Characterization of Optical Pumping of Ti Beam into a Metastable State

Laser cooling and trapping consists of using lights momentum to slow down and eventually confine atoms to small regions of space using light and magnetic fields. These techniques have been demonstrated with many elements in the periodic table, yet most transition metals are still to be addressed. A current effort in the Stamper-Kurn group seeks to implement laser cooling on titanium, eventually trapping and cooling it to quantum degeneracy. Cooling titanium requires that atoms exist in the a5F5 metastable state, an atomic internal state with energy higher than the ground state but with a relatively long lifetime compared to an excited state. One method of creating metastable titanium atoms is by optically pumping titanium from the ground state a3F4 to the y5G5 excited states where atoms can decay to the metastable state. My project focuses on characterizing the efficiency of such method of optical pumping using 379 nm and 844 […]

...Read More about Diego A Pea
L&S Sciences

Investigating the Mechanism of NLRP1 Inflammasome Activation by Dengue Virus Protease

Dengue virus (DENV) is the leading cause of death in dengue-endemic areas. An infection resulting from DENV can manifest as serious human disease, such as Dengue hemorrhagic fever or Dengue shock syndrome. Currently there is no effective vaccine to prevent the infection. My project seeks to understand critical host-virus interactions between DENV and multi-protein innate immune cytosolic complexes called inflammasomes, which initiate downstream proinflammatory signaling. Inflammasomes are typically thought to detect pathogen-encoded ligands. In contrast, NLRP1the focus of this proposaldetects protease activity. I will be focusing on the molecular determinants of human NLRP1 sensing of the DENV NS2B3 protease, and how this recognition event leads to inflammasome activation. A full understanding of the molecular events leading to DENV-mediated activation of the NLRP1 inflammasome is crucial to developing improved mouse models to study host immunity and pathogenesis in the setting of in vivo DENV infection.

...Read More about Rimjhim Agarwal
L&S Sciences

Identifying the Causal Genetic Basis of an Adaptive Trait in Two Diverged Yeast Species through a Novel Mapping Approach (RH-seq)

Finding the causal genetic basis of a complex trait is a challenge of biology. Current methods, such as GWAS and QTL analysis, can identify associations between variants and phenotypes, but this is limited to analysis within the species being investigated and not species-wide traits. Through a novel approach named RH-seq (reciprocal hemizygosity analysis via sequencing), causal variants that underlie interspecific differences can be identified, including those that are the basis of adaptive evolutionary changes. I will be investigating the genetic basis of the relative thermotolerance of Saccharomyces cerevisiae (budding yeast) compared to Saccharomyces paradoxus, two related yeast species that are roughly 20 million years diverged. At 39C, S. cerevisiae grows to a significantly higher density than S. paradoxus. Eight candidate genes have been previously identified through RH-seq performed at 39C. When these candidate S. cerevisiae variants are transformed into the pure S. paradoxus background, the transformants exhibit a small, but […]

...Read More about Faisal AlZaben
Rose Hills

Investigating Root-Multiplicities of Kac-Moody Algebras

Over the summer, we propose to investigate the root multiplicities of (generalized) Kac-Moody Algebras. Our plan is to create an open-source computer package that allows for the computation of root multiplicities of Kac-Moody algebras, building upon the existing tools available to computational mathematicians, for instance, the popular library sage-math. Once we have developed and verified this package against known tables of root multiplicities, we aim to start investigating the root multiplicities of simple graphs, and attempt to address some outstanding conjectures on the distributions of root multiplicities. A greater understanding of the root multiplicities of Kac-Moody algebras would help with questions such as finding natural geometrical realizations of the algebras, and shed light on the connections that have already been found with mathematical physics. Some of these applications may include generalised knot invariants defined over Kac-Moody algebras rather than Lie Algebras, or the study of symmetries of systems and spaces […]

...Read More about Aidan Backus
L&S Sciences

Investigating the Functional Crosstalk Between the Crucial Epigenetic Silencers PRC1 and PRC2

In mammals, the Polycomb Repressive Complexes 1 and 2 (PRC1, PRC2) play crucial roles in maintaining gene expression patterns that enforce cell differentiation during embryonic development. Both complexes silence genes by post-translationally modifying the histone tails of nucleosomes, the smallest structural unit of chromatin. PRC1 plays a role in chromatin compaction by histone ubiquitination, whereas PRC2 reduces expression at the transcriptional level by histone methylation. The importance of these two complexes is emphasized by the fact that mutations in either complex results in embryonic lethality. While PRC1 and PRC2 are essential in maintaining cell identity, the molecular mechanism of PRC1-mediated chromatin compaction and the spreading of silencing marks by PRC2 remains poorly understood. Using cryo-electron microscopy and a novel technique to prevent the denaturation of sensitive protein complexes, we will directly image PRC2-nucleosome interactions to investigate the mechanisms underlying the recognition of specific histone ubiquitination by PRC2 and how it […]

...Read More about Curtis Beck
Rose Hills

Actuating a Spherical Tensegrity Robot using Momentum Wheels

Traditional robots are often ineffective in environments with rough and uncharted terrain. For this reason, robots are underutilized for applications like disaster relief, HazMat, CBRNE (chemical, biological, radiological, nuclear, and explosive) response, and space exploration. The Berkeley Emergent Space Tensegrity (BEST) Lab is developing a tensegrity soft robot, designed to travel over rough terrain after surviving large impacts. The BEST lab robot would be deployed by aerial vehicle, then traverse the unknown area, sending back sensor data and arming first responders with previously inaccessible information. The existing robot moves via shape shifting, and can either sustain a 200m drop or move – not both. I propose a locomotion scheme using momentum wheels instead of shape shifting to address this gap in functionality. My goal is to develop a prototype capable of locomotion after sustaining a 10m drop by the end of summer. My prototype would address this problem, and mark […]

...Read More about Antonia Bronars
Rose Hills

Developing of Reductive Loop Design Principles for Polyketide Synthases

The consumption of petroleum-based gasoline, diesel, and jet fuel continues to affect greenhouse gas emissions and air pollution. Alternative fuel sources are needed, and recent breakthroughs in synthetic biology provide a promising solution: the engineering of microorganisms to generate drop-in biofuels, which are compatible with existing engines. Unlike electricity and natural gas alternatives, biofuels reduce greenhouse gas emissions by recycling the carbon dioxide that is emitted. However, biofuel derived directly from crops or oils may threaten land and/or food security. Thus, this project focuses on expanding the diversity of biofuels by engineering polyketide synthases (PKSs), or complex enzymes found in microorganisms, to generate molecules that can function as drop-in biofuels. We specifically aim to develop the design principles for such PKS engineering by producing fully reduced acids from PKSs that would normally produce hydroxy acids. Not only will this technology assist in developing an accessible, environmentally-friendly fuel alternative, but these […]

...Read More about Sami Chang
Rose Hills

Amino Acid Sensing In The TOR Pathway Of Plants

The presence of nutrients such as amino acids, glucose, or nitrogen and varying growth factors is hypothesized to activate the target of rapamycin (TOR) which initiates eukaryotic cell growth, development, and metabolism. Although TOR is extremely significant to plant cells growth and metabolism, little is still understood about TOR signaling within plants. As such, my project proposal investigates Asparaginyl tRNA synthetase 1 (NRS1) and its likelihood as an amino acid sensor that can stimulate TOR pathways and its importance for plant development. Comprehending how plants can sense the presence of amino acids and then activate TOR is central to breeding crops that are not as affected by nitrogen deficiencies in soil and can survive, despite lacking nutrients or poor growth factors. With the results of my research project, further research can be done to possibly confirm the importance of NRS1 in the promotion of TOR activity and establish and define […]

...Read More about Cindy Chau
Rose Hills

Optimization of CRISPR-Cas9 using an Adeno-Associated Virus (AAV) Delivered Self-Inactivation System

CRISPR-Cas9 is a versatile genome-editing technology that is widely used to modify genome sequences linked to genetic abnormalities. Often, the CRISPR-Cas9 system is used to target or repair disease-causing versions of genes, delete fragments of unwanted DNA, and insert therapeutic gene sequences to treat diseases. However, many studies have shown that CRISPR-Cas9 can cause unexpected mutations and genomic rearrangements in untargeted sites. My research aims to develop a self-inactivation system in effort to limit long-term expression of nuclease-editing protein Cas9 while still maximizing its on-target cuts and reducing off-target effects. To effectively deliver the Cas9-sgRNA complex, I plan to use adeno-associated virus (AAV) due to its highly efficient, targeted gene delivery. In addition, I plan to modulate the kinetics of Cas9 targeting the single-guide RNA to gain better control of Cas9 activity for potential in vivo applications. The goal of this work is to improve current CRISPR-Cas9 applications in not […]

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

Investigating the Regulation of Atg40 Expression During Meiosis

Autophagy is a process of self-eating by which the cell targets specific cargo for degradation. While autophagy was initially believed to primarily be a response to stress or starvation, it is now known that it also plays important roles in cellular homeostasis and organismal development. This process can happen either non-selectively, where cargo is degraded randomly in bulk, or selectively, where degradation of a specific cargo, such as a protein aggregate, organelle, or pathogen, is specified by an autophagy receptor. In budding yeast, selective autophagy of the endoplasmic reticulum is mediated in part by the autophagy receptor Atg40. The work of my lab so far suggests that Atg40 expression is highly regulated, but it remains unknown what factors are controlling its expression. I aim to define the cis- and trans-acting factors required for Atg40 expression in meiosis. Identifying these regulatory factors will shed light on how dramatic changes in cell […]

...Read More about Tia Cheunkarndee
L&S Sciences

Comparative Dual RNA-Seq Transcriptome Profiling of Host-Pathogen Interactions During Chlamydia Trachomatis Infection of Human Primary Endocervical Cells

Microbes pose a wide spectrum of nonpathogenic and pathogenic challenges for the immune system. The encounters are governed by the interactions between the bacteriums adaptations and the hosts ability to mount a protective immune response. Chlamydia trachomatis (Ct) is an especially unique pathogen as the infections it causes in the genital tract are typically asymptomatic. While this suggests that Ct possesses an effective set of tools to cloak itself as a lesser threat to the immune system, these tools still vary in success, as Ct strains elicit different immune responses depending on the cell type the bacterium infects. Hence, I propose to use a new technology called dual RNA-seq to analyze how human primary cells from patients vary in their response to infection with Ct and determine factors that distinguish successful immune responses from unsuccessful ones. Overall, by tracking Ct and host genes simultaneously, this data could lead to preventative […]

...Read More about Siddharth Chittaranjan
L&S Sciences

Uncovering the Physical Properties of Fingerprint Treads Under Dynamic Wet Conditions

This summer, I will be looking into the natural phenomenon of wet-induced fingertip wrinkling and the possible dynamic benefits which could come with implementing and mimicking its main properties in a mechanical system. Similar to how tire treads can improve a cars efficiency and safety on the road during heavy precipitation and how shoe treads help prevent slips, the organic wrinkling found in water-saturated human fingertips can possibly provide analogous effects for a persons grip success with wet objects or underwater scenarios. However, this possible connection has barely been addressed by engineers and doctors, as any type of effective wrinkling pattern is absent in current models of hand prostheses and less than five research papers address the influence of fingertip wrinkling on the mechanics of grasping.Through a systematic series of friction and shear force testing, I hope to gather enough data to determine a set of design guidelines for robotic […]

...Read More about Ethan Chung
Rose Hills

Investigating Root-Multiplicities of Kac-Moody Algebras

Over the summer, we propose to investigate the root multiplicities of (generalized) Kac-Moody Algebras. Our plan is to create an open-source computer package that allows for the computation of root multiplicities of Kac-Moody algebras, building upon the existing tools available to computational mathematicians, for instance, the popular library sage-math. Once we have developed and verified this package against known tables of root multiplicities, we aim to start investigating the root multiplicities of simple graphs, and attempt to address some outstanding conjectures on the distributions of root multiplicities. A greater understanding of the root multiplicities of Kac-Moody algebras would help with questions such as finding natural geometrical realizations of the algebras, and shed light on the connections that have already been found with mathematical physics. Some of these applications may include generalised knot invariants defined over Kac-Moody algebras rather than Lie Algebras, or the study of symmetries of systems and spaces […]

...Read More about Peter Connick
L&S Sciences

The Particular Language of Shahan Shahnour

My research will serve as an inquiry into the particular language of the prosaic and poetic works of Armenian-French writer Shahan Shahnour, nom de plume Armen Lubin. Shahnour was a part of the Menk generation (so named after the Armenian word for “We”), a literary group of Armenian migrs living in Paris in the 1920’s, having survived the Armenian Genocide and fled the Ottoman Empire. Within the frame of exile and mourning a lost homeland, Shahnour’s novel in Armenian and Lubin’s later poems in French illuminate a unique language space that can be linked to French philosophers Gilles Deleuze and Flix Guattari’s notion of a “littrature mineure.” Shahnour’s particular language parallels a symbolic third territory in which the writer finds himself displaced from both the country of origin and the country of residence. The creation of this conceptual in-between space operates on a technical level through unique syntactic constructions and […]

...Read More about Hannah Cox
Humanities and Social Science

I Regret To Inform You That Your Private Information Has Been Compromised

Privacy is one of the central issues of our time. All things being equal, we assume that most people prefer privacy; it is a foundational right enshrined in the penumbras of the 1st, 3rd, 4th, 5th, 9th, and 14th amendments of the U.S. constitution as well as in several state constitutions (including those of California, Massachusetts, and Washington) and the Universal Declaration of Human Rights. Despite our appreciation of privacy, police officers wear body cameras, customer loyalty programs track purchases, and the Transportation Safety Administration performs full body scans. This paradox illuminates the deep ambivalence in modern American society about privacy, and a largely untapped area of research in sociology. This research seeks to understand the deeper cultural logics inherent in shifting views on privacy in the modern world as well as the evolution of its meaning historically in the U.S. context.

...Read More about Savannah Cragin
SURF SMART

Numerical Simulation of the Ejecta Velocity Distribution of Type Ia Supernovae

Type Ia supernovae (SNe Ia) are generally thought to be the thermonuclear disruption of a carbon-oxygen white-dwarf star, but their formation scenarios and exact progenitor systems are still ambiguous. SNe Ia are used as standardizable candles used for measuring distances in the universe. Famously, SNe Ia are being used to determine the acceleration at which the universe is expanding (i.e., Hubble constant). Knowing more about the formation and progenitor of SNe Ia may help correct some assumptions made when using SNe Ia to measure distances. The photospheric velocity of SNe Ia measured from the strong Si II 6355 absorption line in their spectrum at the time of peak brightness is one such parameter useful to study various properties of SNe Ia. Recent studies reveal that the distribution of SN Ia velocity does not originate from a uniform class. I will be exploring the plausibility of the theory that the non-uniformity […]

...Read More about Keto, De Zhang
L&S Sciences

Exploring Mechanisms Behind the Oxygen Dependence of Listeria Monocytogenes Intracellular Replication

Listeria monocytogenes is a pathogen often found in poorly preserved food , especially dairy products. L. monocytogenes can survive with or without oxygen as well as inside or outside of host cells. During infection, L. monocytogenes must pass through the low-oxygen environment in the intestines before entering the high-oxygen target tissue. It thus stands to reason that both aerobic and anaerobic growth processes might be important for L. monocytogenes pathogenesis. Recently, it has been shown that essential components of aerobic respiration are critical for intracellular replication in vivo. However, the specific role of aerobic respiration within host cells remains unclear. Here, I propose conducting three experiments about the role of aerobic respiration in L. monocytogenes pathogenesis. I will use both forward and reverse genetic approaches, for which I will both analyze pathogenic phenotypes from gene functions and vice versa. Such bidirectional approaches allow me to probe for possible roles of […]

...Read More about Davy Deng
L&S Sciences

Probing Unknown Proteins from a Unique Genetic Island in Vibrio Cholerae

The current treatment for cholera infection is hydration with sanitary water and salts to replenish the nutrients and water lost through diarrhea. The World Health Organization estimates that 120,000 people die each year from cholera infection alone, with the majority of deaths in developing countries which have neither the infrastructure nor resources to treat patients. Current vaccines are ineffective; therefore, researchers are turning to alternative ways to stop the spread of cholera. While trying to understand a unique genetic island that Vibrio Cholerae uses to protect itself from viral infection, we found two genes. The first was named TafA and is a seemingly harsh toxin for both the infected cell and neighboring V. Cholera around it. TafB, the second gene, when co-expressed with TafA seems to detoxify TafA in an unknown mechanism. In my project, I will work to purify these proteins and analyze them to see how they interact […]

...Read More about Peter DePaola IV
Rose Hills

Modeling and Testing of Eco-friendly Piezoelectret Sensor for Anthropocentric Pressure Measurements

The ability to measure vibrations is a vital engineering problem. From measuring pulse for health diagnostics to sensing pressure on a touch screen for a smart phone, the applications vary far and wide. In our group we study the use of polymer-based devices called piezoelectrets to measure pressure signals for a variety of applications. Our microfabricated polymer approach yields superior flexibility, piezoelectric coefficients, and costeffectiveness when compared to traditional ceramic material competitors. The devices themselves also vary in material composition and geometry depending on the application. In this project we explore the potential of using environmentally friendly materials for the fabrication of a piezoelectret pressure sensor without compromising performance.

...Read More about Danielle Diaz
SURF SMART

Breaking the Stereotype Ceiling: A Study on Stereotype-Inconsistent People

Humans are cognitively cheap. To preserve precious cognitive resources, we take cognitive shortcuts, one example being the detrimental use of stereotypes. Simply, we prefer to mentally process information about people when that information is consistent with our stereotypes about them. So what happens when someones identity contradicts the stereotypes that society has about them? Because relations between Black and White communities remains one of the most problematic racial issues in America, I have narrowed my research question to focus on this inter-group context. I hypothesize that White Americans prefer to interact with stereotype-consistent vs. stereotype-inconsistent Black Americans. Further, I propose that perceived authenticity is a critical variable that will mediate the proposed hypothesis. I predict I will find multi-methodological evidence of this effect across self-reported liking, salivary cortisol, attributions of trust, nonverbal behavior coded from videotapes, and cognitive impairment measured with a cognitive reaction time measure. This project will help […]

...Read More about Zoe Elina Ferguson
Humanities and Social Science