions they induce in the corresponding theory, can be explored by looking at their consequences in lower dimensions. My research will investigate the lower-dimensional behavior of […]

...Read More about Orion Ning
L&S Sciences

Eurabia and the Great Replacement Along the Fault Lines of Civilizations

The notion of a “Great Replacement” and the Eurabia thesis are two Islamophobic conspiracy theories with similar roots and trajectories. They both articulate the fear that, with the support of European elites, Muslims are demographically replacing Europeans, threatening to extinguish “Western culture” and replace it with a global Islamic civilization. Circulation of these theories has accelerated since 2015, alongside a rise in white supremacist violence. The theories themselves are linked to Zionist political thought, but they build on long-standing antisemitic tropes, and have occasionally been taken up in service of antisemitism, especially in the United States. I will investigate the transit and resonances of these theories in Israel/Palestine and Turkey — two Middle Eastern contexts which are often imagined to exist along “civilizational fault lines” between the Muslim and Western worlds. My project explores how the Muslim- and Jewish-majority states situated along these purported “fault lines” respond to or latch […]

...Read More about Olivia Nouriani
Humanities and Social Science

Quantitative Characterization of Enlarged Perivascular Spaces in CADASIL

Perivascular spaces are cerebrospinal fluid filled areas that surround the brain’s blood vessels and are involved in waste clearance and molecule distribution. When these perivascular spaces become enlarged (ePVS), they become visible on MRI and may represent a response to blood brain barrier pathology and neurodegeneration. Cerebral arteriopathy dominant arteriopathy with sub-cortical infarcts and leukoencephalopathy (CADASIL) is an autosomal dominant inherited small vessel disease that causes deterioration of small blood vessels, strokes, and cognitive impairment as early as the fourth and fifth decades of life. Due to their presence along the brain’s blood vessels, ePVS may serve as a particularly relevant biomarker for understanding CADASIL disease progression and vascular contributions to cognitive impairment and dementia. Despite their relevance to this disease, ePVS have not yet been rigorously quantified in CADASIL. My project aims to quantitatively characterize ePVS in CADASIL and test our hypothesis that ePVS load and spread are associated […]

...Read More about Bradley Oh
L&S Sciences

Fictional Cops, Real Brutality: The Police Procedural as Propaganda

How do fictional cops enable and validate real police brutality? My research surveys a wide selection of procedural television from the 1950s to the present, examining each show in its context to understand the cultural, political, and sociological work done by narratives that cast police officers as “good guys” in a reality where that may not be the case. From standard procedurals like The Rookies to more modern, “progressive” programs like Brooklyn Nine-Nine, I hope to examine how television manufactures consent among the American public to justify over-policing and its consequences. Using policing as a starting point, I aim to investigate the greater American attitude towards violence and how violence in the United States is evaluated as either acceptable or excessive. This project will take an interdisciplinary approach that synthesizes history, folklore studies, legal studies/criminology, sociology, media studies, and political science to understand how effective propaganda is created and what […]

...Read More about Ava Olson
Humanities and Social Science

Exploring the impact of culturally tailored culinary interventions: Reducing blood pressure through dietary change among Filipinx Americans

Among all Asian American subgroups, Filipinx Americans have consistently shown to suffer from the highest rates of hypertension. Despite this alarming fact, little research has been done to investigate culturally sensitive interventions to help control blood pressure and reduce rates of hypertension in this specific community. The purpose of my research will be to investigate whether the development and implementation of a culturally tailored culinary intervention used to control hypertension, such as a heart healthy Filipinx recipe cookbook, is effective for encouraging dietary change and ultimately reducing blood pressure in Filipinx- Americans currently diagnosed with hypertension. In this research project, I will work with key individuals in the local Filipinx community to help me develop and design a heart healthy Filipinx recipe cookbook. After the development of the cookbook, I will begin the implementation of my culturally tailored intervention in the study population. My ultimate goal for this research project […]

...Read More about David Pack
Rose Hills

Investigating interactions between the circadian and reproductive systems in female reproduction

Female reproductive health is a pervasive issue in the medical field as 16.2% of married women ages 15-49 are affected by infertility. Recent studies reveal that poor female reproductive health arises, in part, from circadian disruption. Due to modern lifestyles, humans lack exposure to natural sunlight during daytime and receive excess artificial lighting during nighttime, which disrupts circadian rhythms. COVID-19 quarantining has exacerbated this issue, and despite knowing how harmful circadian disruption is for female reproductive health, the anatomy and physiology behind how the circadian and reproductive systems communicate remain nebulous. This project will determine how the suprachiasmatic nucleus (SCN), the master circadian clock of the brain, coordinates the activity of Kisspeptin (Kp) and RFRP-3 neurons (neurons that positively and negatively regulate reproduction, respectively) to allow for ovulation. Viral tract tracing in mice will determine the neurochemical pathway between the SCN and Kp/RFRP-3 neurons, and optogenetic techniques will determine how […]

...Read More about Shuka Park
L&S Sciences

Measuring Nematically Ordered Superconductivity with Resonant Ultrasound Spectroscopy

Most iron, and much nickel-based superconductivity is found in the same region as a magnetically ordered state. The transition temperatures for these magnetic states have in turn been found to be strongly correlated with those of “nematic” phase transitions reducing the lattice symmetry from tetragonal to orthorhombic. Given the intersection between these nematically fluctuating regions and superconducting phases in so many unconventional superconductors, several questions naturally arise. This first of these is of course what connection exists between the nematic phase and superconductivity. But, beyond that, the origin of the nematic phase itself isn’t completely clear in and of itself. And the existence of the aforementioned magnetic phase creates a confounding variable, making it challenging to disentangle nematic from magnetic order in the effects on superconductivity. BaNi2As2 is a nematically ordered superconductor with no observed long-range magnetic order. Using resonant ultrasound spectroscopy (RUS), I hope to extract complete symmetry information […]

...Read More about Gabriel Perko-Engel
L&S Sciences

Constraining Type Ia Supernovae Luminosities

Type Ia supernovae (SNe Ia) are a category of exploding stars, and serve as one of the most important tools for probing our universe today. Because of their extreme and consistent luminosity, they are widely used to measure distances to faraway galaxies. Determining these large-scale distances allows a better understanding of the universe’s expansion, and thus of dark energy itself, the driver behind the expansion’s acceleration. Several recent studies have suggested that the luminosities of these supernovae can be better standardized if we factor in the properties of their host galaxies, such as the galaxy’s mass or age. This project aims to statistically correlate these properties with models of SNe Ia luminosities. We also pursue a new method of standardizing these luminosities, which would ultimately improve the cosmological applications of distance measurements with SNe Ia, advancing our understanding of dark energy.

...Read More about Druv Punjabi
L&S Sciences

Using Low-Cost Sensors to Evaluate Community-Scale Air Pollution Trends

Particulate air pollution contributes to millions of premature deaths worldwide annually and has major climate feedback effects. This is particularly true of black carbon (BC), a component of particulate matter (PM) that results from incomplete combustion sources and has not been as thoroughly assessed as other air pollutants. Gathering particulate air pollution data within communities most affected by industrial activities and vehicle traffic is necessary in developing solutions to mitigate the social and health inequities that result from exposure. My team at LBNL aims to analyze spatiotemporal trends of PM and BC concentrations in vulnerable California communities using our low-cost sensor technology. Our goal is to use high-density air sensor networks to understand the trends in BC concentrations and BC/PM ratios over daily, weekly, and seasonal periods. This will allow us to identify localized regions where air pollution levels are highest as well as the magnitude of different pollutant sources. […]

...Read More about Lilou Redon-Gabel
Rose Hills

Metagenomic Analysis of the Microbiomes of Fijian Women with Chlamydia trachomatis Infection

Chlamydia trachomatis (Ct) is the most common bacterial cause of sexually transmitted infection (STI) in the world. The Pacific Islands have some of the highest rates of Ct infections, with Ct often asymptomatic and remaining undetected in the population. My project will study Ct in Fijian women by analyzing the microbiomes of the vaginal and rectal anatomic sites. I will use a metagenomic approach, involving shotgun sequencing and bioinformatics software, to learn about Ct genome variation among these anatomic sites, compare microbial diversity in the presence and absence of Ct, and determine the relationship between microbiome composition and Ct acquisition. By detecting Ct and other STIs in women who have tested Ct negative using conventional diagnostic assays, I will show that metagenomic testing is more sensitive than existing diagnostic tests. I am interested in the following research questions: What is the effect of Ct infection on the microbiome, and how […]

...Read More about Gracie Richards
Rose Hills

Androcentric Tendencies in Storytelling to Children

From infancy, people are told stories. The patterns, morals, and relationships in these stories help children form schemas to interpret the world. While cultures have prominent stories that are passed down to most children (e.g. Romeo and Juliet), people spontaneously invent narratives for purposes of entertainment, distraction, or teaching. My research aims to understand how androcentric bias (the bias that centers the experiences of men over the consideration of other genders) functions at an interpersonal, individual level during storytelling; more specifically, how a character’s agency or communality in a story influences the likelihood that someone will tell a child a story with a male protagonist. These conditions are chosen because agency, an essential function of being human, has become specifically associated with masculinity, while community is associated with femininity. With an awareness of how androcentric bias functions in storytelling, people can consciously shift from androcentric descriptions to more gender-neutral language […]

...Read More about Lauren “Aris” Richardson
Humanities and Social Science

Characterizing Genes Underlying Serpentine Adaptation in Monkey Flowers

High metal content, low levels of essential nutrients, and poor water retention make serpentine soil a uniquely challenging environment and a source of strong selective pressure. The yellow monkey flower, or Mimulus guttatus, an annual wildflower native to the western United States, has adapted to these harsh conditions; coupled with its wide range, this ability to survive on serpentine soil makes Mimulus guttatus a model organism for studying how plants adapt to local environments. This study will focus on three genes — involved in root architecture and the uptake and transport of essential nutrients — that show key variations between on- and off-serpentine populations. The CRISPR-Cas9 system will be used to generate plants with nonfunctional variants of these genes, which will provide important insights into the role these genes play in Mimulus guttatus’s ability to survive in serpentine conditions.

...Read More about Allison Rothrock
Rose Hills

Microtektites of Gorgonilla Island, Colombia: Insights into the Cretaceous-Palaeogene Mass Extinction

The Cretaceous-Paleogene (K-Pg) mass extinction, 66 million years ago, is considered a major landmark in Earth’s history with the demise of many prehistoric taxa and development of modern species. Famously known for the extinction of the dinosaurs, this event is linked to a high-energy meteor impact on the coast of Chicxulub, Mexico. However, the actual extent to which the impact influenced global changes remains obscure due to the vaporization of the meteor upon impact and satisfactory preservation of the K-Pg rock record. Thus, studies have analyzed microtektites, tiny bedrock-derived droplets of glass produced by the high-energy impact, to better infer impact dynamics and chemical signatures associated with the extinction. Even so, these studies are limited to North and Central America, with geochemical readings of the samples largely obscured by post-depositional weathering. My project aims to investigate microtektites from a newly discovered, largely unaltered deposit in Gorgonilla Island, Colombia, utilizing electron […]

...Read More about Paolo Sanchez
Rose Hills

Sasanian Subjects and Their Faith

The Sasanian Empire is known to have had a vast number of faiths within it. Despite this, most of the Persian sources of this time only refer to the known Zoroastrian elements of the royal pantheon. By studying these sources, as well as other records around this time, it is possible to learn if the majority of Iranian subjects held the same faith as their rulers, or if there was a difference. This topic will be approached in two major segments, which encompass the analysis of primary and secondary sources. Analysis of these sources will allow a final understanding of the Sasanian rulers’ religion relative to that of their subjects. The first step is to review primary sources created during the Sasanian Era. These sources mainly include the Sasanian Royal Inscriptions, rock reliefs, and Kerdir’s Inscriptions. The second step is to review secondary, scholarly sources about the Sasanian Empire, which […]

...Read More about Sepanta Sarraf
Humanities and Social Science

Intergenerational Trauma and Cultural (Re)Connection in Korean-American Young Adults

Past research shows an alarming phenomenon in which Asian-American young adults are suffering uniquely high suicide rates and risk of deadly mental health complications. In disaggregating that data more specifically with Korean Americans (KA), evidence suggests that there may be even more risk due to cultural, societal, and political issues in both Korea and in the US, past and present. In my research, I look into the question of what leads to such high suicide rates in KA young men. Specifically, I will utilize in depth interviews with 20 participants in convenience and snowball sampling to examine the role of intergenerational trauma and cultural (re)connection in mental health complications among 1.5 and 2nd generation KA young adult males and how connecting to culture, roots and heritage can provide a path to care. I hope to deepen culturally specific understanding of KA young male mental health to aid in coping with […]

...Read More about Jae Won “Jake” Sim
Humanities and Social Science

Digitized Minor Histories of Dance in Singapore’s National Archives

This dance history project is focused on identifying materials in the archive that record the contributions and major stage works of Santha Bhaskar, a prolific Singaporean-Indian dance choreographer whose career has spanned six decades between the 1960s and the present day. The primary resources for this project are the Singapore National Archives, Singapore National Library and the Singapore National Heritage Board, all of which have archives available for online access. In this project, I will collate and organize materials – newspaper reports, press clippings and photos related to Bhaskar’s contributions to Singapore’s cultural history, her dance experiments, dance institutions, and foreign diplomatic tours. Through this project, I will acquire the ability to 1) navigate online archives, 2) discern the value of materials encountered thus and 3) gain the technical proficiency in reading archival records along or against master-narratives of culture and nationhood. My mentor will provide guidance in developing a […]

...Read More about Kara Smale
SURF SMART

Targeted Gene Editing in Cheese-Rind Microbial Community

Microbial communities are ubiquitous and intimately involved in environmental cycles, human health, and industrial processes. Despite the fact that microbes live in diverse microbiomes, much of our knowledge about them comes from studying isolates. This creates gaps in understanding of how microbes interact with each other in communities. One such interaction is the production of siderophores in low iron environments. Iron is required for essential functions such as respiration and DNA synthesis. Siderophores, small iron chelating molecules excreted into the environment, are the most prevalent method bacteria use to scavenge iron. This process is dependent on community interaction because some microorganisms are able to acquire iron using siderophores produced by a different species. My project will investigate this siderophore “cheating” and its effect on the fitness of members in the microbial community of the cheese rind. This work will be conducted through observational sequence-based approaches as well as perturbing the […]

...Read More about Sara Smith
Rose Hills

Street and Sidewalk Codes: Studying Day Labor Solicitation Ordinances as Symbolic Legislation

Have you ever wondered why governments pass risky legislation–legislation that is likely to fail and goes against an administration’s own livelihood? My research will focus on symbolic law and the practicality of day labor solicitation ordinances. In the late 2000s, day labor solicitation bans emerged as an attempt to police and drive out Latino day workers from their communities. Many of these bans were legally challenged, ruled unconstitutional, and stopped from ever going into effect. Despite the legal challenges, some administrations pursued this regulation anyway, costing them millions in legal fees. Prior research on day labor solicitation ordinances has focused on the discriminatory practices and constitutionality that day labor bans entail. Yet, little is known about why local governments pursue day labor ordinances knowing the financial and legal risks. In a single case study, I will examine the back-and-forth litigation of Oyster Bay, New York’s day labor solicitation ban. Using […]

...Read More about Michelle Soto-Melgar
Humanities and Social Science

Characterizing Cell Type Diversity Among Wide-Field Cells

Understanding the diversity of cell types in the brain is critical for understanding how we interact with the world around us. Previous neuroscience research has not clearly defined the cell types that exist among wide-field cells, a population of cells that are critical to the visual integration pathway. Wide-field cells have potentially wide-ranging impacts on human disease, so having a better understanding of the proteins wide-field cells produce could help elucidate the causes of various disorders in humans. I will aim to categorize the biomolecular cell types in genetic mouse lines using immunohistochemistry (IHC) and in situ hybridization (ISH) to monitor the proteins expressed by wide-field cells, as well as the mRNA present in wide-field cells. The activity and downstream connections of wide-field cells are mediated by their expression of proteins. Knowing the molecules wide-field cells express will shed light on their function and connectivity, allowing for the investigation of […]

...Read More about Ilaria Stewart
Rose Hills

DNA Metabarcoding of Mosquito Gut Contents

When mosquitoes bite a host, they extract blood as a source of nutrition for their eggs. The DNA contained within mosquito blood meals can be extracted and identified using a method called DNA metabarcoding. Millions of DNA sequences of known organisms are contained within bioinformatic databases and extracted DNA sequences can be matched up to these known sequences. Using DNA metabarcoding of mosquito blood meals, I will map out mosquito predation from 5 locations across the state of California to test the hypothesis that mosquito predation will vary across locations, due to the different ecosystem types in these different regions.

...Read More about Blake Stoner-Osborne
Rose Hills

Cost and Construction Analysis of Concrete Gridshells

Thin-shell concrete structures are material-efficient and low-mass building systems with the ability to cover large spans and building envelopes. The geometry of shells and their corresponding gridshells plays a vital role in many performance factors such as their structural stability, constructability, costs and environmental impact. Therefore, exploring different design alternatives in the early stages of the construction workflow can have a significant impact on the overall performance of these building systems. Motivated by these challenges, the goal of this research is to evaluate the environmental impact, cost efficiency, and constructability (torsion and bending) of gridshell structures to enhance their overall performance. In this project, I will work on how to formulate the cost, bending, and torsion analysis modules by generating a parametric 3D module with respect to cost analysis and bending measurements. Afterwards, these developed modules will be integrated into an already developed larger project which accounts for the structural […]

...Read More about X Sun
SURF SMART

Expanding a Computational Platform for the Engineering of Chimeric Polyketide Synthases

Polyketide synthases (PKSs) are a family of enzyme complexes that synthesize a diverse class of secondary metabolites including clinically important antibiotic, antifungal, and anticancer compounds. In order to accomplish this, PKSs utilize a modular assembly with a wide variety of catalytic building blocks, passing molecular intermediates between modules until a product is finished. Due to their unique modular nature and deterministic mechanisms, PKSs have inspired engineering efforts to biosynthesize various useful new molecules. However, designing active variants still face difficulties due to a lack of understanding for the reasons behind successful or inactive enzymes, frequently resulting in nonfunctional systems. For this reason, my project will expand ClusterCAD, a computational platform that provides sequence and structure search tools useful for identifying parts necessary to build new chimeric PKSs. Specifically, I will annotate new database entries and implement support for irregular catalytic modules. The addition of novel mechanism elucidations and support for […]

...Read More about Xavier Tao
Rose Hills

Characterizing the assembly and ecological succession of the C. elegans gut microbiome composition during larval development

Bacteria inhabit almost every surface on Earth, from tabletop to hydrothermal vents. Thus, it’s unsurprising that a diverse community of microbes also thrives within the human gut. However, these residents aren’t stowaways, as strong evidence has emerged in the last decade that a well-balanced community of gut bacteria is indispensable to human health. And yet, our understanding of the genetic factors involved in selecting what gut microbes can colonize and persist remain limited. This summer, I research the effect of host genetics on the composition of the gut-microbiome, focusing on the effect of individual genes on compositional changes occurring during early development in the model organism Caenorhabditis elegans. This unprecedented work will not only constitute the first experimental investigation into the role of individual genes in the initial establishment of the gut microbiome composition of any animal host, but also contribute more generally to our understanding of the fundamental rules […]

...Read More about Kenneth Trang
Rose Hills

Un raro verdor': Potentiality in post-industrial poetry from García Lorca to Pizarnik

My research hinges on a question of resonance. What, I pose, do we as readers hear echoed in the self-effacing abstraction of Argentine poet Alejandra Pizarnik’s 1962 Árbol de Diana from the Romani-influenced folk narrative of Spaniard Federico García Lorca’s mid-1920s Romancero Gitano? The urgency of this issue stems from the post-industrial crisis of subjectivity, wherein, per Marxist theory of estrangement, the mechanical gears of capitalism mediate not only financial transactions, but also inter- and intra-personal relations. In an economic system founded on conceptual predetermination, per the logic of exchange-value, art must open spaces of potentiality for free judgement – spaces, therefore, where the individual might experience their individual subjectivity and that of a collective. My research considers selections of non-orthodox Marxist critical theory, especially that of early 20th century Frankfurt School philosopher Theodor Adorno, of the conditions under which lyric poetry may open such doors. I begin with García […]

...Read More about Ryan Tuozzolo
Humanities and Social Science

Mathematical Modeling of Actin Crosslinkers during Clathrin-Mediated Endocytosis

Clathrin-mediated endocytosis is a crucial cellular event during which vesicles at the cell surface containing nutrients, receptor molecules, and viral proteins are formed and brought into the cell interior. The process works via the formation of a clathrin-coated vesicle which is internalized against membrane tension with the assistance of a branched actin network. In mammalian cells, this process is incompletely understood, especially at later stages of internalization. Mathematical modeling efforts have successfully been able to evaluate the mechanism by which actin filaments can generate force to spur internalization, but so far, only minimal models have been created. In order to fully understand and model the behavior of branched actin networks during internalization, it is important to add in additional proteins such as actin filament crosslinkers and cofilin, which would more accurately capture the mechanism by which force generation and internalization occur. This research aims to determine the impact of these […]

...Read More about Karthik Vegesna
L&S Sciences

A Novel Computational Model For Bovine Intervertebral Disc Joint Level Mechanics

Being able to understand and predict the behavior of bovine intervertebral discs under different mechanical stresses is important because bovine discs are often used as a stand-in for human discs in disc biomechanics studies. Current computational methods of modeling stress and strain mechanics in the disc are very inconsistent because they are unable to reliably and accurately depict fiber mechanics, due to the fact that they treat a non-homogenous, fibrous part of the disc (the annulus fibrosis) as a homogenous structure. This newly developed computational model is better able to predict the behavior of the disc as it more accurately models the annulus fibrosis as a structure made up of separate fiber bundles. With this improved model, the scientific community will be able to more accurately predict the mechanical stability of a disc with simulated repair or degeneration. However, this model has yet to be experimentally validated. My project is […]

...Read More about Joanna Veres
Rose Hills

Steroidal Regulation of Kir7.1 as a Treatment for Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is an endocrine disorder that affects nearly 13% of reproductive-aged females. It is typically caused by hyperandrogenism, which allows PCOS to manifest itself in different forms. This also contributes to infertility due to anovulation, which affects nearly 50% of PCOS patients. Anovulation presents an opportunity to discover the mechanism underlying PCOS. Ovarian smooth muscle cells (SMC) express Kir7.1, a potassium channel that controls the excitation and contraction of SMC. Kir7.1’s function is affected by hormonal imbalance, demonstrated through its activation by dehydroepiandrosterone (DHEA), and therefore can be altered in PCOS patients. Given the function of Kir7.1, hyperandrogenism in PCOS patients may cause the overactivation of Kir7.1 which inhibits ovulation. In the Lishko Lab, we aim to investigate steroid selectivity of Kir7.1 and explore its physiological role in ovaries through the use of pharmacological profiles and in vitro ovulation respectively. We aim to determine if regulation of […]

...Read More about Citlalli Vergara
Rose Hills

Heat Capacity for Ni intercalated TaSe2

Superconducting qubits, typically made from conventional metals such as aluminum or indium, are one of the best candidates for scalable quantum computing. However, these qubits are highly susceptible to environmental noise. To make the system more robust, scientists proposed to use topological qubits, a more exotic type of superconducting qubit made from a class of superconducting materials called spin-triplet superconductors. Due to the scarcity of naturally existing spin-triplet superconductors, the intrinsic properties thereof are largely under-explored, and there exist few good candidate materials for the next generation of quantum computers. In this project, I will investigate the physical properties of a novel metallic compound, nickel-intercalated tantalum diselenide, which has the potential to be a spin-triplet superconductor and used as a building block for error-resistant quantum computers. I will perform calorimetry measurements at cryogenic temperatures on grown samples in order to map out phase boundary lines as the nickel concentration of […]

...Read More about Wendy Wan
L&S Sciences

Uncovering Ferrosome Function with Random Barcode Transposon Sequencing

Compartmentalization lies at the heart of understanding cell biology. The eukaryotic cell is composed of organelles, each of which carries out a unique function. As the newly discovered complexity of the prokaryotic cell is becoming further understood, bacterial organelles are becoming an essential detail to comprehending how bacteria function. The Komeili group recently discovered a novel membrane-bound organelle called the ferrosome. It is hypothesized that the ferrosome may play a part in iron storage or bacterial stress response. Yet, the question remains: what is the function of the ferrosome? My project seeks to answer this question by employing Random Barcode Transposon Sequencing, a powerful new method used to annotate gene function. I will determine which genes become conditionally essential in the absence of ferrosomes. Finding out the ferrosome’s function can reveal how bacteria produce, use, and store iron. It can also have broader implications in organelle biogenesis and bacterial stress […]

...Read More about Alexandra Weiss
Rose Hills

Using Listeria Monocytogenes to Change the Suppressive State of the Tumor Microenvironment to a Proinflammatory State

Immunosurveillance is the immune system’s ability to detect foreign pathogens, such as bacteria, viruses, and cancerous cells in the body. Many cancers evade immunosurveillance, through the use of mechanisms, which allow them to exist and spread undetected. Checkpoint blockade therapy – an immunotherapy treatment method in part developed at Berkeley – counters the “breaks” of immunosuppressive cells, imposed on inflammatory immune cells within the tumor microenvironment. Many current immunotherapies use Listeria monocytogenes as a way to induce immune cells that were previously exhausted to regain their effector phenotype and control cancer. However, about half of the patients fail to respond to treatment. This may be because immunosuppressive cells within the tumor microenvironment dampen any immune response leading to unresponsive inflammatory cells. I propose that changing the injection method from intravenous (IV) to intratumoral (IT) injection will counter these shortcomings because an immune response will generate directly within the tumor. My […]

...Read More about Elina Wells
Rose Hills

Net Primary Productivity and Carbon Sequestration of Amendment-Treated California Grassland Soils

Soil biogeochemistry has become a field of great interest in the fight against climate change. As Earth’s largest terrestrial carbon reservoir, soils have a huge potential to absorb and store atmospheric carbon dioxide, if managed properly. This project expands upon this premise, investigating how various amendment applications such as compost, ground rock, and biochar impact carbon dynamics within California grassland soils. To determine the impacts of these amendments, soil samples taken from amended and unamended plots at the Sierra Foothills Research Center will be analyzed for bulk carbon content. Comparing carbon content across the different treatments will help reveal the most effective amendment for carbon sequestration. In addition to the laboratory analysis, remote-sensed vegetation indices such as NDVI (Normalized Difference Vegetation Index) will be used to estimate grassland NPP (Net Primary Productivity) for each plot. This is an important metric because it reflects the amount of carbon stored in living […]

...Read More about Dan Willett
Rose Hills

Articulating Hong Kong Identity: Leftist Organizing in the Global Financial Center

In response to perceived violations of Hong Kong’s special autonomy, as enshrined in the “One China, Two Systems” framework, by mainland China, mass protests broke out in the city from 2019-2020. Viewing the city’s unique geopolitical position through cultural scripts, popular media framed the city’s pro-democracy movement in distinct ideological terms, stating that the residents of the financial hub were fighting for freedom and capitalism in the face of increased encroachment by “communist” mainland China. However, this tidy framework suggesting protestors took on right-leaning identities fails to account for the complex realities of organizing. Indeed, the recent movement showcased protestors choosing leftist tactics such as anarchist protest structures and unionization under the banner of Localism, an ideology calling for Hong Kong independence. Current scholarship however, ignores left-right ideologies in favor of the dominant pro-democracy versus pro-Beijing divide, despite the seemingly low predictive power of cultural scripts. My investigation thus fills […]

...Read More about Ian Wong
Humanities and Social Science

Spatiotemporal dynamics of type II actin nucleation-promoting factors at clathrin-coated pits

Clathrin-mediated endocytosis (CME) is an intricately-coordinated cellular pathway that is crucial for cellular growth, maintenance, and nutrient uptake. Functionally, CME internalizes receptors from the cell membrane, and nucleation of the protein actin protein has been shown to provide crucial forces for this internalization process. While well-characterized in yeast cells, the exact roles of actin in mammalian CME still requires further investigation. Using CRISPR/Cas9 genome-edited human induced pluripotent stem cells (hiPSCs), I will study the timing and regulation of branched actin network assembly by the proteins ABP1 and CTTN, which are type II actin nucleation promoting factors. I will also use the CRISPR/Cas9 system to generate a protocol for knockout cell lines to be used for future protein studies. This summer and beyond, I will build upon my skills in live-cell imaging microscopy, data analysis, and cell culture work. All of these experiments and studies will culminate in a fundamental understanding […]

...Read More about Amy Yan
Rose Hills

Investigating Transposable Element Activity in the Adaptive Radiation of Hawaiian Spiders

Adaptive radiations are rapid bursts of diversification of a single ancestor that give rise to many ecologically different species. While the ecological and evolutionary aspects have been extensively studied, little is known about the genomic mechanisms that produce such high genetic and phenotypic diversity. Transposable elements (TEs), DNA sequences that can change their position within a genome, are one potential genomic component, since they can quickly produce a wide variety of mutations when active. McClintock (1984) first proposed that TE activity may increase in response to “challenges to the genome.” Since adaptive radiations frequently occur when a species colonizes a new area, novel environmental and ecological conditions may trigger the deregulation of the genome and activate TEs. Using the adaptive radiation of Tetragnatha spiders, which display various stages of adaptive radiation across several Hawaiian islands, this project will utilize transcriptome data and genomic sequencing methods to test the expectation that […]

...Read More about Heidi Yang
Rose Hills

Modelling Demand for Source-Checking on Instagram: A Revealed Preference Approach

The importance of citing reputable sources is common knowledge for anyone communicating information, but less is known about whether audiences actually investigate the sources, an increasingly important practice due to the prevalence of misinformation on social media. This is a crucial determinant of whether misinformation can spread online that is often overlooked: even if there is a sufficient “supply” of credible sources, they will not be utilized if media consumers do not have sufficient “demand” for source-checking. Extending this economic analogy, this “demand” also decreases with the effort needed to check the source, analogous to the “price” of source-checking. As such, the goal of this project is to construct an economic model of Instagram users’ demand for source-checking when faced with varying costs of doing so. This could allow us to predict how source-checking behavior changes when sources are harder to find. I hope to determine this relationship experimentally by […]

...Read More about Owen Yeung
Humanities and Social Science

Exploring Core-Exciton States and Transitions in Four-Wave Mixing (FWM) Experiment

Probing core-exciton dynamics and its coupling behavior with carriers and optical fields by utilizing nonlinear wave-mixing spectroscopy can uncover the fundamental electronic and optical properties for materials and provide insights for electronic device manipulation. The nonlinear attosecond Four-Wave-Mixing (FWM) spectroscopy, using one extreme ultraviolet (XUV) light pulse followed by two optical pulses with controllable delays, has recently been used to evaluate gas-phase and condensed-phase materials. My project aims to use this technique to explore the core-exciton absorption in tungsten disulfide, a two-dimensional semiconductor and transition metal dichalcogenide. Photon energy range of the XUV pulse is suitable for exploring core-level spectra, while the optical pulse probes the core-exciton state evolution and decoherence through decay. During this project, the absorption spectra, population decay time, and core-exciton state evolution can be displayed experimentally, while the corresponding core-exciton wave function in real space and oscillator strengths between the bright and dark excitonic states can […]

...Read More about Ruoyi Yin
L&S Sciences

Conformational Shifts of the 26S Proteasome After Pore Loop Mutation

The 26S proteasome is the last stop of the main protein degradation pathway in our cells, and it allows us to keep our bodies healthy by degrading old or non-functional proteins. The motor of the proteasome is responsible for engaging, unraveling and pulling the targeted protein into the core, where it is degraded. The pore loops, six in total, are located on the motor and are the parts of the proteasome that physically interact with the targeted protein. These six pore loops pull the protein to the core like hands pulling a rope downward, switching position like hands would from top to bottom of the protein “rope” by using ATP. When a protein substrate tail is initially engaged by these pore loops, the arrangement of the entire proteasome complex shifts to begin degradation of the targeted protein. My research will explore the effect of pore loop mutations on the shift […]

...Read More about Sahar Zarafshan
Rose Hills

Seismic Detection of Groundwater Aquifers in Critical Montane Meadow Ecosystems

Riparian meadows in the Sierra Nevada facilitate access to near-surface groundwater, a resource critical to sustaining the productivity and biodiversity of the larger montane ecosystems. Historically, the groundwater flow is consistently recharged by snowmelt percolating down from snowpack at higher elevation. However, climate change is depleting this critical snowpack, destabilizing the groundwater flow and consequently the ecosystem. Using seismic surveys I conducted last year, I will produce cross-sections of a characteristic meadow. These will provide information on the near-surface groundwater distribution and composition and geometry of the soil and rock bedding. I can then evaluate how the landscape affects the relative volume and movement of groundwater. Understanding these subsurface controls on groundwater availability will inform meadow conservation efforts.

...Read More about Allison Zau
Rose Hills

Electrophysiology of Pacemaker Neurons in the Upside-Down Jellyfish, Cassiopeia

Behavior in the upside-down jellyfish, Cassiopea, an animal without a centralized nervous system (CNS), is controlled by their decentralized net of ganglia that initiate pulsing activity. This activity decreases at night, during sleep, and we study how this activity is regulated. Pacemaker neurons hold the intrinsic ability to generate rhythmic bursts of action potentials that play an integral role in the function of nervous systems from humans to jellyfish. For this project, I will perform electrophysiological recordings on pairs of pacemakers during behavioral recordings to detect the action potential of the leading pacemaker and its associated waveform. Models predict that leaders also hyperpolarize the competing pacemakers, and by recording pairs of pacemakers we will be able to detect both signals. Following these recordings, I will then perform spike-sorting and clustering algorithms to identify characteristic waveforms, and determine how they change between wake and sleep. This quantitative analysis in Cassiopea will […]

...Read More about Lilian Zhang
Rose Hills

Tonal Variation on "bu" in Mandarin-English Code-Switching

In our present world that faces an unprecedented amount of language contact, code-switching has become an increasingly common sociolinguistic phenomenon. In particular, code-switching between tonal and atonal languages poses interesting questions that are yet to be studied in tone research. In Mandarin Chinese, the negator “bu” is documented to change from a falling tone to a rising tone before another falling tone (Chao, 1965). Considering Mandarin syntax and the structure of Mandarin syllables, I propose the hypothesis that “bu” has a rising tone before monosyllabic English words and a falling tone before polysyllabic English words. A pilot study (2020) featuring four Mandarin-English bilinguals found results that didn’t perfectly match, but nonetheless support, the hypothesis. The goal of this project is to build on the pilot study, refining the experiment design, collecting additional data, and performing more rigorous data analysis. The results of this study could shed light on how tonal […]

...Read More about Cynthia Zhong
Humanities and Social Science

Desiccation resistance across Californian Tetragnatha populations

As anthropogenic climate change progresses, there is an increasing need to understand how organisms tolerate hot, arid conditions without desiccating, or drying up. In many arthropods, aridity tolerance is impacted by the outer covering of their bodies, the cuticle, especially its waxy outer layer, the epicuticle. This layer can help retain moisture by reducing evaporation rates. The chemical composition of the cuticle may impact moisture retention, and thus the ability of arthropods to persist under global heating. We plan to analyze specimens of two spider species (Tetragnatha versicolor and T. laboriosa) from populations in various regions of California. Both species are distributed throughout the state near bodies of water, though they have different habitat preferences, with T. laboriosa typically found in drier environments. We will evaluate how quantities, lengths, and double bond counts of methyl-branched cuticular hydrocarbons vary across populations, which may allow inference on the role of specific compounds […]

...Read More about Zachary Zollman
Rose Hills

PTSD Symptom Dynamics and Development after Sexual Assault: An Idiographic Network Analysis

Sexual Assault (SA) is a highly prevalent form of trauma – around 43.6% of women and 24.8% of men in the US will experience some form of SA in their lifetime. The physical and mental health consequences experienced by SA survivors place a tremendous burden on society, as SA is correlated with greatly increased risk for psychopathology, especially Post-Traumatic Stress Disorder (PTSD). However, little has been uncovered about the day-to-day PTSD development immediately following SA. How do PTSD symptoms interact with each other over time? How is this dynamic interplay related to long-term PTSD outcomes, and does this vary by person? The present study proposes to shed light on these questions using an idiographic network approach, aiming to best model the within-person relationships between symptoms and behaviors in a sample of SA survivors within one month of SA. This study will clarify patterns of association between PTSD symptoms on a […]

...Read More about Zoe Zong
Humanities and Social Science