The phyllosphere, the microbiome of the leaf surface, is a highly tractable model system, and is particularly adept for empirical studies on microbial ecological and evolutionary dynamics. One open question is how prior local adaptation on a plant host influences the efficacy of microbial biological control agents. Using an experimental evolution approach, in which changes in populations are measured over multiple passaging events, a naturally occurring, defensive phyllosphere bacteria, Pantoea dispersa, was evolved on tomato seedlings. Preliminary assays found that this bacterium has evolved increasingly negative effects on seedling health, suggesting a potential degradation of protective traits. Over the summer, I will help conduct dose-response assays on tomato seedlings to examine how the defensive ability of P. dispersa against the common plant pathogen, Pseudomonas syringae, has evolved over time. Understanding these ecological-evolutionary dynamics in the plant phyllosphere is critical for the implementation of effective biocontrols.
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.
The perception of a stimulus is strongly influenced by the background surrounding it. In mammals, this figure-ground perception to identify stimuli from the environment is crucial for survival, such as detecting predators. My project aims to explore the neural mechanisms behind figure-ground perception, especially focusing on the role of vasointestinal peptide positive (VIP) and somatostatin (SOM) interneurons in the primary visual cortex (V1). To explore the mechanism, I will first develop a novel mice behavioral task that can accurately quantify figure-ground modulation. Then, I will use optogenetics to activate or silence VIP and SOM neurons to explore how these perturbations affect mices performance in the task. In doing so, I aim to uncover how VIP-SOM disinhibitory circuit contributes to figure-ground perception.
Mitochondrial dysregulation has emerged as a cause for certain forms of Parkinson’s disease. Investigations of the mechanisms linking mitochondrial function to Parkinson’s have focused on the degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNc-DA neurons). Norepinephrine-releasing neurons in the locus coeruleus (LC-NE neurons) rely on mitochondria for their daily activity in healthy individuals and also severely degenerate in Parkinson’s. Both SNc-DA neurons and LC-NE neurons are crucial for maintaining various aspects of wakefulness, but it is unclear whether mitochondrial dysregulation in each neuron population distinctly impacts sleep disturbances characteristic of Parkinson’s. For my project, I will address the hypothesis that mitochondrial dysregulation in LC-NE neurons versus that in SNc-DA neurons will have different effects on sleep in a mouse model, which could provide insight for targeted therapies to improve sleep in patients. Toward this goal, I will study mice using a targeted genetic approach where a key […]
Understanding the genetic basis of organ regeneration remains a central challenge in the field of developmental biology. Teeth are a classic model for organogenesis, since many homologous ectodermal organs (e.g., teeth and hair) follow similar patterns of development and regeneration. Threespine stickleback fish are a powerful model organism for studying tooth regeneration in vertebrates because they possess the ancestral dental phenotype of polyphyodonty, in which teeth are continuously replaced throughout adult life. Past research has shown that Foxc1 regulates Bmp6, a gene important for viability, growth, and tooth patterning in threespine stickleback fish, and maintaining quiescence, a period of rest, in mouse hair follicle stem cells. My project aims to study whether Foxc1a and Foxc1b are required for regulating tooth regeneration in threespine sticklebacks. I hypothesize that Foxc1a and Foxc1b play homologous roles in reestablishing quiescence in fish tooth stem cells as Foxc1 does in past studies of mouse […]
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 […]
Suppose that we have a (finite or infinite) series of independent, identically distributed real-valued random variables (increments of time). From this series, we can form a random walk. We can consider the partial sums of this series and analyze the average value of the walk the partial sum divided by the number of increments up to that point at each of its time increments. This project is focused on studying the distribution of the maximum average value of a random walk through a variety of computational algorithms. While there already exists an explicit formula for the probability that the maximum average value is at most any given real number 0 x 1, this formula presents computational challenges for small values of x. What is especially interesting is the asymptotic aspect: how quickly does the probability that the maximal average is at most x approach zero as x approaches zero from […]
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 […]
Contactin-associated protein-like 2 (CNTNAP2) mutations are strongly associated with autism spectrum disorder, which presents with repetitive behaviors. Research has shown that mice lacking CNTNAP2 exhibit decreased numbers of GABAergic interneurons throughout the brain, and that the number and function of these interneurons in the striatum are associated with the presentation of repetitive behaviors. Recent work has shown that enriched environment rearing restores GABAergic interneuron numbers in the striatum and rescues behavioral deficits in rodent models of neuropsychiatric disorders. I will be looking at how different rearing conditions affect striatal gene expression and behaviors in CNTNAP2 knockout mice. My project will explore the interactions between genes and the environment, particularly the potential for environmental aspects to alter striatal interneuron cell types and the presence of repetitive behaviors. The goal of my project is to help provide insight into how environmental factors may influence neurodevelopmental disorders.
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 […]