Non-linear Tensegrity Control System Design for the ULTRA Spine

Current robotic designs have limited movement because they involve rigid bodies and links that are connected through restrictive joints. Conventional actuation of these joints is usually achieved through motor and hydraulic control. In contrast, many macroscopic biological systems have evolved to produce locomotion through the actuation of tensile links to control their rigid counterparts. This allows for lighter and better dynamic systems that are capable of safer and more efficient motion. These biological systems can be modeled with a principle known as tensegrity, a combination of tension and integrity. A tensegrity system refers to an internally stable structure that is built from a network of compressive and tensile members. When applied to robotics, tensegrity structures can achieve large degrees of freedom while remaining extremely lightweight and robust. During my fellowship, I will be working in Professor Agoginos Berkeley Emergent Space Tensegrities (BEST) Lab in order to research a control system […]

...Read More about Zeerek Ahmad
Rose Hills

NKG2D Ligand Induction by Viral Proteins

Natural Killer (NK) cells are an important part of the Innate Immune System, surveying the body to recognize and eliminate cells determined to be abnormal. NK Cells can be activated through ligands that bind to excitatory receptors on the cell. The most well-studied excitatory ligands have been the NKG2D family of ligands, which bind to NKG2D receptors on NK Cells. Im using MCMV, Mouse Cytomegalovirus, as a model to study NKG2D ligand regulation in cells infected by viruses. M18, a protein in MCMV, by itself is necessary and sufficient for induction of the Rae-1 family of ligands, which are sub-group of NKG2D ligands. M18 does not exist as one peptide chain, but rather in two forms that are produced by cleavage, and I plan to determine where M18 is cleaved in post-translational modification and how this cleavage potentially affects Rae-1 induction. Discovering the cleavage site and how cleavage affects Rae-1 […]

...Read More about Billal Ahmed
L&S Sciences

Cluster-based parallel processing of DT-MRI acquisitions for real time probabilistic fiber tracking

Using acquisition data from Diffusion Tensor Magnetic Resonance Imaging (DT-MRI), an MRI variant that can map the diffusion of water, medical researchers have been able to image neural bundles in the brain, known as white matter tracts. Fiber tractography has been used extensively for clinical diagnosis of many neurological disorders and is used by neurosurgeons for surgical planning. Dipy, an open source project, provides a rich suite of fiber tracking algorithms accessible to any medical center in the world. Computing the fiber tracks using its probabilistic models, however, are computationally expensive. My project this summer is to integrate standard parallelization frameworks into dipys probabilistic models. I plan on leveraging industry standard cloud computing tools to accelerate the computation of these fiber tracts. The goals of my project are to enhance dipys probabilistic models for richer image processing, to provide real-time fiber tracking analytics to UCSF surgical planners, and to provide […]

...Read More about Amit Akula
Rose Hills

Integration Time in the Avian Auditory System

Temporal discrimination of acoustical signals plays a key role in how we perceive sounds. It affects the perception of loudness, timbre and pitch and it determines the rate at which we can parse phonemes in speech. A robust way to assess temporal integration is to determine the flicker-fusion rate: the rate at which a train of clicks is heard as a continuous sound with a low pitch instead of as a series of short sound elements. This rate is approximately 40Hz in humans corresponding to our lower bound of pitch discrimination and an upper bound for parsing phonemes. Songbirds have been used extensively in neurophysiological and behavioral research designed to understand the perception and production of learned communication calls because they are one of the few animals, other than humans, that are capable of vocal learning. Although it is known that songbirds have frequency resolution similar to humans, it is […]

...Read More about Milan Amin
L&S Sciences

Astigmatism-related Amblyopia Treatment

Vision is a vital sense that many people reply on to navigate through their daily lives, and yet people with amblyopia (commonly referred to as lazy eye) can have their vision and depth perception severely impacted by this condition. With my mentor in the Levi Lab, I sought to develop an effective treatment for astigmatism-related amblyopia and test it in a clinic trial. The treatment is a perceptual learning task where the patient looks at a computer that presents different orientations of a black and white pattern. The task of looking at the pattern repeatedly is done to hopefully train the eye to focus using the astigmatic part of the eye, to ultimately improve the visual input from that eye, and improve their binocular vision.

...Read More about Michelle Antonucci
Rose Hills

Neoproterozoic carbon anomalies in the rock record

A worldwide abundance of glacially deposited sediments in early Neoproterozoic strata suggests the onset of a great global cooling event that began approximately 720 million years ago. Sometimes referred to as the Snowball Earth Hypothesis, this period of massive climactic change resulted in the propagation of glaciers at very low latitudes, and potentially covered the entire surface of the planet with ice. Determining the geographical, climatological, and biological changes that happened prior to the onset of this event can allow us to better understand the processes that led to such a dramatic climate anomaly. This summer, I will be mapping, sampling, and analyzing pre-glacial Neoproterozoic rocks in the region around Negash, Ethiopia. By combining data from 13C ratios from carbonate rocks with radiometrically-dated ages gleaned from multiple volcanic ashes interspersed among the carbonates, we will be able to better constrain and determine the speed and duration of significant climactic anomalies […]

...Read More about Eliel Anttila
L&S Sciences

Analysis of neurodegeneration-associated TREM2

The prevalence of neurodegenerative diseases has reached an unprecedented level and is now a prominent threat to the health and wellbeing of our aging population. As a result, the demand for effective therapies has become of paramount importance. Studying proteins involved in neurodegeneration allows researchers to outline cellular pathways leading to disease, which in turn helps provide targets for drug molecules. Recently, scientists discovered a link between different neurodegenerative diseases and specific point mutations in triggering receptor expressed on myeloid cells 2 (TREM2). TREM2 is normally expressed at the cell surface and is believed to play a key role in the immune response of the brain. Recent studies suggest that mutant versions of TREM2 are defective in the transport of the protein to the cell surface. This summer, I will analyze mutant forms of TREM2 to determine where in the cell these defects are present in an attempt to understand […]

...Read More about Renan Aparicio
Rose Hills

Mechanism of DNA Spacer Acquisition during CRISPRCas Adaptive Immunity

Found in many species of bacteria and archaea, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated (Cas) proteins provide an adaptive defense mechanism against foreign invaders such as viruses and plasmids. By integrating segments of the foreign DNA into the CRISPR locus of the host genome, the bacteria remember the invaders and can subsequently produce CRISPR RNAs (crRNAs) to destroy the foreign DNA complementary to the crRNA. In particular, Cas9 plays a major role in using the short RNA as a guide to search for any DNA sequences in viruses and plasmids that match the RNA sequence, cleaving and destroying them. Although the CRISPR pathway has been extensively studied, the mechanism of new spacer acquisition is still poorly understood. In 2015, it was discovered that four proteins Cas1, Cas2, Csn2 and Cas9 are involved in acquiring these spacers in the bacteria Streptococcus pyogenes. Using a combination of […]

...Read More about Lawrence Bai
Rose Hills

The Remediated Bakhtin: Heteroglossia and New Media

According to the 20th century theorist Mikhail Bakhtin, the distinguishing feature of the novel lies in its ability to incorporate multiple dialects and forms of language into itself and better mirror the diversity of language that naturally occurs in reality. In his argument for this theory, Bakhtin relies on a cultural analysis of the genres development and ignores the impact of technological innovation in media that may have crucially affected the development of the genre. My project seeks to analyze Bakhtins theory in relation to similar studies that incorporate the development of media and extrapolate these relations in regards to the internet. In doing so I seek to answer the following questions: What has been the impact of the internet on heteroglossia, diversity, of language? Does Bakhtins theory of the novel still hold in consequence of this impact? And ultimately, what is the relationship of the novel genre to the […]

...Read More about Travis Bartley
Humanities and Social Science

Building a Movement from the Inside: An Organizational History of the Prisoner Hunger Strike Solidarity Network to Support Prisoner-Led Resistance at Pelican Bay

In Spring of 2011, prisoners inside Pelican Bay State Prison contacted prisoner-rights and anti-prison activist organizations announcing prisoners would be beginning a rolling hunger strike and that they needed support making sure their voices and demands were heard and acted on outside prison walls. The Prisoner Hunger Strike Solidarity coalition (PHSS)- originating in the Bay Area and made up of grassroots organizations, family members, formerly incarcerated people, lawyers, and individuals- to amplify the voices of CA prisoners on hunger strike was formed. Though the hunger strike has ended, the demands of the prisoners have not been met, and prisoners alongside PHSS continue to fight to get these demands met. My research will create an organizational history of PHSS in order to determine whether this model of prisoner-led resistance can be replicated elsewhere, keeping in mind the unique history of radical bay area social movements. I hope to aid organizers and […]

...Read More about Rosella Bearden
Humanities and Social Science

U.S Public Perception of Measles, 1900 - Present

Measles was once a nearly ubiquitous childhood plague, a rite of passage with sometimes deadly outcomes. However, the disease has all but disappeared in the vaccination era – few people cross paths with the measles, few know anyone who has been infected. The veritable erasure of the disease from public life stems from widespread use of the measles vaccine, whose success effectively revolutionized societys relationship with measles from one of grudging resignation, to a near ignorance. It is the nature and details of this change in perception that I will explore this summer. Via a case study of the measles experience in 20th century United States, I will investigate how the introduction of preventative health measures moderates the publics relationship with disease, transforming perceptions of harm and danger previously inherent to the illness. I will systematically survey the dynamic public attitude toward measles throughout the last century, as presented in […]

...Read More about Marina Blum
Humanities and Social Science

Modern Science and Tibetan Buddhism

Over the past two decades Tibetan Buddhism and modern Science have been seriously engaging each other in topics of consciousness, origins, and happiness. The excitement of the possible convergence between science and spirituality in a conversation that has been historically polarized between secular and religious values has overshadowed investigative research that aims to understand the quality and impact of the interaction. To start this process, I will look at the lasting effects of two programs; Science For Monks (SFM) and the Emory Tibet Science Initiative (ETSI) on Tibetan Buddhist communities in India. I will do this by investigating and documenting the existence and utility of science in major Tibetan Buddhist monasteries in South India, specifically Sera, Drepung, and Gaden. At each location I will document physical changes to the monastery that have resulted from SFM and ETSI and conduct interviews with monks who have attended their workshops. What is the […]

...Read More about Kathryn Boden
Humanities and Social Science

Investigating Age Related Decline of Germline Regeneration in an Amphipod Crustacean

Regeneration is an organisms ability to regrow and compensate for damage to specific cell lineages, and the extent to which it can occur varies greatly among species. My research focuses on the germline, which is the cell lineage entrusted with producing and maintaining gametes that contribute to the creation of offspring. The ability to regenerate the germline is predominately observed in species that can undergo total body plan regeneration such as flatworms and sponges. Parhyale hawaiensis however, is an amphipod crustacean that has been shown to regenerate its germline post-hatching despite not having full body plan regenerative capabilities. I am testing the limits of this novel process by ablating the germline in adults and observing if mature Parhyale retain this ability. In order to investigate this pathway I am using the CRISPR/Cas9 genome editing system and the NTR/Mtz cell ablation method to create a transgenic lineage that I will use […]

...Read More about Lucas Brenes
Rose Hills

Identification of Interactor Binding Domains on Usp44

Ubiquitin is a protein that serves as a molecular tag for either degradation of its targets by the 26S proteasomes or for a wide variety of other functions such as DNA repair, transcription, endocytosis, membrane transport, or protein localization in a proteasome independent manner by covalently attaching to its target proteins. Deubiquitinases (DUBs) are proteins that mediate ubiquitin removal and processing to play regulatory roles in multiple cellular processes. The deubiquitinase (DUB) Usp44 is a critical regulator of cell division that acts as a tumor suppressor by preventing premature anaphase during mitosis. During cell division, Usp44 protects mitotic checkpoint complex from the anaphase-promoting complex (APC)-driven disassembly, which allows it to regulate transition from metaphase to anaphase. Beside this well-known function, Usp44 may also play a significant role in regulating stem cell pluripotency and differentiation in neuronal lineages. Previous work has identified and characterized Usp44 binding partners. Most of the binding […]

...Read More about Denny Cha
L&S Sciences

Pseudomonas aeruginosa Hijacks Cell Death Pathways

Pseudomonas aeruginosa is an opportunistic pathogen responsible for a significant number of antibiotic resistant infections. It can infect almost any site of the body, but typically targets damaged epithelial tissues such as corneas of contact lens wearers, potentially leading to blindness. P. aeruginosa uses a Type 3 Secretion System, a needle-like structure, to introduce bacterial exotoxins into host cells which can cause cell death. P. aeruginosa has also been found to replicate intracellularly and occupy protrusions in the plasma membrane known as blebs. Previous studies from the Fleiszig lab have shown that caspase 1, an enzyme that can induce pyroptotic cell death, plays a role in initiating bleb formation. We hypothesize that caspase 1 activity and the induction of pyroptosis is needed for bacterial intracellular survival and replication to occur.

...Read More about Stephanie Chang
Rose Hills

Evaluation of Post ACL Injured Knees

Injuries to the ACL are very common in the young and active population, and this can often lead to posttraumatic osteoarthritis (OA), sometimes as early as in their third decade of life. Like idiopathic OA seen in older individuals, posttraumatic OA causes pain, impaired function, and overall decreased quality of life, but occurs at a much younger age after injury. ACL injuries are commonly treated with surgical reconstruction of the ligament, replacing the torn ACL with a graft. However, surgical reconstruction does not perfectly correct for tibiofemoral joint kinematics. Moreover, these subtle changes in knee kinematics can lead to early joint degeneration overtime. Since the mechanism behind OA development after ACL injuries is poorly understood, there is little development of preventive measures that could help this particular population. The purpose of my project is to correlate biomechanical alterations after ACL injuries and articular cartilage changes to better understand how ACL […]

...Read More about Ellison Chen
Rose Hills

The role of Gpr75 in the beta cell response to autoimmunity

Despite the growing prevalence of diabetes, the exact biological mechanisms leading to the onset of this disease still remain painfully unclear. Type 1 diabetes in particular is caused by an autoimmune attack to an individuals insulin secreting beta cells; this cell population cannot be regenerated and an adverse condition known as hyperglycemia ensues. The immune cells and chemokines present in the pancreas at the onset of this autoimmune response are of interest when considering this disease. Recent studies have suggested that the activity of a particular G-coupled protein receptor may influence the onset and progression of beta cell destruction. The goal of my project is to study this G-coupled protein receptors role in regulating beta cell function, as well as investigate any potential interactions between this receptors and the molecules of the immune system present in type 1 diabetes.

...Read More about Justin Choe
Rose Hills

Imitation, Emulation, and the Meaning of Originality in Painting Versus Cinema

How do issues of authorship and originality function within fine art and cinema? What are the similarities between painting and film? What are the fundamental differences, especially those relating to the meaning and worth of emulation within the two mediums? My research will attempt to answer these questions using two case studies: Orson Welles’ 1973 film F for Fake, and the paintings of the infamous Elmyr de Hory, Hungarian art forger extraordinaire who imitated the style of countless painters (Degas, Derain, Dufy, Matisse, Modigliani, Picasso, and Vlaminck to name a few), and traveled the world painting counterfeits in hotel rooms along the way, prompting a manhunt for one of art history’s greatest and most prolific art forgers. Using postmodernist texts as a foundation and employing rigorous filmic and formal analyses of F for Fake and Elmyr de Hory’s forgeries respectively, my research will challenge prevailing conceptions of the integrity of […]

...Read More about Scarlet Cummings
Humanities and Social Science

Investigating Alzheimer's: Network Theory Approach

The leading hypothesis suggests that the progression of Alzheimers disease (AD), the major cause of dementia, is driven by the accumulation of misfolded amyloidB proteins into plaques within the brain. The presence of these plaques in some cognitively healthy adults has complicated our understanding of AD and has raised the question of what exactly triggers cognitive decline. Recent studies employing network theory have revealed that the answer may lie in the details of the disruption of the brain network by the amyloidB plaques. This summer I will use fMRI and PET imaging data to simulate the progressive effects of plaque deposition on the topology of the functional brain network.

...Read More about Leonardino Digma
Rose Hills

Characterization of Gene Flow Through Experimental Secondary Contact by Molecular Assay

Speciation has long been studied in the field of evolutionary biology, but many questions remain regarding the specific genomic interactions between diverging species. To study the genetic events involved in the development of reproductive isolation and speciation, I will focus on the Drosophila nasuta fruit fly clade which is currently in the process of diverging. I will use molecular assays to characterize gene flow through experimental secondary contact between recently diverged Drosophina nasuta subspecies and draw conclusions about the level and type of reproductive isolation between the subspecies pairs. My results will ultimately be analyzed alongside the results of mating and fertility assays and whole genomic sequencing conducted within the Bachtrog lab to facilitate a better understanding of the extent and kind of reproductive isolation between recently diverged subspecies. This research will provide a framework for future investigations of the genetic and phenotypic reasons behind genetic incompatibilities and their role […]

...Read More about Jennifer Ding
Rose Hills

The Gospel of Nicodemus and Early English Drama

During the middle ages the apocryphal Gospel of Nicodemus was wildly popular throughout Europe, and was translated into nearly every vernacular language. This non-canonical religious text contained a piece of theology that has fallen into obscurity, Christs harrowing, or descent, into Hell. In Middle English the Harrowing of Hell occurs as a narrative poem in three manuscripts, spanning the late 13th century to the early 14th century. A striking aspect of these poems is that they appear to straddle the line between what we consider poetry and drama. The poems sparse descriptions, ensemble cast of biblical characters, and almost entirely spoken action has led some recent scholars to determine the poem is, in fact, an early play explicitly intended for dramatic performance. My research project intends to question this hypothesis by comparing the Middle English Harrowing of Hell poems to their source in the Gospel of Nicodemus, looking for clues […]

...Read More about Alexander Flores
Humanities and Social Science

Learning Contact-Rich Tasks with Haptic Input

Robots are typically deployed in highly controlled environments, but for robots to become usable in everyday situations, they must be able to learn to adapt to the environment. Reinforcement learning is a popular framework in robotics for teaching robots motor skills in unknown environments through a trial-and-error process. Recently, methods have been developed that allow optimization of high-dimensional control policies, which enables the use of powerful tools from machine learning such as neural networks to decide on which actions the robot should take and when. My project involves using various types of neural networks in tandem with high-dimensional sensor data (such as pressure, torque, and visual) to learn manipulation tasks.

...Read More about Justin Fu
Rose Hills

Regulating Lignocellulose O-acetylation

Plant biomass represents the most abundant collection of polymers on this planet. As a dominant carbon sequestration system, an upwards of 150 billion tons of biomass is produced worldwide each year, but humans currently utilize only 2% of this resource. Thus, there is a large margin to accommodate recent interests in lignocellulosic plant biomass as feedstock for biofuels and other commodity chemicals. A major bottleneck in the generation of commercially competitive biofuels from lignocellulosic plant biomass is the presence of acetate throughout the plant cell wall as this chemical hinders the access of enzymes required to depolymerize the biomass and is a potent fermentation inhibitor to many microbes. To date, three proteins families have been identified as participants in the O-acetylation of plant cell wall polysaccharides the Altered Xyloglucan9 (AXY9) protein, the Reduced Wall Acetylation (RWA) and the Trichome Birefringence-Like (TBL) proteins. Though our understanding of the participants involved in […]

...Read More about Brett Garabedian
Rose Hills

Modeling of COSI Detector Fields for Charge Transport Simulation

In Compton telescopes with crossstrip germanium detectors, interactions on the detector strip borders where charge is split between strips result in significant signal loss that degrades spectral resolution. Thus, modeling this charge loss mechanism is essential for making corrections and maximizing the resolving power of the instrument. Yet despite this, the mechanism is not entirely understood. My project seeks to model charge collection and transport in the detectors of the Compton Spectrometer and Imager (COSI), a balloonborne gamma ray telescope operated out of the Space Sciences Laboratory. The research hopes to answer three main questions: What mechanism causes this charge loss? How can the charge loss be described in a numerical model? How can this model be used to apply corrections to the COSI data pipeline? Using Monte Carlo techniques, it is hoped that we can address these questions and extend the results to the next generation of detectors, which […]

...Read More about Cory Gerrity
L&S Sciences

Search for Dark Higgs and Dark Photons at BaBar

The majority of matter in the universe is dark matter which does not interactwith light. In several physical models dark matter includes a dark photon (A’) which plays a similar role to that of the photon in the normal sector. In addition,recent experiments at CERN have confirmed the existence of the Higgs boson, a particle which mediates the Higgs field that gives other particles mass. Now physicists are proposing theories beyond the Standard Model which introduce additional Higgs states, with one of them (A0), having a lower mass than the one found at CERN. Preliminary searches for A0 and A’ at the SLAC National Accelerator Laboratory have not taken advantage of the tools currently available to handle the large amount of raw detector data. My analysis will improve uponthe work done in these searches by using machine learning techniques to enhance the selection rates of events which produced A0 and […]

...Read More about Alexander Giuffrida
Rose Hills

Buddhist Statues and Transformation Images: The Peacock King at Dazu

The Dazu Rock Carving is the only Buddhist cave site in China representing the development of Buddhist teachings during the Song dynasty (960- 1279). My research mainly investigates the Buddhist statues of Dazu site, with a special focus on Mahamayuri Vidyaraja, or the Great Peacock King at Baodingshan, Dazu. The Great Peacock King, a deity who can cure all evils in Esoteric Buddhism and who always rides on a peacock, is rarely depicted in other Buddhist caves. Dazu has three statues of him, however, at Baodingshan, Northern Mountain and Shimen Mountain. The adjacent site, Anyue, has another one. More importantly, these four iconic images are extremely similar, with the exception of differences in transformation images (bianxiang), the narrative images of exemplary stories derived from Buddhist scripture at the rear of each statue. The similarity of formal language among these Great Peacock King statues and the diversity to their associated transformation […]

...Read More about Ruiyao Gong
Humanities and Social Science

Proteasomal Inhibition by KSHV Protein ORF68

A virus can have two distinct life cycles: lytic, which produces new virus, and latent, in which the virus remains silently integrated into the DNA of the host. The ultimate goal of a latent virus like Kaposis sarcoma-associated herpesvirus (KSHV) is to get its viral genes integrated into the host genome, and eventually produce viral proteins in order to generate more virus. These viral proteins interact with the host cell organelles and proteins in order to hijack host machinery for viral use. A KSHV viral protein, ORF68, interacts with and inhibits the activity of the host cell proteasome. The proteasome is an ATP dependent, multi-subunit, multi-protein complex that is part of many cellular pathways in the cell, including protein degradation and quality control. Studies have shown that proteasome inhibitors can be used as novel cancer therapies. The proteasome degrades unneeded or misfolded proteins and plays roles in regulating the cell […]

...Read More about Apurva Govande
Rose Hills

Robotic Model to Investigate Crab Burrowing

By understanding how physiology, behavior and the environment all contribute to animal multifunctionality, we can better understand animal motion and translate these discoveries into new technologies in the fields of robotics, prosthetics and rehabilitation. Ghost crab (ocypode quadrata) burrowing is particularly valuable for understanding multifunctional appendage design. To access burrowing data (like forces produced by the crabs legs, the effect of the crabs motion and the importance of the crabs anatomical features) and systematically vary them, I am constructing a robotic model based on actual ghost crab appendages. Robotic models and engineering methods similar to those I am employing have a long history of supporting biological research. These models not only offer new insights into animal biomechanics but can also lead to entirely new robotic technologies.

...Read More about Nicole Greene
Rose Hills

Investigating the Thalamocortical Circuitry Underlying Somatosensation

Understanding the neurophysiology of sensation in mammals has been a major topic of research for over a century. My project aims to shed light on the neural circuitry underlying the sensory perception of body position, known as proprioception, by investigating its role in object localization. Our ability to proprioceive is mostly subconscious and facilitates several skills including typing on a keyboard without looking. As with other senses, specific sensory receptors that mediate proprioception, termed proprioceptors, have been identified. Research using whisking behavior in rats and mice as a model has also suggested that specific sets of neurons in the brain, particularly the posterior medial nucleus of the thalamus (POm), respond selectively to movement and the primary somatosensory cortex (S1), which is involved in the processing of touch signals, makes direct connections to POm. However, an understanding of the role of these projections in the sensory perception of body position is […]

...Read More about Sandon Griffin
Rose Hills

Characterization of Immune Response in Repeat Dengue Infections of the Nicaraguan Pediatric Cohort Study Using Dengue Reporter Virus Particles (DENV-GFP 1-4)

Four serotypes of the dengue virus (DENV1-4) circulate globally, causing more human illness than any other mosquito-borne virus. DENV infections can be both asymptomatic and symptomatic, resulting in dengue fever or the more severe and life-threatening forms of the disease, dengue hemorrhagic shock/dengue shock syndrome. DENV infections confer life-long immunity against re-infection with the same serotype; however, they may either protect against or enhance a subsequent infection with a different serotype. An important step in assessing this topic is the determination of the amount of anti-DENV antibodies produced by the immune response to these infections, as well as the degree to which they neutralize each of the four DENV serotypes. My SURF project involves reconstructing the immunological history of children in the Nicaraguan Pediatric Dengue Cohort Study run by Dr. Eva Harris and Nicarguan collaborators (now in its 11th year) by documenting their first, second, and third infections with different […]

...Read More about Aryan Haratian
Rose Hills

Tracing the molecular footprints of extreme sexual selection - The genetics of sexual suicide in black widow spiders

Since its foundation in the early 20th century, ethological research has provided countless fascinating insights into the evolutionary significance of animal behavior. While the adaptive importance of behavior is often well understood, its molecular causes are still poorly known. Behavioral adaptations are often driven by sexual selection, one extreme example has been found in the males of the black widow spider species, Latrodectus hasselti and L. geometricus. As the result of strong sexual selection, these Latrodectus species have evolved obligate sexual cannibalism in which males somersault their abdomen on the fangs of the female during courtship, ensuring their death. My aim is to use Latrodectus as a model system to investigate the molecular basis of suicidal mating behavior. To do so I will be comparing the RNA transcriptome from several male brains to look for differential gene expression between suicidal and non-suicidal males. By analyzing the transcriptome from sub-adult and […]

...Read More about Katie Hitchcock
Rose Hills

Functional domain analysis of type I myosins in clathrin-mediated endocytosis

Clathrin-mediated endocytosis (CME) is a process through which cells internalize pieces of their plasma membrane (PM) and extracellular substances. Cells regulate signal transduction, membrane homeostasis, and nutrient uptake through this ancient and highly-conserved pathway. Previous research demonstrated that type I myosins are critical for endocytic internalization. The yeast type I myosin Myo5 is composed of a motor head linked to a multi-domain tail. Myo5 motor activity is necessary for PM internalization, and its tail domains are predicted to bind various cellular structures. Little is known about the precise role of Myo5 in yeast CME. I will apply a combination of genetic manipulation and fluorescence imaging toward building a functional domain analysis of Myo5 by quantitating the effects of mutations in the Myo5 protein. These studies will increase our understanding of the fundamental mechanisms responsible for the crucial process of endocytosis. Because the endocytic machinery is widely conserved, what we learn […]

...Read More about Jessica Hong
Rose Hills

Induction of PD-1 expression on NK cells by Tregs

Several lines of evidence support a role for Natural Killer (NK) cells in the immune response to tumors. We recently found that PD-1, a receptor capable of powerfully suppressing the functions of T cells, is expressed by NK cells. However, the cellular networks responsible for PD-1 expression on NK cells are not known. Here, we propose to study the contribution of Regulatory T cells (Tregs) in inducing PD-1 expression on NK cells, by using both an ex vivo and in vivo approach. The proposed research plan will provide important knowledge on the cross-talk between NK cells and Tregs in the context of an immune response to a tumor.

...Read More about Joy Hsu
L&S Sciences

Development of Retinal Direction Selective Circuit

A basic question in neurobiology research is how neural circuits are wired up to perform computations. A classic example of neural computation is that which underlies the visual systems ability to detect the direction of moving object. Input to the retina is encoded by photoreceptors, which are point detectors of light and by themselves cannot determine the direction an object moves. However at the output of the retina, there is a class of neurons that signal robustly when object moves in one direction over any other. These direction-selective cells have been the focus of extensive research and the neurons that comprise the circuit that perform the computations are well defined. The Feller lab is interested in how the connections between these neurons, i.e. the direction selective circuit, emerge during development. My research aims to study the development of the synapses the connections between neurons within the direction selective circuit. Specifically, […]

...Read More about Ching-Hsiu Hsu
L&S Sciences

Connecting the Game of Chomp and Young Tableaux

The Game of Chomp (also called Northeast) is a two-player game on a rectangular chocolate bar consisting of m-by-n squares. Players take turns eating chocolate squares on the board. If a player eats a square, they must eat all squares lying above (north) and to the right (east) of that piece. Whichever player eats the lowest left corner chocolate square (poisoned) loses (Gale). For my project, I am trying to apply Sprague-Grundy value from Game Theory and Young diagrams from Algebra to characterize winning strategies for Chomp or provide evidence of the complexity of solving general m-by-n Chomp.

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

Looking Outward: Awe Reduces Bias and Prejudice

Implicit bias refers to a prejudiced attitude or stereotype activated outside of conscious awareness. While there has been a great deal of research examining factors that affect implicit attitudes, there is a dearth of research on the effects of emotional statesparticularly positive emotionson implicit bias. I seek to address this gap by examining the influence of awe on implicit bias. Awe is an emotional response to vast stimuli that transcend current frames of reference and stimulate a need for the formation of a new cognitive framework to accommodate the experience. The experience of awe is associated with more systematic processing, present moment awareness, outward focus, and feelings of belonging to broader groups. These attributes lead to the hypothesis that experiencing awe will be associated with less implicit bias. This study will be an important contribution to research examining the effects of positive emotions on automatic processes and to the psychological […]

...Read More about Bradley Hughes
Humanities and Social Science

Target-Specific Input Architecture of Cingulate Cortex Pyramidal Neurons

Many recent studies have shown that the brains frontal cortex strongly modulates the information processed in the primary sensory cortices. A strong contributor of this modulation, each of the frontal cortical pyramidal neurons can project axons to multiple different brain regions (e.g., thalamus, midbrain, striatum, and other cortical areas) and therefore have fundamentally different roles. However, it is still unknown whether the frontal cortical pyramidal neurons innervating different targets receive inputs from overlapped brain regions or from segregated regions. My research will focus on the cingulate cortex (Cg), the frontal cortex modulating visual response and controlling eye movement in mouse models, and I will use a unique Cre-dependent trans-synaptic tracing method based on pseudotyped rabies virus to examine the input architecture of the Cg pyramidal neurons targeting the primary visual cortex (V1) or the superior colliculus (SC). I am enthusiastic that this study will ultimately result in a more thorough […]

...Read More about Daniel Jeong
Rose Hills

Activism in the Context of Violations in Indian Conflict Zones: A Multi-Actor Approach

While it is the largest democracy in the world, Indias human rights record with respect to conflict zones has been unsteady at best. In many areas of the country with past and ongoing conflicts, the commission of human rights violations of the government has been continuous and widespread. The failure of the Indian state to investigate these human rights abuses committed by its own departments has created a structure where, in these areas of conflict, basic human rights have been suspended and faith in the democratic system, the police and the justice system is dangerously low. In a bleak context where this abuse in conflict zones is a public secret of the Indian government, my research project aims to juxtapose this environment of human rights violations on one hand, with the traces of activism observed in these areas on the other by asking the question: (How) has the dehumanizing experience […]

...Read More about Dipin Kaur
Humanities and Social Science

Stochastic Bias on 2LPT (2nd order Lagrangian Perturbation Theory)

The large scale matter distribution allows to answer the fundamental questions about the Universe including the cosmological constituents and the origin of the Universe. The Universe seems homogeneous on a very large scale (~100 kpc), yet on the smaller scales such as on the order of clusters and galaxies, the cosmological structures exhibits non-Gaussianity. This non-Gaussian matter field created by non-linear gravitational evolution is proved to be hard for modeling. Since the majority of matter is almost non-interactive dark matter, the science we learn from a direct observation has a certain limitation. Therefore, a computational simulation has been a useful tool to study mass fluctuation fields. From analyzing data from the cosmological N-body dark matter simulations, I try to find a better way to correlate the dark matter field and the halo field based on the second order Lagrangian perturbation theory.

...Read More about Avery Kim
L&S Sciences

Exploring Deception Using Brain Imaging

In most deception experiments, the situation presented to human subjects in unrealistic, lacking a social dimension, unreflective of the emotionally charged nature of a lie, and does not possess a valid paradigm to assess intention. By incorporating economic games informed by neuroscience modalities, the necessary context can be established to rectify the aforementioned flaws. With accurate monitoring of the subject populations in the economic game, the subjects reactions and behavior can be used in functional Magnetic Resonance Imaging (fMRI) to provide the needed realistic element to deception research. It would be important and fascinating to discover the neural basis for the extent, emotional foundation, and intention behind lying. There are a number of questions to test: How sensitive to personal gain are people when deciding to lie? To what extent do people care about the losing partys loss? What role does emotion play in the calculation to lie? Delving into […]

...Read More about Nikhil Kotecha
Humanities and Social Science

Genetic Mechanisms of Heteroresistance in KPC-producing Klebsiella pneumoniae

Antibiotic resistance in the Enterobacteriaceae family, which includes Gram-negative bacteria E. coli and Klebsiella, has become a serious public health problem. Many bacteria of this family produce extended-spectrum beta-lactamases (ESBLs), which are enzymes that can degrade most beta-lactam antibiotics. Therefore, carbapenems, a type of beta-lactam drug, are increasingly the drugs of last resort for ESBL-producing bacteria. However, an enzyme called Klebsiella pneumoniae carbapenemase (KPC) threatens to render carbapenems completely ineffective, leaving few choices for treatment in patients with infections caused by KPC-producing species. In fact, the CDC has designated carbapenem-resistant Enterobacteriaceae (CRE) as urgent threat pathogens. The goal of this project is to investigate the genetic mechanisms of heteroresistant KPC-producing species, which are bacteria that show drug susceptibility in vitro, but quickly become resistant after exposure to antibiotics. Using transposon mutagenesis assays, I aim to identify potential genes involved in mediating the heteroresistant phenotype. This research will help to identify […]

...Read More about Mallika Lal
L&S Sciences

Using Bay Annulated Indigo for OPV

Organic Photovoltaic cells (OPV) are on the rise of changing modern technology. An advantage of photovoltaic cells is that it utilizes chemicals based on their properties that can harness energy from the suns radiation and provide a voltage. This green way of approaching power supply will help save Earths natural reservoirs and impede atmospheric pollution. However, standard organic photovoltaic cells (OPV) that uses P3HT and PCBM mixtures have only a power conversion efficiency (PCE) up to 4.5%. This inefficient percentage is what hampers OPV from excelling in todays technology. My research will be using a substitute for P3HT with Bay Annulated Indigo (BAI) and explore its derivatives in attempt to find resulting compounds that yield better absorption in the UV-VIS regions.

...Read More about Jason Lam
Rose Hills

Analysis of Cockroach Tarsus Applied to Running on Horizontal Rods

American Cockroaches exhibit a large versatility of movement; they are able to transverse over varying substrates in different orientations. Over the last decade, scientists have studied the tarsus, or foot of the cockroach, looking specifically for certain features that allow the cockroach to make such transitions. So far, three distinct structures; the claw, the euplantulae, or a set of overlapping friction pads, and the arolium, which is an adhesive protrusion; have been found to act in tandem during movement. My research for the summer will investigate the capabilities of the cockroach to run rapidly and make gait transitions on horizontal rods. Currently it is unknown how the complex leg morphology of the cockroach is used to attach to the rod in both upright and inverted running, and how these changes affect the performance. Ultimately, the goal of this research, which will continue on to my senior thesis, is to learn […]

...Read More about Crystal Lee
L&S Sciences

Identifying novel genetic modifier(s) for cataracts in mouse genetic models

Cataracts, which are a clouding of the lens in the eye, affect nearly 22 million Americans age 40 and older, and are the leading cause of blindness worldwide. By the age of 80, more than half of the American population will have had cataracts or cataract surgery. To maintain lens transparency, connexin protein subunits are crucial in forming intercellular gap junction channels for the transportation of metabolites, ions, and secondary messengers. Previous studies have shown that knocking out connexin in the 129SvJae mouse strain results in dense cataracts, while disrupting the same connexin in the C57BL/6J (B6) mouse strain results in very mild cataracts. The Gong Lab has mapped several loci in the B6 background that contain genes suppressing cataract severity, and identified periaxin, a cytoskeletal scaffolding protein, as a genetic modifier for nuclear cataract formation. We have mapped a new gene to mouse chromosome 2 that we hypothesize is […]

...Read More about Lucy Li
Rose Hills

sRNA and mRNA Localizations in E. coli

Bacterial survival depends on the cells ability to adapt to diverse environmental pressures. Many of these adaptive pathways involve small non-coding RNAs (sRNAs) that bind to the 5 untranslated region of their target messenger RNAs (mRNAs). Depending on the sRNA, the interaction between sRNA and mRNA either silences or activates mRNA translation. Although sRNAs are important regulators of gene expression, their signaling properties and regulatory mechanisms remain unclear. Identifying the localization of sRNAs, their target mRNAs, and their site of interaction is key to gaining new insights into bacterial gene regulation. Therefore, in the proposed study, I will first seek to characterize the localization of several sRNAs and their target mRNAs in the model bacterium Escherichia coli (E. coli). Second, I will test whether the protein Hfq, known to facilitate sRNA function by binding both the sRNA and mRNA, has an effect on their localizations. To visualize the sRNAs and […]

...Read More about Chris Lin
Rose Hills

Culture, Memory, and Identity in Hong Kong Food Writing & Literature

People revere food as if it were Heaven. This Chinese idiom highlights the essential role that food has always played in Chinese culture and history. It is commonplace to see cuisine and wine appear in Chinese classical and modern literature. When food appears in literature, we experience it with all our senses and gain a deeper understanding of its significance. In consideration of the lack of studies on Hong Kong food literature, I will investigate the interaction between literature and food in colonial and postcolonial Hong Kong by carrying out close textual reading and literary analysis of Yasis works as an important example of Hong Kong food literature. How do food writing and literature contribute to documenting the history and culture of Hong Kong, representing the colonial and postcolonial experience, preserving Hong Kongs collective memory, exploring and defining local consciousness and cultivating the political and cultural identities?

...Read More about Queenie Kwan Yee Lo
Humanities and Social Science

Kinetic Analysis of the Fluorine-Specific Thioesterase FlK

FlK is an enzyme found in the soil bacterium Streptomyces cattleya, in which it confers resistance to the toxic metabolite fluoroacetate by breaking down its activated form, fluoroacetyl-CoA. Interestingly, FlK has evolved to discriminate between fluoroacetyl-CoA and its nonfluorinated analogue, the metabolically crucial acetyl-CoA, displaying a million-fold higher catalytic efficiency for the former. Although previous work has elucidated some of the mechanisms of fluorine specificity in FlK, the role of the arginine residue at site 120 (Arg120) has not yet been explored. Recent research suggests that Arg120s positively charged side chain is positioned in FlKs active site close to the substrate fluorine atom, and therefore may be involved in correctly positioning fluoroacetyl-CoA for catalysis by stabilizing the fluorine. I will carry out Michaelis-Menten and pre-steady-state kinetic analyses of both wild-type FlK- and mutant FlK-catalyzed reactions in order to investigate the function of Arg120. This knowledge will enrich our understanding of […]

...Read More about Nicholas Lue
Rose Hills

Redundancy Post Gene-Duplication in Moss EMF2

Gene duplication is a driving force in evolution – the genetic redundancy created by a gene duplication event can enable one gene copy to rapidly accumulate mutations and take on new functions, while the other copy performs the original function. Previous studies suggest that large-scale genome duplication closely preceded major evolutionary events such as the divergence of vertebrates, but the exact occurrences and evolutionary consequences of gene duplication have yet to be fully understood. The model moss Physcomitrella patens contains three homologs of the gene EMF2, which appear to have been recently duplicated in a lineage specific manner. I will be investigating the functional importance of each of the EMF2 genes by characterizing single and multiple mutant phenotypes and examining EMF2 protein expression patterns throughout development, focusing on spatial and temporal redundancies. Studying these genes will provide insight into how gene duplication in epigenetic regulators can lead to both novel […]

...Read More about Lynn Ly
Rose Hills

Infant Locomotion, Cognition and Early Language Acquisition

My research seeks to examine the functional consequences of locomotor experience. Current research insists that the onset of walking leads to psychological changes that have not been appreciated or expected. Some studies show that an infant’s receptive and productive language seem to improve dramatically after acquiring the ability to walk. However, critics are doubtful because this finding is based off of survey data gathered from parental report. I believe that a direct measure of infant language comprehension can serve as a converging research operation and provide more persuasive evidence. I seek to establish an experimental procedure for testing language comprehension on infants between twelve to sixteen months of age. I will also create a converging research operation by comparing data gathered under experimental setting to data from standardized tools (ex: parental report). My goal is to find out whether or not the link between infant language acquisition and the onset […]

...Read More about Lucy Ma
Humanities and Social Science

The Political Role of Religious Appeals in India

Indian Muslims, a recent UC Berkeley study discovers, are more likely to elect politicians who use Islamic symbols in campaign materials. This stands in contrast to Indian Hindus, who have no preference for candidates who appeal to their vote through Hindu symbols. Asymmetric outcomes, therefore, permeates how religious identities are politicized between India’s two largest religious populations: Hindus and Muslims. India, however, is a nation of enormous religious diversity. In consideration of religious politicization among Indias numerous religious minorities there is little to no research in the field of political science. My research involves administering and analyzing an electoral survey of Christians, Muslims and Hindus in four cities across the state of Kerala, India. From analysis into the data, I hope to provide a more nuanced understanding of religious appeals in Indian politics as well as offer footing for greater scholarship into religious minorities in the country.

...Read More about Alex Mabanta
Humanities and Social Science

Who Would Rule Over Immortal Gods and Men: The Preservation of Cosmic Order in Hesiods Theogony

Within pantheistic ideology there is a clear, central conflict: the birth of a new deity poses a threat to the existing cosmic order. This complication will be my focus this summer as I perform close analyses of the Archaic Greek poems that have since provided the canonical representations of the Olympian pantheon: Hesiods Theogony and the Homeric Hymns. A specific episode in the Theogony known as the Typhonomachy will be my launch point for examining in greater depth female deities in their maternal role, and the way in which their ability to give birth to and train a new god influences the divine political structure.

...Read More about Cecily Manson
Humanities and Social Science

Development of New KIR and HLA Genotyping Method

The amount of genomic information being gathered in the NCBI Sequence Read Archive (NCBI SRA) has been increasing exponentially over the past 8 years. Although the volume of genomic data being stored has recently reached the 2000 terabyte mark, methods for analyzing these data have struggled to keep pace, especially in the area of reinterpreting sequence for highly variable genomic regions. My honors thesis work will focus on development of new methods for immunogenetic data analysis, creating interoperable systems based on publicly available data. This summers project involves the integration of the PING software tool, developed by Dr. Paul Norman, Senior Research Scientist at Stanford University and Dr. Jill Hollenbach, Assistant Professor at UCSF, with the NCBI SRA and the Immuno Polymorphism Database-KIR (IPD-KIR). The integration of PING with these databases will create a new, seamless method of killer-cell immunoglobulin-like receptor (KIR) genotyping for the whole genome and whole exome […]

...Read More about Wesley Marin
Rose Hills

Evaluating Reproductive Isolation with Drosophila nasuta Fertility & Mate Choice Assays

The study of reproductive isolation, or the inability of two species to mate and produce fertile offspring, continues to be an area of groundbreaking evolutionary research. Both the mode of reproductive isolation (pre-zygotic or post-zygotic) and the genetic distances between species can tell us a great deal about when and how ancestral species diverged to form clades of distinct species. In order to uncover any patterns in pre-zygotic and post-zygotic isolation as species diverge, I will be studying the stage, timing, and sex-specific nature of reproductive isolation in Drosophila nasuta flies and correlating these data with the genetic distances between these species. Using fertility and mate choice assays, I will be gathering data on the generational timing of reproductive isolation in Drosophila nasuta species, the sex ratio of inter-species offspring, and the extent to which intra-species or inter-species mating is preferred in order to discover reproductive patterns in the evolution […]

...Read More about Melissa Markowitz
Rose Hills

Intuition in Mathematical Problem Solving

Science is a synonym for analytical thought, rigor, meticulousness and rationality. However, some of the greatest scientific discoveries, inventions and even proofs relied on the complete opposite of that intuition. In mathematics, mother of all sciences, intuition is routine: there is no point in dedicating decades to proving a conjecture if one does not have an intuition that it is solvable. Existing research has approached intuition primarily through a linguistic lens; my research project will extend the reach of intuition to the domain of mathematical problem solving. More precisely, I will examine peoples intuitive (unconscious) ability to make estimations about arithmetic problems. My research also includes investigating symbolic distance effects which are a phenomenon when the time to compare two symbols varies inversely with the distance between their referents. This research has implications for understanding the role of unconscious processing in problem solving, intuition, and mathematical cognition.

...Read More about Elena Martynova
Humanities and Social Science

The Role of CTAGE5 in Autophagy

Autophagy is a fundamental pro-survival cellular process by which superfluous proteins and damaged organelles are delivered to the lysosome for degradation and reuse.. Numerous human disorders have been linked with dysfunction in autophagy including heart disease, cancer, and neurodegeneration. The molecular mechanisms of autophagy are currently not well understood. My project goal is to study how the autophagosome, the double membrane vesicle which contains cargo and fuses with the lysosome membrane, is generated. Based on previous studies, we hypothesize that the CTAGE5 protein plays a role in autophagosome biogenesis. I plan to generate a CTAGE5 knockout cell line in mammalian cells with the CRISPR-Cas 9 system of gene editing so that I can compare my knockout cells to the wild-type cells using various autophagy assays, immunofluorescence, and immunoprecipitation. Ultimately, I hope to uncover the interaction of CTAGE5 with autophagy-relevant proteins in order to determine its function in autophagy.

...Read More about Anandita Mathur
L&S Sciences

Investigating the Properties of Plant-Specific Splice Factor Proteins RSZ32 and RSZ33 and Their Role in Gene Regulation

Alternative splicing is a fundamental mechanism used by higher eukaryotic organisms to produce different outcomes from the same gene transcript through selection of variable splice sites. Alternative splicing gives plants the ability to modulate gene expressions in order to conserve energy resources and optimize interactions with their environment. There are many different plant-specific alternative splicing events and while they have been catalogued on a genome-wide scale, there remains little detailed knowledge about the specific, molecular mechanisms of these pathways. I am interested in studying a plant-specific alternative splicing pathway discovered in Arabidopsis thaliana which involves the Plant 5S Ribosomal RNA Mimic (P5SM) cassette exon. The aim of my project is to study two plant-specific splice factors, RSZ32 and RSZ33, by investigating their properties, functionality, and interaction with P5SM to regulate splicing. Through this project, I hope to deepen our insight on the plant-specific alternative splicing mechanism that is key to […]

...Read More about Bao Nguyen
Rose Hills

Designing Spatial Interactions for the Internet of Things

The Internet of Things (IoT) refers to the emerging network capability between ordinary objects and promises novel interactions between devices and between people in everyday scenarios. For example, in an IoT-networked smart-house, temperature sensors embedded throughout the building sense changing environmental conditions and strategically close windows to conserve energy. Traditional user interfaces for programming interactive devices focus on single-device programming, but a programming interface for IoT networks must account for coordinating large amounts of devices as well as the autonomous nature of the devices themselves. My research focuses on building a user interface to allow anyone to create complex IoT networks quickly. I will extend the flow-based programming paradigm (FBP), a drag-and-drop user interface technique popular in content-creation software tools, to allow users to coordinate many components at a time in variable environments. I will then test the interface against control interfaces in a user study where participants prototype networks […]

...Read More about Jasper O’Leary
L&S Sciences

Low-level Feature Representation of Music in the Human Brain

Music is often considered a universal language, an important component of every culture. It is a complex natural stimulus, composed of a hierarchy of basic acoustic components. However, not much is known about how the human brain represents these components. This summer I will investigate the cortical representation of low-level acoustic features, such as pitch, tonality, and spectral (frequency) components. I will analyze functional magnetic resonance imaging (fMRI) data and map computational models of music to brain activity to understand the hierarchical organization of basic acoustic features in the human cortex. This summer project will hopefully be the first step towards a future in-depth study of the cortical relationship between music and other natural structural sounds, such as speech.

...Read More about Lucine Oganesian
Rose Hills

Effects of Prior Host Infection Status on New Infections

Grapevine leafroll disease (GLD) has spread to all grape-growing regions and is one of the most important viral diseases affecting grapevines worldwide. GLD has adverse effects on fruit quality and plant health, leading to significant economic losses. Grapevine leafroll associated virus 3 (GLRaV-3) is the primary causative virus involved in GLD. Given the economic importance of grapes and the consequences of GLD, it is crucial to develop efficient ways of managing this disease. Recent studies have demonstrated that abiotic conditions such as plant nutrient status, accumulation of inorganic metals, temperature, and plant water status can alter viral dynamics, increase resistance to pathogens, and confer benefit to plant hosts under stress. The goal of my research is to test the effects of nutrient availability on plant susceptibility to GLRaV-3 infections and symptom severity. My research will provide insight for novel management approaches for plant viral diseases.

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

Research Proposal for General Chemistry Lab Development

The undergraduate chemistry curricula at UC Berkeley has been undergoing a series of changes in the past years to update the experiments and increase their relevancy to students as they move on through their college careers. The main goals of this curriculum redesign are centered on creating experiments that give students an understanding and appreciation for green chemistry, and designing curricula that embodies authentic practice allowing students to experience science as it occurs outside the classroom setting and giving them insights into how research is realistically conducted. The project I am focusing on is a continuation of an experiment we designed the past year revolving around the aquatic toxicity of commonly used pesticides. The aim is to complete the lab module, currently only two experiments, with a third experiment which allows chemistry students to conduct an in vivo assay of their specific compound, giving students an insight into toxicology and […]

...Read More about Prithvi Pande
Rose Hills

Microbiological Contamination in Local Water Sources and Related Waterborne Illnesses in Rural Tanzania

The human right to water is indispensable for leading a life in human dignity. It is a prerequisite for the realization of other human rights -UN Economic and Social Council General Comment No. 15 Although the Millennium Development Goal (MDG) to reduce by half the number of people without access to improved sources of water by the year 2015 was supposedly met in 2010, about 748 million people around the world, especially in rural areas, are still without improved clean water sources. For my research project, I will be working with the non-profit African Immigrants Social and Cultural Services (AISCS) on assessing microbial contamination level in different water local sources and characterizing prevalence of related waterborne diseases such as diarrhea among the local population. The collected data and geospatial analysis will try to not only establish safer locations for drinking water precedence in the case of differential microbiological contamination level […]

...Read More about Jooyoung “Paul” Park
L&S Sciences

The Role of Bioactive Lipids in Smooth Muscle Physiology and Asthma

Asthma is caused by chronic inflammation in the lungs, which leads to inappropriate contraction of smooth muscle cells that surround the lung airways, causing them to narrow and impair breathing. Contraction of the smooth muscle occurs when the level of calcium ions inside the cells increases, and relaxation only occurs once muscle cells return to their resting state. This relaxation process is regulated by a potassium channel, the BK channel. Chronic inhibition of BK channels can result in airway muscle hyper-contraction and eventually lead to asthma. The steroid hormone, progesterone, inhibits the BK channel, and asthma is known to worsen during pregnancy or during hormone therapy, when blood progesterone levels are elevated. The purpose of this research is to determine how the BK channel is regulated by progesterone. My project will identify new pathways that regulate airway smooth muscle excitability and explain why asthma worsens with elevation of progesterone levels. […]

...Read More about Divya Patel
L&S Sciences

Myopia Growth Factor Gene Expression Regulation

Emmetropization is the process in which the eye adjusts its length based on the defocus it receives in order to achieve better clarity of vision. Ocular refractive errors such as myopia (near-sightedness) or hyperopia (far-sightedness) occur when there is a dysregulation in emmetropization, resulting in a mismatch of the eyes axial length and optical power creating blurred vision or defocus. Understanding the underlying mechanisms to this process is thus crucial to a cure for myopia which is a disease that affects hundreds of millions world-wide. Prior research in the chick-model reveals three growth factors of particular importance to the development of refractive errors. Defocus sign-dependent bidirectional regulation of Bone Morphogenetic Protein-2 (BMP2), BMP4, and BMP7 gene expressions has been demonstrated in the retinal pigment epithelium (RPE) of the eye, a layer that separates the light-sensitive retina from the eyes outer structural layers. In my study, we will use different paradigms […]

...Read More about Eileen Phan
L&S Sciences

Inductive Inferences

A defining feature of human language is its creativity; we can express an infinite number of ideas from a limited number of words. One well-analyzed source of such creativity is the rules of grammar, which let us combine words into sentences in new ways. However, we know much less about another source of creativitythe flexible use of words, known as lexical flexibility, which allows us to use one word to express multiple different meanings. For example, the word chicken can mean both an animal and meat. My research, with the final goal of a senior thesis, asks how children initially learn such flexible words, and in particular, whether they initially understand that the different meanings of these words are in fact distinct. Of critical interest is whether children will generalize facts from one meaning of a flexible word to another, distinct meaning, and whether this depends on the two meanings […]

...Read More about Patricia Pierry
Humanities and Social Science

Development of a time-based reconstruction algorithm to constrain the Spill-In/Out Effect at the Daya Bay Experiment

Neutrinos present some of the greatest mysteries within the Standard Model of Particle Physics. They are nearly massless and electrically neutral, making them very difficult to detect. That said, neutrinos have been observed to oscillate over time between their three flavors. The primary target of the Daya Bay Reactor Neutrino Experiment has been to measure the exact value of the mixing angle 13, which describes this oscillation. The Experiment, which started taking data in 2011, is based in Southeast China. The eight detectors, situated in three experimental halls, analyze antineutrinos emitted from six powerful nuclear cores. While the Daya Bay Experiment has obtained the most accurate measurements of 13 to date, there still exist sources of error. My goals this summer will be to reduce these errors by improving rate and energy spectrum measurements. I will tackle the largest outstanding source of error in the experiment, known as the spill-in/out […]

...Read More about Varun Raj
Rose Hills

Effect of Blueberries on Antioxidant Gene Expression

Obese individuals have significantly greater amount of damage in their DNA compared to lean individuals, however the consumption of blueberries has been shown to decrease that damage in obese. I will be trying to figure out the mechanism by which blueberries reduce the amount of DNA damage.

...Read More about Jay Ramsay
Rose Hills

Narration and Perspective-Taking in Children

Relatively recently there has been a surge of interest in investigating the social value of fiction. For example, some researchers claim that fiction fosters the development of perspective taking abilities by serving as social practice as the reader mentally simulates narrated events. By perspective taking abilities I mean the capacity to understand another persons thoughts, feelings, and point of view. Extending upon such research, I plan to investigate via an experimental study with young children whether or not the narrative point of view from which a story is told (i.e. first vs. third person) affects childrens perspective taking abilities. I have decided to work with children because there is strong evidence for the occurrence of a developmental shift in these abilities between the ages of 4 and 5 years, so I can determine if narration enhances these early developing abilities. I hope that this study will improve our understanding of […]

...Read More about Sari Rickansrud
Humanities and Social Science

Surface Potential Mappings on TMD P-N Junctions

P-N junctions are the basis of most modern electronicsthe foundation for the diodes and transistors that make up our computers. Current research in low dimensional transition metal dichalcogenide (TMD) heterostructures aims to make these junctions smaller. TMD p-n junctions are made of atomically thin, stacked TMD layers and have been hailed for their novel properties, diverse applications, and potential to revolutionize electronics. My research project will provide improved understanding of the performance, functionality, and limits of atomically thin, stacked TMD p-n junctions. I will use Kelvin probe force microscopy (KPFM)a powerful variant of frequency modulated atomic force microscopyto map the surface potential of a nanoscale p-n junction, which will help determine the electronic properties of the junction.

...Read More about Griffin Rodgers
L&S Sciences

Student-faculty interactions: Understanding Mexican-American Community College Students

My research project explores the role student-faculty interaction has on community college students and their goals to transfer to a four-year university. I am specifically focusing on Latina/o students who are more likely to attend community college and who are also one of the major underrepresented groups in four-year universities. This being said, however, there are also limits in homogenizing the entire group of Latina/o community college students. For this reason, I plan to look at Latina/o subgroups separately in order to get a deeper and meaningful understanding of each group and the role student-faculty interaction has in their goals to transfer to a four-year university. Over the course of my summer research I focused on three specific subgroups: Mexican-American, Guatemalan, and Salvadorian students attending Los Angeles Community College District. In the future, I plan to extend this research to include more Latina/o subgroups and more community colleges around the […]

...Read More about Giovanni Roman
Humanities and Social Science

What in the World is This? Discovering Meaning Through Situational Narrative

Imagine two hot air balloons that leave the ground at the same time. As they rise, one of them moves faster than the other and the distance between them grows as they get higher. Proportionality is everywhere in our world, as are many other mathematical concepts that we dont consider day-to-day, which teachers often refer to real-world situations in the math classroom. However, educational reformers debate whether students should begin learning concepts from abstract producers or concrete situations. The embodied cognition approach reconciles these two approaches, suggesting that we should enter a new bodily scheme and then ground this in concrete situations and abstract towards symbols. This summer, Ill work with an interactive device that facilitates visualizations of proportion and sheds light on learners conceptual understandings that originate from bodily experience. What narratives do students bring from their own experiences, and how can we use fabricated narratives to ground an […]

...Read More about Dana Rosen
Humanities and Social Science

A Data-Driven City-Scale Electricity Demand Model

As our society focuses on reducing the drivers of global climate change, a primary goal is to look at the ways in which we can generate and use electricity in a more efficient and environmentally friendly manner. These challenges require broad and complex solutions. However, in order to implement these, it is imperative that broad swaths of the population be well informed in the nuances and technical complexities of electrical power systems. That is where Griddle comes in. The brainchild of researcher Michael Cohen, Griddle is an educational game that promises to bring realistic simulations that explore the challenges of reinventing power systems to a broader population. For my research, I will be working to develop a data-driven electricity end-use model for cities based on their population, economic, land-use, and climate characteristics, among others. While the model will be used for simulation within the game, there are other practical benefits […]

...Read More about David Rothblum
Rose Hills

Protecting Paradise: The Politics of Citizenship in American Samoa

Multiple memberships are increasingly common in the universe of citizenship. American Samoans are American non-citizen nationals of the United States; that is, they are nationals but without birthright citizenship. My proposed SURF projects examines the inherent conflicts and contradictions of these overlapping memberships in light of a lawsuit, Tuaua v. United States, filed by a group of five American Samoans in 2012 who sought to obtain the full rights and privileges of U.S. citizenship. The proposed research will analyze the implications of this landmark case, as well as for the general case of overlapping citizenships. Specifically, I will compare differences in attitudes toward citizenship and its relation to political and cultural identification between the diaspora in U.S. states and the residents of the islands of Samoa. This research seeks to clarify an aspect of a developing global phenomenon of targeted exclusions, and its preconditions and effects on identity and migration […]

...Read More about Tua-Lisa Runsten
Humanities and Social Science

Unmasking the Monstrous Ontology of Seonggoe in Neoliberal South Korea

In South Korea, the global financial crisis of 2008 coincided with the upsurge in Facial Contouring Surgery (FCS) the shaving of the cheek and jaw bones into a sculpted baby face among people of all genders in their early 20s, specifically college students and graduates. Western media has reduced this boom to just another fad, but Western influences on young Koreans aesthetic choices are insufficient to explain this. Consumers who benefit from these procedures project on their faces a selective yet homogenous narrative identity that best suits the demands of todays competitive, neoliberal(ized) job market. I depersonalize the face as an emblem of a persons individuality, and analyze it as the aesthetic externalization of the emerging intersubjective temporality and affect that derives from the rapidly polarizing class topography. The waning possibility of class mobility is attributable to the erosion or anachronism of traditional temporality, as signified by the alarmingly low […]

...Read More about Jinoh Ryu
Humanities and Social Science

Breast Cancer, Bodies, and Boundaries: Queering Solutions for Equitable Healthcare

My mother once told me: I tell doctors that my partner is my sister so she can be present during my appointments and hospitalization without prejudice. My mom, who identifies as an LGBT individual, was diagnosed with breast cancer when I was a first year at UC Berkeley. Although the LGBTIQA communities are diverse and represent a wide range of identities, the discrimination and stigma surrounding these social and gendered minorities is common, including in healthcare. In the US context, discrimination and ignorance by health professionals create disparities in LGBTIQA health where health care, access, and needs are denied. Breast cancer is prevalent among the LGBTIQA communities, and there are many factors that have influence on why this community is often left untreated or receives poor health care. Little data is available on breast cancer in the LGBTIQA communities: my research seeks to develop solutions for better healthcare by exploring […]

...Read More about Courtney Sarkin
Rose Hills

The Structural Basis of Cbl Specificity

The protein Cbl is a key component of receptor tyrosine kinase transduction, acting both as an E3 ligase and as an adaptor in the ubiquitination pathway. In fact, overexpression of Cbl has been found to inhibit tumor growth; therefore, understanding Cbls specificity will be key to the development of relevant therapeutic drugs. Interestingly, Cbl is known to ubiquitylate over one dozen targets, and its specificity for tyrosine kinases is achieved by its unique activation mechanism. Recent work has found that Cbl recognizes multiple lysine residues from the same substrate and certain lysines appear to be targeted for ubiquitination. However, no mechanism has been developed to explain how this occurs. This summer, I will be investigating the molecular basis of the selectivity of Cbl on protein tyrosine kinases. To address this question, I will use structural biology and biochemistry; specifically, I will express and purify various versions of Cbl substrates, perform […]

...Read More about Lochan Shah
Rose Hills

Peroxide and Persulfate in ISCO

In Situ Chemical Oxidation – A Close Look at Peroxide and Persulfate Benzene is an organic compound that causes birth defects, cancer, a decrease in red blood cells and many other health impediments upon inhalation. Benzene is just one of many toxic chemicals flowing through our groundwater. Pumping out contaminated water to treat harmful chemicals is ineffective because it is too inefficient and slow, which is why in situ chemical oxidation (ISCO) is necessary. ISCO degrades harmful compounds in the soil, removing both the cost of pumping and injecting groundwater as well as the ecological impact of injecting wells and removing large quantities of water. There is a gap in knowledge surrounding ISCO regarding persulfate and peroxide, which are oxidants that are currently used by industry in ISCO. My research objective is to demonstrate how these two oxidants will trigger each other and become reactive intermediates, which then oxidize contaminants. […]

...Read More about Ila Shimabuku
Rose Hills

An Adiabatic Demagnetization Refrigerator

The cosmic microwave background (CMB) is ancient light radiation emitted during initial expansion of the universe. Theorists believe that gravity waves (like light waves, but related to gravity rather than to electricity) bounced around in the early universe and left measurable imprints on the CMB. Searching the CMB for these imprints can be done with a technique called bolometry, which works by measuring the heat that photons transfer to a superconducting wire. Because radiation background noise from instruments drops at low temperatures, colder bolometry equipment gives more precise results. Our lab, the Experimental Cosmology Group, manufactures bolometer arrays for several different CMB measurement experiments, and as such we need a variety of very powerful refrigerators in order to test and develop the next generation of bolometers. To further this end I will be constructing a new refrigeration system which will use a pulse tube refrigerator, a helium10 refrigerator, and a […]

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Rose Hills

Towards Understanding the Hierarchical Organization of Mirror Neurons in humans: An Electrocorticography Study

One of the most intriguing, yet controversial recent findings in neuroscience is the discovery of the mirror neuron system (MNS). These visuo-motor neurons discharge both when a monkey does a particular goal-directed action and when it observes another individual doing a similar action. The result of this mechanism is thought to be the capacity to recognize that an individual is performing an action, to differentiate this action from others analogous to it, and to use this information in order to act appropriately. This mechanism has been proposed as the basis for social cognition. Additionally, deficits in social understanding, such as those seen in autism spectrum disorder have been linked to deficits in the MNS. In this project I will utilize the temporal and spatial advantages of Electrocorticography (ECoG) in neurosurgical patients, to assess, for the first time, whether the MNS can be differentiated into subpopulations, which are tuned to different […]

...Read More about Jeni Stiso
L&S Sciences

Effects of catalyst supports on hydrogenation kinetics of 2,5-dimethylfuran

There is a growing need for the development of a clean, sustainable energy supply from renewable sources. Among the many options currently under investigation, a promising route involves the conversion of plant-based biomass into biofuels. In order for this process to be viable at an industrial scale, one of the steps that must be optimized is the conversion of biomass-derived chemicals into products that can be used as additives to existing fuels such as gasoline or diesel. In particular, the optimization of the hydrodeoxygenation of intermediate platform molecules is crucial in efficiently generating a product with high energy content that can be easily mixed with existing fuels and effectively incorporated into the worldwide fuels supply. My research project will focus on investigating the kinetics of the hydrodeoxygenation reaction by determining the effect of reaction conditions and different heterogeneous catalyst systems on the hydrodeoxygenation of model compounds in order to better […]

...Read More about Joseph Tang
Rose Hills

Spectroscopic Analysis of Surfaces for Quantum Information Processing with Trapped Ions

One of the most promising ways to create a universal quantum computer is using trapped ions. We confine ions in electromagnetic fields and store quantum information in them by addressing their internal and motional states with lasers. However, electric field noise emanating from the surface causes anomalous heating in these ions, creating noise which impedes quantum processing. One possible source of this is hydrocarbon contamination on the surface. My research will focus on identifying and characterizing the molecular structure of the contamination by probing its molecular bonds using a Fourier Transform Infrared (FTIR) spectroscopic analysis supported by grazing angle polarization modulation (PM) to boost sensitivity, a method which has never been done for this purpose. My research will contribute towards mitigating the unwanted ion motion. Particularly, I will progress the development of a quantum computing platform that will be capable of performing algorithms with reduced rates of decoherence. Furthermore, my […]

...Read More about William Tokumaru
Rose Hills

The Pendulum of Opinion: Union Membership Effects on Confidence in Labor, 1975-2014

Research on the decline of organized labor has tended to focus on the decreasing rates of union membership in the national or international context, while ignoring public support for organized labor. Those social scientists who have focused on union support, on the other hand, have not included union membership in their analyses. I will synthesize these two perspectives on de-unionization by analyzing 42 years of data from the General Social Survey that include measurements of both union membership status and support for organized labor. The 29 General Social Surveys conducted between 1972 and 2014 provide nationally representative, repeated cross-sectional survey data. Using these data, I will conduct a statistical analysis of confidence in labor as a function of union membership while controlling for age, political affiliation, race, region of residence, sex, and social class. Integrating union support and union membership may allow for a more complete understanding of the future […]

...Read More about John Towey
Humanities and Social Science

Deciphering Spaces: The Mermaid and the Soul

The mermaid has been symbolic of desire and danger, beauty and monstrosity, and the human and non-human. Residing in the constant flux of paradoxes, the mermaid remains a beautiful enigma to all that encounter her. She is perceived at a distance, yet remains within close proximity because she is our reflection. As a reflection of the self, the mermaid is a product of the human imagination, reconfigured and transformed to articulate our personal reality. There is more to the mermaid that promises truth, and I hypothesize the truth is in the mermaid being a projection of the human soul. To test my hypothesis, I intend to psychoanalyze various literary texts, focusing on the figure of the mermaid and her interactions with mankind by linking the following: the symbolic depictions between land and sea, how these symbolic depictions of space attribute themselves to gender representations, and ultimately to articulate gendered spatial […]

...Read More about Leah Tyus
Humanities and Social Science

Lithic and Spatial Analysis of Kharaneh IV

I will be analyzing/making sense of a collection (~30,000 pieces) of lithic materials from a 20,000 year old archaeological site in the Azraq Basin of Jordan. I will then put all the information obtained from the lithic remains into a GIS and run various statistical and spatial analysis, which will allow me to quantify my results and help understand the structure of the site through time and space.

...Read More about Joshua Varkel
Humanities and Social Science

Investigating the Interaction Between RIP1 and RIP3 in T cell Necroptosis

Necroptosis, a regulated form of necrotic (inflammatory) cell death, has been shown to naturally occur in activated T-cells, a type of white blood cell crucial in cell-mediated immunity. Presently, the death domain- containing kinase protein RIP1 is suggested to recruit the key necrotic regulator protein RIP3 to form a necrosome, a protein complex, and induce necroptosis under certain conditions in T cells; however, exactly how these two proteins interact with each other to mediate between the two cell death types, necroptosis and apoptosis, is not well understood. The molecular pathways of necroptosis and their roles in T cell homeostasis are also not well defined. Through a tagged RIP3 construct, I will investigate the interaction between RIP1 and RIP3, as well as their possible interactions with other death promoting proteins, by isolating and studying the necrosome after T cell activation and treatment. Elucidating the interaction between RIP1 and RIP3 during necrosome […]

...Read More about Winnie Yao
L&S Sciences

Survey of Gestational Diabetes Mellitus and Pregnant Women in Mysore, India

Gestational Diabetes Mellitus (GDM) is a condition of glucose intolerance onset during pregnancy, and is associated with increased risk of complications during pregnancy and increased likelihood of bearing overweight infants. Worldwide GDM affects approximately 4% of women, and studies suggest that GDM may be more common in Indian women. Early screening and treatment of women with mild GDM has been shown to reduce the likelihood of complications during pregnancy and prevent the onset of type-2 diabetes. Given the growing public health concern of GDM and type 2 diabetes in India, there is a pressing need to find a simple and feasible test for GDM. Relaxin is an insulin homologue produced in pregnant women, and has been demonstrated to be significantly higher in diabetic women compared to their normal counterparts, indicating that relaxin could provide a convenient marker for GDM. This project aims to determine whether elevated plasma levels of relaxin […]

...Read More about Annie Yau
Rose Hills

Causal Role of the dmPFC in Goal-Directed Behavior

The prefrontal cortex (PFC) plays an important part in purposeful, goal-directed behavior through the representation and maintenance of internal goals. In particular, the PFC has been implicated in post-error correction, an important aspect of adaptive cognitive control whereby animals perform better immediately after punishment than after reward. However, the contributions of the PFC to this phenomenon on a trial-by-trial basis are still unclear. Our hypotheses are that the PFC affects overall performance because of its contribution to stimulus-based decision-making and that outcome responses in the PFC underlie the phenomenon of post-error correction. My project will use optogenetics to test whether PFC activity underlies individual components of goal-directed behavior, and our results will be an important contribution to understanding the functions of the PFC.

...Read More about Michelle Zhang
Rose Hills