Mellon Zhang

Neural network models have traditionally been viewed as a black box, with tremendous capabilities in a variety of domains, yet with inexplicable inner workings. Past attempts at analyzing neural networks include analyzing model results and learned weights in an effort to design explainable artificial intelligence, as well as early efforts to determine the full capabilities of neural network models. My project seeks to continue in this tradition by investigating the logic-building aspect of neural network models. More specifically, I aim to investigate whether a novel program synthesis neural network model builds internal logical structure during the course of a simple rule-learning task, and whether the model’s logic-building process shares similarities to humans, demonstrated in biases such as a preference for simplicity or brevity.

Connor Tumelty

Epigenetic information refers to chemical modifications to DNA and histones that can be inherited independently of the genetic sequence of a gene. These modifications control the expression of the gene and can alter the organism’s phenotype. In nature, a number of epialleles (alleles with identical sequences yet different epigenetic states) have been identified and often contribute to vast phenotypic diversity among a population of organisms. It is currently poorly understood whether epialleles can be engineered within plant systems. If possible, this could expand the toolbox available to plant breeders and engineers seeking to specify the phenotypes in their crops. I propose to perform an important proof-of-concept experiment to demonstrate the feasibility of engineering epialleles, using a visually obvious marker gene in the model plant Arabidopsis thaliana. I seek to understand if DNA methylation patterns can be engineered and if this epigenetic mark is stably inherited over multiple generations once it […]

Joanna Veres

Living on Earth, gravity constantly exerts a mechanical load on the spine, which puts pressure on the discs and causes them to gradually lose height throughout the day. However, this constant mechanical load is greatly reduced while in environments with microgravity such as on the international space station. Due to long-term mechanical unloading in the presence of microgravity, astronauts have an incidence of disc herniation 4.3 times that of the general population. Being able to better describe the physiological changes to the IVD caused by prolonged time spent in microgravity would help the medical community understand the sensitivity of disc homeostasis to mechanical loading and therefore more fully know the role of mechanical loading in disc herniations. Given that 2 percent of the worlds population has herniated discs at any given time, having a better understanding of this affliction could be used to try and create preventative care in order […]

Phoebe Wang

Dengue virus (DENV) infects an estimated 105 million people every year. More than 500,000 of these cases develop into a severe form of disease characterized by leakage of plasma from the vasculature. If left untreated, these symptoms may progress to fatal outcomes such as hemorrhage, hypovolemic shock, and organ failure. Studies have suggested that DENV non-structural protein 1 (NS1) plays an important role in the pathogenesis of severe dengue through interactions with endothelial and immune cells. In addition, the Harris Lab has recently shown in vitro and in vivo that DENV NS1 activates the inflammasome, a family of cytosolic innate immune sensors, leading to a protective immune response to DENV in a murine model of DENV infection. However, the molecular mechanisms behind DENV NS1-induced inflammasome activation remain unknown. For my project, I plan to identify the functional protein domains of NS1 involved in inflammasome activation by using NS1 chimeras containing […]

Joshua Wong

My project will investigate how mating status (virgin or mated females) affects how Drosophila, commonly known as fruit flies, will intake bitter substances when mixed in solutions with sugar. Because mated females have been shown to intake more nutrients like sugars or amino acids for the purpose of egg production, I want to investigate if mated females will also tolerate more intake of bitter (aversive) compounds that are mixed with sugars. This dynamic is super interesting because fruit flies have two different mechanisms to avoid aversive compounds: one activates bitter gustatory receptors, and the other inhibits sugar consumption. Together, these two processes allow fruit flies to avoid potentially toxic compounds, even in mixed solutions with both appetitive (sugar) and aversive (bitter) compounds. Furthermore, if this is true, then I want to investigate and illustrate the genetic and molecular mechanism that allows this process to occur, which would signify that mated […]

Jinze Wu

My research project is simulating the layered honeycomb material BaCo2(AsO4)2 at low temperature and high applied in-plane magnetic field, since BaCo2(AsO4)2 is theorized by the Kitaev honeycomb model to exhibit Kitaev Quantum Spin Liquid (KQSL) behaviors. Currently, the Kitaev honeycomb model is still a very new theory to explain the quantum spin liquid states, and any simulations that corroborate or contradict the experimental results will be examined within the theoretical framework of this model in order to identify possible inconsistencies between the model and the experimental results. This topic will be part of my senior honors thesis project, which expands the simulation to other candidate materials of Kitaev physics. These simulations will help to provide explanations for the magnetic behaviors of BaCo2(AsO4)2 in experiments, and any discrepancy between simulation and experimental results will be examined to determine whether the discrepancy is the product of holes in the theoretical framework of […]

Xavier Tao

Currently, most chemotherapy drugs used for cancer treatment target specific upregulated or dysfunctional pathways, rather than specific cancer-driving mutations. This results in adverse side effects or reduced applicability, since the drug can also affect normal pathways of healthy cells. In many tumors, cancer-driving mutations alter amino acid residues into cysteines. Due to cysteine’s unique chemical properties, these mutations are an ideal target for covalently binding molecules. This approach is especially useful in undruggable proteins lacking traditionally targeted binding pockets. In this regard, the Nomura Research Group has applied target-based screening of its cysteine-reactive compound library to identify hit compounds that covalently bind target proteins. In this project, I will express, purify, and screen human proteins with common cancer-driving mutations. Subsequently, I intend to utilize established chemoproteomic platforms to characterize hit features like proteome-wide selectivity and on-target engagement. My project ultimately intends to identify and characterize therapeutically useful chemical compounds targeting […]

Ngoc-Thanh Tieu

Vietnam’s demographic transition to increased urbanization and rapid economic development have led to a nutrition transition from traditional to nontraditional, processed diets. Vietnam endures a double burden of malnutrition, the simultaneous prevalence of childhood stunting, thinness, overweight, and obesity. However, these outcomes have not been distributed evenly, particularly when comparing child growth status between different ethnicities. There is a need to explore the prevalence of child malnutrition among Vietnam’s ethnicities, examine if there are significant differences between them, and, lastly, examine potential risk and/or protective factors associated with these outcomes. My research is a secondary analysis across five rounds on 1961 Vietnamese children from the Young Lives Cohort Study from 2002 to 2017. Community, household, and individual child characteristics (using variables modeled from the ecological framework) were collected from children aged 1, 5, 8, 12, and 15. I hope my research will encourage more research focused on recognizing each ethnic […]

Kenneth Trang

Bacteria inhabit nearly every surface on Earth, from tabletops to hydrothermal vents. Thus, it is unsurprising that a diverse community of microbes, or microbiome, also inhabits the human gut. However, these residents arent simple stowaways, as gut bacteria actively modulate host development and physiology. Therefore, as different species of bacteria modulate host physiology differently, understanding the factors that determine which bacteria can and cannot colonize the gut is of increasing importance. Host genetics, diet, and geography were all shown to play important roles in determining microbiome composition. The goal of the proposed project is to examine the role of parental transmission to progeny, which, beyond its functional consequences, may have further implications for understanding the evolution of host-microbiome interactions. Last year, I characterized the ecological succession of Caenorhabditis elegans gut microbiome during larval development as part of my honors thesis project. This summer, I will explore the dauer larval stage […]

Ryan Quan

Mitochondrial DNA Depletion Syndromes (MdDSs) are a set of diseases characterized by severe pathological effects on the liver and brain. These syndromes are implicated by low/absent levels of mitochondrial genomes, circular strands of DNA housed in the mitochondria (mtDNA) that encode for proteins important for respiration. Thus, maintenance of this genome is thought to be critical for cellular health. However, the mechanism behind the tissue-specific pathologies of these syndromes remains unclear. Recent evidence suggests that the essentiality of mtDNA for cell viability and division may vary across different conditions. Recent experiments done in Dr. Samantha Lewis’s laboratory found that fibroblasts depleted of mtDNA are viable and may retain mitochondrial membrane potential. The goal of my project is to identify candidate genes that allow for the continued resilience of cells depleted of mtDNA. Data from my project will help determine the extent to which mtDNA and its expression is essential for […]