Genetic Analysis of Evolved Tooth Gain in Sticklebacks

Understanding the genetic mechanisms that underlie morphological evolution is a long-standing goal in biology. The threespine stickleback (Gasterosteus aculeatus) is an emerging model organism with features ideal for studying the molecular basis of morphological evolution. Several stickleback populations display evolved differences in tooth number, likely adaptive to match different diets. These differences in tooth number are largely controlled by a Quantitative Trait Locus (QTL), a genomic region controlling a quantitative trait. This QTL is located on chromosome 21 and contains an excellent candidate gene: Bone Morphogenetic Protein 6 (Bmp6). I will use two approaches to test the hypothesis that Bmp6 underlies the chromosome 21 tooth QTL. First, I will use a reverse genetics approach with TALENs (TAL Effector Nucleases) to generate loss-of-function Bmp6 alleles to assess the role of Bmp6 in tooth patterning. Second, I will use a forward genetic approach of recombinant mapping to further fine-map the tooth QTL.

...Read More about Rachel Agoglia
L&S Sciences

Unsupervised Feature Learning for Object Recognition

My research this summer focuses on object recognition for robotics. The goal is to have a robot be able to look at several objects and be able to not only identify each object, but also figure out how each is positioned. I will apply deep learning algorithms that have proven useful in other vision tasks to this problem.

...Read More about Pedro Amaral
Rose Hills

Improving Sintered Cadmium Telluride Nanocrystals Films for Photovoltaics by Controlled Halide Surface Chemistry

Cadmium Telluride (CdTe) is an alternative semiconductor to silicon for photovoltaic applications. Its advantageous physical properties allow it to absorb an equal amount of light with a fraction of silicons thickness; this means lower material costs. However, lack of fundamental research renders this material less efficient than silicon. Recent attempts at reducing manufacturing costs of CdTe solar cells investigate solution deposited nanocrystal (NC) films, i.e.semiconductor ink. During solar cell fabrication, CdTe films must be exposed to CdCl2 and heated to improve device performance. My research will investigate the effect of CdCl2 on heated CdTe NCs films. I will first synthesize solution-stable CdTe NCs (i.e. ink), then modify the NC surface with CdCl2. Next, I will fabricate CdTe layers by heating solution-deposited CdTe NCs and evaluate the films electrical and optical properties. Ultimately, I strive to discover which deposition and CdCl2 parameters lead to the best film performances for solar cells.

...Read More about Rami Ariss
Rose Hills

The Role of Nonhematopoietic Cells in Tuning Natural Killer Cell Responsiveness

In the Raulet lab, we are interested in studying the ability of a subset of innate lymphocytes called Natural Killer (NK) cells to respond to stimulation (responsiveness). NK cell responsiveness mainly depends on their ability to engage with a family of proteins called Major Histocompatability Complex Class I (MHC-I) molecules commonly expressed throughout the body. However, whether a particular cell type is responsible for setting the levels of NK cell responsiveness is still outstanding. During the summer, I will develop part of a bigger project aimed in identifying the cellular component important for tuning the responsiveness of NK cells particularly focusing on the role of MHC-I on non-hematopoietic cells (nHCs). Once we establish the cellular type involved in tuning NK cell responsiveness, we could be able to modulate NK responsiveness towards hyper- and hypo-responsivity, to be applied in cancer therapies or for the improvement of graft rejection.

...Read More about Camillia Azimi
Rose Hills

Designing and Implementing a Compact, Low Power Capacitively Coupled Contactless Conductivity Detector for Use in a Point of Care Diagnostic Device Coupled with a Microfluidic Chip

Quantitative portable medical diagnostics devices have the potential to transform medicine by providing a range of analytics that cannot be provided by classical binary readout assays. We are developing a next-generation portable clinical diagnostic device with low-power consumption that produces digitized data. To accomplish this we will utilize a detection method called, capacitively coupled contactless conductivity detection (C4D), with microfluidic electrophoresis for detection in a low-power compact cheap plastic microchip. C4D directly detects ions using two external electrodes via capacitive coupling between the electrode and the solution in the microchannel. By passing a high frequency sinusoid through one electrode and picking up the signal with a second electrode, the conductivity of the solution between the electrodes is monitored and the presence of specific ions can be determined. This detection method will be optimized for detecting biomarkers associated with diseases critical to humanitarian efforts, such as HIV and malaria.

...Read More about Cameron Baradar
Rose Hills

Role of the Medial Prefrontal Cortex in Learning and Memory: Integrating Antagonistic Effects of Reward Signals

Cadmium Telluride (CdTe) is an alternative semiconductor to silicon for photovoltaic applications. Its advantageous physical properties allow it to absorb an equal amount of light with a fraction of silicons thickness; this means lower material costs. However, lack of fundamental research renders this material less efficient than silicon. Recent attempts at reducing manufacturing costs of CdTe solar cells investigate solution deposited nanocrystal (NC) films, i.e.semiconductor ink. During solar cell fabrication, CdTe films must be exposed to CdCl2 and heated to improve device performance. My research will investigate the effect of CdCl2 on heated CdTe NCs films. I will first synthesize solution-stable CdTe NCs (i.e. ink), then modify the NC surface with CdCl2. Next, I will fabricate CdTe layers by heating solution-deposited CdTe NCs and evaluate the films electrical and optical properties. Ultimately, I strive to discover which deposition and CdCl2 parameters lead to the best film performances for solar cells.

...Read More about Nadir Bilici
Rose Hills

Martyrdom Imagery in the Church of Santi Nereo e Achillo: Establishing the Lineage of Catholic Iconography through Theatrical Arrangement

The reassertion of Catholicism’s essential principles after the Council of Trent had a major impact on religious art production in 16th century Italy. Consciously putting together reliques from the early years of Christianity with Rinascimento painting techniques, the new visual programs created within Roman churches became the place where sacred space and ideas could be rebuilt, generating a new meaning for the Catholic community. I will travel to Rome to investigate the emergence of the discipline of Archaeology as the crucial event that allowed early Christian antiquities discovered in the Catacombs to be reinvested in churches during the Counter-Reformation. My research will focus mainly on the modest basilica of Santi Nereo e Achillo where infamous scenes of Christian martyrdom are believed to have been composed by Renaissance painter Pomarancio to understand how this gruesome imagery participated in the establishment of the Roman Catholic Church’s claims for historical legitimacy.

...Read More about Mathilde Bonvalot
Humanities and Social Science

Study of the over-expression of Thioredoxin h in Sorghum bicolor and its effects on seed protein digestibility

Sorghum is an important staple crop in the semi-arid tropics of Asia and Africa as it feeds millions of the poorest people in these regions. It provides some degree of nutritional content for humans, but is considered an inferior grain because of its significantly lowered protein digestion. Since sorghum is being consumed in populations where undernourishment is of concern, it is extremely important to consider the accessibility of its nutritional content.

...Read More about Stephanie Byun
L&S Sciences

Exploring the Helicase Domain of Dicer

My primary work revolves around a eukaryotic pathway known as RNA interference (RNAi) where small RNA molecules regulate gene expression. As the main enzyme responsible for generating these small RNAs, Dicer measures and cleaves a diverse population of RNA molecules into mature fragments primed to control genes. The two main substrates are hairpin RNAswhich are cut into microRNAs (miRNAs)and long duplex RNAswhich are cut into small interfering RNAs (siRNAs). Although many studies have analyzed Dicers ability to cleave RNA, there are still many unanswered questions about how Dicer selects its RNA substrates, which can lead to large changes into which genes are eventually regulated. Dicer is a large protein composed of many distinct parts. One elusive part of the protein is the helicase domain, which is involved in the processing of specific RNA substrates. My research aims to examine how the Dicers helicase domain recognizes the RNA substrates to influence […]

...Read More about Jessica Chan
Rose Hills

Characterizing the Tumor Suppressive Functions of MIR-449 miRNAs in the E-myc B Cell Lymphoma Mouse Model

Cancer is a potent disease that occurs when cells acquire certain mutations that cause uncontrollable cell growth. MicroRNAs (miRNAs) are small non-coding RNAs that have been associated in cancer development. In our research, we specifically study the tumor suppressive effects of miRNAs on B cell lymphoma, a type of blood cancer in the lymph nodes. We have determined that the deletion of mir-34a or mir-34bc (tumor suppressive miRNAs) accelerate lyphomagenesis. More recently, it has been shown that there is a homologous cluster of miRNAs, the mir-449 family, suggesting similar functions. While the ultimate goal is to understand how these miRNA clusters interact and collectively act in a tumor suppressive role, I aim to understand the effects of losing the mir-449 cluster alone on lymphomagensis. I propose to determine the extent of acceleration of lymphomagenesis due to the loss of mir-449, and whether this acceleration is through proliferation or cell death.

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

The Mechanism of Nor-1 Mitochondrial Translocation during Thymocyte Negative Selection

Nor-1 is a protein that can promote death of CD4+ CD8+ double positive thymocytes, cells in the process of maturing into T cells. In the thymus, these double positive thymocytes undergo a process called negative selection, in which any thymocytes that recognize self-molecules that our own body produces are killed. This makes sure that our body mounts an immune response when it encounters a foreign pathogen. Failure during this negative process results in autoimmune diseases such as systemic lupus erythematosus (the go-to disease whenever someone is sick in the episodes of House), Graves’ disease and rheumatoid arthritis. Presently, the exact molecular mechanism of negative selection is poorly understood. Nor-1 can induce apoptosis (cell death) by assisting in translations of new proteins, but it can also promote cell death by moving into the mitochondria and turning on Bcl-2 into a pro-apoptotic molecule by exposing its killer BH3 domain1. The mechanism for […]

...Read More about April Choi
L&S Sciences

Improving the Large Underground Xenon (LUX) Dark Matter Detector

The Large Underground Xenon, or LUX, collaboration has spent the last few years constructing a dual-phase liquid xenon detector which is sensitive enough to detect weakly interacting massive particles (WIMPs), the primary candidate for dark matter. The detector is finally running and has been taking data since February of this year. With the first round of data in hand, I will analyze LUXs current level of performance. I will look for unexpected drops in its photo-detection rates and other signs that previously unaccounted for factors are limiting the detectors efficiency. The ultimate goal is to determine whether the detector is running as well as it needs to before the second round of data is taken. If it isnt, I will make recommendations for methods of measuring and investigating the factors I have studied.

...Read More about Derrek Coleman
Rose Hills

Specific Active Site Inhibition of Members ofthe DEAD-Box Protein Family

DEAD-box proteins are vital to the central dogma of biology. They are involved in all aspects of RNA biology including ribosome biogenesis, mRNA export, RNA-protein complex remodeling and much more. Since DEAD-box proteins have been implicated in pathways of viral infections, like HIV, and many types of cancers, they are critical to human health. The two most formidable hurdles in researching this family are their highly similar active sites and that most are essential for life. This makes studying individual DEAD-box proteins difficult, so many of their functions remain unclear. My project will focus on designing chemical inhibitors for a single DEAD-box protein in order to develop methods for further investigating the entire DEAD-box family. This work will reveal the potential of chemical inhibition of DEAD-box proteins for treating disease and shed light on the biological functions of specific DEAD-box proteins.

...Read More about Kendall Condon
Rose Hills

Producto de La Ley: Immigrant Policy and Literature

The Chinese Exclusion Act is considered the most racist law in U.S. history; it entailed quarantining immigrants for up to two years on Angel Island, resulting in a collection of poetry carved by the detainees onto the walls of the detention barracks. Given the tumultuous history of immigration from south of the border, where is this poetry for Mexican and Central American immigrants? While immigration has been extensively studied through various academic perspectives, the literature from the immigrants themselves has largely remained untouched. By identifying the trajectory of literature by undocumented immigrants, I will analyze how policy may have driven the changes in language and style of this corpus of literature and, conversely, what the literature reveals about policy itself. In creating an aesthetic for The Literature of the Undocumented, I will argue for its differentiation from Chicano Literature, under which the literature is currently (mis)categorized.

...Read More about Kiara Covarrubias
Humanities and Social Science

Investigating the Effects of Electric Field Noise from Metallic Surfaces on Ultra-Low Temperature Ion Traps at Low Frequencies

The objective of this work is to study electric field noise from metallic surfaces at low frequencies observed in ultra-low temperature ion traps. This source of noise has been a major issue for ion trapping experiments because it heats up the cold ions several orders of magnitude faster than what was expected. This heating is a serious problem and hinders progress in the use of ions, as dependably controllable qubits, toward a scalable quantum computer. The expected benefits from this research is the determination of the frequency scaling of this anomalous heating, which will shed light on the origin of this noise and, in turn, on ways to mitigate it.

...Read More about Thamine Dalichaouch
Rose Hills

Correlating Maximum Intrinsic Luminosity and Spectroscopic Features of Type Ia Supernovae

Type Ia supernovae are the thermonuclear explosions of critical mass white dwarves which have reached the Chandrasekar mass through accretion of mass from their binary companion. The near constancy of their maximum intrinsic brightness is the key to the use of these events in cosmological studies. Unfortunately, systematic errors associated with the diversity of type Ia supernovae continue to limit their usefulness as standard candles. I will use a very large spectroscopic and photometric data set gathered by the Palomar Transient Factory (PTF) in order to identify correlations between the stretch parameter of type Ia light curves and a variety of parameters derived from type Ia blackbody spectra. Combining the correlations between photometric and spectroscopic parameters I hope to obtain a new correction to type Ia maximum intrinsic luminosity. Furthermore, I would like to apply this new correction to obtain a new value for Hubbles constant using the PTF data.

...Read More about Joseph DeRose
L&S Sciences

Uncovering the Role of Global mRNA Degradation during the Gammaherpesvirus Lifecycle

I will be working with the Murine gammaherpesvirus 68 (MHV68), a member of the Herpesviridae family consisting of over one hundred viruses capable of infecting a wide array of hosts. My gene of interest, muSOX, is a viral gene that targets and cleaves cytoplasmic host mRNAs and is the mouse analog of the SOX gene in the human gammaherpesvirus. A former graduate student constructed an MHV68 virus that is defective for host shutoff (HS). The HS virus has a single point mutation R443I and is incapable of targeting and degrading host cytoplasmic mRNAs. This summer, my job will be to confirm that phenotypes observed in the HS virus are due to only absence of host shutoff activity and not an unintended consequence of the R443I mutation. To do this, I will be creating another MHV68 virus that is defective for host shutoff and contains a different point mutation, L132F.

...Read More about Mansee Desai
Rose Hills

Charge Transport in Millikelvin Germanium

Dark matter is ubiquitous in this universe yet has not been detected directly. The leading candidate particles for dark matter are Weakly Interacting Massive Particles (WIMPs). The Cryogenic Dark Matter Search utilizes measurement of ionization and phonons in order to discriminate between background particles and rare WIMP interactions. Achieving complete charge collection by the ionization readout is challenging due to trapping within the low temperature Germanium detectors. The charge transport experiment will provide great insight into the phenomenon of charge trapping and this information will have wide implications in low temperature semiconductor physics. Examining the trapping curves will also allow us to better understand the charge collection mechanism for the CDMS detectors. With this information we can more accurately distinguish between background particles and rare WIMP interactions, eventually leading to the detection of dark matter.

...Read More about Akash Dixit
Rose Hills

The Socialized Being: How the Words "As If" Operate within Selected Novels of Henry James

I am currently exploring the question of the ways in which the phrase as if — as it appears in novels by Henry James, particularly What Maisie Knew — implicates integration into a social existence in which the curious and problematic acceptance of both reality and unreality is required of the self, particularly the pre-adolescent self. This is a vital question because, first, it offers a foundation from which to examine the complex interplay between several important novelistic factors: the self in relation to the other, the socialization of the child, the divide between the conscious and unconscious mind, and the necessary falsehoods perpetuated by social existence (to name a few). Second, the words as if and the work these words do within the novel as a literary genre is a topic which has received little attention and, yet, is of paramount importance in regard to both novelistic form and […]

...Read More about Emily Doyle
Humanities and Social Science

Healthy Corner Stores Movement

Many communities in the San Francisco Bay Area struggle with food insecurity or the lack of access to healthy and affordable food, making them more likely to suffer from diet-related diseases such as obesity and diabetes. Because these communities have a base of corner stores where people already shop, such as liquor stores or other smaller-scale stores, bringing healthy options to local corner stores may be a more effective strategy than developing larger supermarkets. My project will examine whether the federal governments strategies of providing financial incentives to storeowners is an effective way of increasing the availability of healthy food. I will also learn how local and state governments can make the process of corner-store conversion not only more appealing but easier and less demanding for storeowners. My research will involve looking at government policies as well as interviewing storeowners and other key players in the healthy corner store movement.

...Read More about Alina Enoiu
Humanities and Social Science