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

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

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

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