Plants, like other multicellular organisms, possess a complex set of defensive measures deployed upon stimulation of the immune system. In the case of insect herbivory, these defensive measures depend upon specific pattern recognition receptors (PRRs). These PRRs enable the plant to detect herbivore associated molecular patterns (HAMPs). The Inceptin Receptor (INR) is a known herbivore receptor found in legumes, which detects Inceptin 11 (In11), a peptide fragment unique to the oral secretion of Spodoptera exigua. Beyond the plasma membrane much of the pathway from In11 detection to immune response is unknown. This research investigates possible signaling kinases downstream from INR. Receptor-Like Cytoplasmic Kinases (RLCKs) are known to mediate both specific immune and developmental signaling cascades in Arabidopsis thaliana. This suggests that they may play a role in the signaling network of herbivore induced immune responses. In this work we systematically investigate seven RLCKs of interest from three clades within the legume RLCK protein family which are upregulated by In11 treatment in the common bean (Phaseolus vulgaris). To better understand their effects, selected RLCK’s are transformed into the plant model organism Arabidopsis thaliana via Agrobacterium tumefaciens, and homozygous transgenic lines overexpressing the RLCKs are isolated. To examine the effects of over-expressing RLCKs on immunity, classic immune assays will measure their effects on Reactive Oxygen Species (ROS) and the phytohormone Ethylene production during immune activation. This research provides insights into plant immune signaling specific to caterpillar herbivory. In the future, this research may enable the intentional amplification or modulation of plant immune response to reduce losses in crops susceptible to herbivore infestation, a growing concern for food security in the near future.

Plants utilize cell surface protein receptors to recognize insect herbivory through the detection of Herbivore Associated Molecular Patterns (HAMPs) Following the detection of HAMPs, plants initiate specific immune responses, often measured by the increased production of the hormone ethylene gas and by Reactive Oxygen Species (ROS). The Inceptin Receptor (INR), which is specific to legume plants, recognizes the HAMP Inceptin11 (In11). The binding of In11 to INR initiates a signaling cascade, leading to an immune response. However, the signaling mechanism activated by INR is unknown. The Receptor-Like Cytoplasmic Kinase (RLCK) gene Herbivore Induced Kinase 1 (HIK1) is upregulated by In11 treatment in the bean species Phaseolus vulgaris. The goal of this research is to determine if HIK1 and other RLCKs are downstream proteins required for INR signaling. Because of the genetic intractability of P. vulgaris, I transform Arabidopsis thaliana with RLCK genes using Agrobacterium tumefaciens infiltration. Isolated genetic lines are then used to analyze the effect each RLCK has on immune signaling. Transgenic plants are treated with bacterial associated molecular patterns to trigger an immune response, then tissue samples of the leaves are measured for ROS and ethylene gas production. Results are then compared with ROS and ethylene gas production of wildtype plants. If the studied RLCKs are involved in downstream INR signaling, the transgenic plants will have increased ROS and ethylene gas production. I anticipate HIK1 to have the strongest increase in ROS and ethylene gas production due to the upregulation of HIK1 after In11 treatment in P. vulgaris. Understanding the INR signaling pathway is vital for engineering of plants that are resistant to insect herbivory without the use of pesticides.

The emergence and spread of antimicrobial resistance (AMR) in bacterial populations pose a significant threat to global health. A key factor in this process is the horizontal gene transfer (HGT) of resistance genes carried by mobile genetic elements (MGEs). This study focuses on understanding how mutations in plasmids influence the rate of HGT and its implications for the spread of AMR. Plasmids are small, extrachromosomal DNA elements that can transfer between different bacterial cells, a process crucial in spreading antibiotic resistance genes. These plasmids often use a mechanism known as conjugation for transfer, a process encoded by approximately 30 genes in the transfer (tra) operon. This research aims to understand how changes in the tra operon affect the plasmid's ability to move between bacteria. This movement can be either horizontal (between different cells) or vertical (from parent to offspring during cell division). Our project is divided into two main aims. The first is creating a library of mutated plasmids. I modified a large, well-studied conjugative plasmid, the F plasmid, and introduced specific mutations into the tra gene. This step is achieved using a method called Lambda Red recombination, a technique suitable for large plasmids where standard cloning methods fall short. The second aim is to measure the rates of vertical and horizontal gene transfer (VGT and HGT) in these mutated plasmids. We employed the Luria-Delbrück method for precise estimation of these transfer rates. Understanding the trade-off between VGT and HGT is crucial in predicting and controlling the spread of AMR. By mapping the relationship between specific mutations in the tra operon and their impact on gene transfer rates, our study contributes to a broader understanding of how antibiotic resistance spreads through bacterial populations. This knowledge is vital for developing strategies to combat the increasing threat of antibiotic-resistant bacteria.

Existing studies show the importance of migration in ensuring both the livelihood and safety of migrants around the world, and that factors such as ethnicity and caste have a significant impact on an individual’s ability to migrate. My study aims to further explore the association between caste/ethnicity and the order of starting, intermediate, and most recent destinations a migrant passes through. To do so, I perform a sequence analysis on places traveled to by participants of the Chitwan Valley Family Study (CVFS) dataset. CVFS focuses on the Chitwan Valley region in Nepal, a country that hosts a variety of ethnic groups and has a wide range of destinations that its inhabitants migrate towards, with a much higher rate of human migration than other countries of similar population size or GDP. Using the dataset, I also search for common factors between caste groups, such as the kinds of intermediate locations they may travel to before heading to a more permanent destination, and how long certain castes take to migrate either due to legal issues, their own caution or the resources available to them. I expect people of lower caste to face more difficulty in migrating due to how caste profoundly influences social life in the region. This transforms how we view the impact of caste or ethnicity on migration, not just isolated to the Chitwan region but across any region involving the migration of multiple ethnic groups. It is also relevant to note that sequence analysis has little pre-existing use in migration sociology, especially when focusing on migration across multiple continents. Therefore, this study presents a new method of studying migration along with a better understanding of what goes on between the assumed starting and most recent point of a migrant’s journey.

The measurement problem is the challenge of reconciling the probabilistic and deterministic aspects of Quantum Mechanics. In this study, our primary aim is to unravel the measurement problem by investigating the possibility that quantum collapse occurs according to the probabilities presented by Born's Rule due to a perturbation on the system, appearing during the measurement process. Our group employs a multifaceted approach, where we examine the interplay between time dynamics and classical limits, alongside the influence of time-(in)dependent perturbations. Computational simulations serve as our primary tool in this exploration. One part of our group worked with a 3-well system with a time-independent perturbation, another part looked at a 2-well system with a time-dependent perturbation, and the last part saw what a time-independent perturbation does to a 2D-well system. We anticipate that our investigations will uncover critical parameters that are expected to yield probabilities consistent with Born's Rule, a foundational principle of Quantum Mechancis. This research points towards a potential reconsideration of quantum collapse as a dynamical, affected by the perturbation introduced by measurement. While preliminary, these findings contribute to the ongoing discourse in Quantum Mechanics and may offer insights for future theoretical developments and applications.

Nepal, despite its heavy reliance on agriculture, is witnessing a decline in agricultural productivity and an increasing dependence on food imports. This phenomenon, coupled with factors such as land fragmentation and labor shortages, has led to a masked "Silent Green Revolution" reminiscent of past agricultural movements. Agrochemical overuse and over-intensification has raised concerns about the long-term sustainability and health implications of such practices. In this paper I explore interplay between agricultural practices, farmer health, and environmental sustainability in Nepali farming communities. With the help of a translator, I orally conducted a Farm and Farmworker Health Survey in Phoolbari and Baluwa, two villages in the Kavrepalanchok District with both commercial and subsistence farmers. I found that while commercial farmers favored agrochemicals for their cost-effectiveness, subsistence farmers preferred organic alternatives for their safety and sustainability. However, there was a general lack of awareness among farmers regarding the symptoms of pesticide exposure and proper safety measures like Post Harvest Intervals and Personal Protection Equipment, indicating a need for targeted health and procedure awareness programs. Furthermore, the study highlighted the potential health risks associated with agrochemical use, including exposure to carcinogenic heavy metals like cadmium and glyphosate residues. These findings underscore the urgent need for sustainable agricultural practices that prioritize the health of both farmers and consumers. By centering traditional farming methods and indigenous knowledge and implementing initiatives that address occupational safety and provide proper training and infrastructure, Nepal can pave the way towards a more sustainable and equitable agricultural future.

Cannabidiol (CBD), a non-psychoactive cannabinoid compound found in cannabis, has been reported to attenuate morphine tolerance and can potentially be used as an alternative to opioids in treating chronic pain. Previous work has established connections between morphine tolerance and Reactive Oxygen Species (ROS) production through JNK-mediated Peroxiredoxin 6 (PRDX6) activation. Excess ROS production promotes desensitization of opioid receptors, which in turn leads to opioid tolerance. CBD administration is associated with decreasing pain-related Reactive Oxygen Species (ROS) production, and it was hypothesized that CBD directly interacts with JNK, blocking JNK’s activities. This project aims to investigate the connections between CBD administration and ROS production to determine CBD’s effects on JNK-mediated ROS production. To quantify ROS production through fluorescence imaging, I will transfect wild-type HEK 293 cells with oROS, a genetically encoded sensor, which fluoresces proportionally to ROS production. Coverslips of HEK 293 cells expressing oROS are treated with buffer (control) and CBD before administration of Tumor Necrosis Factor alpha (TNFα), a known activator for JNK released during pain states. After imaging with oROS, I will quantify ROS production and compare this between groups with and without CBD pretreatment to determine CBD’s activity on inhibiting JNK-mediated pro-inflammatory pathways. I predict that relative to the control, cells treated with CBD will have significantly less ROS production. If the results are consistent with this prediction, CBD could be a potentially promising co-treatment with opioids in managing chronic pain as it can potentially attenuate opioids' side effects like tolerance. 

In the context of computer-aided design, researchers have studied how to reconstruct an input geometry in CAD by decomposing it into CAD primitives. Such reconstruction is useful for creating CAD designs for manufacturing applications. What we want to study is also object decomposition but towards a different goal: understanding object affordances and interactability. For example, a handle of a basket can be grasped or hung from a sticky hook, and we recognize this affordance or functionality because it has a certain shape (e.g. hook or rod). Prior research has identified eight types of shape primitives that are common in everyday objects, but the existing tagging process requires a high degree of modeling expertise. We aim to create a more automatic and easy-to-use tagging tool. Our proposed research is to develop user-in-the-loop methods for tagging shape primitives given an object geometry. This takes advantage of human intuition for how objects function and interact. We start with building an interface, where users sketch over the input mesh to indicate the region for fitting and select the type of primitive to be fit. On top of this, we plan to crop the selected mesh data to generate a reduced mesh that encompasses only the area selected by the user. Finally, we utilize differentiable rendering techniques to automatically optimize the shape parameters of user-selected primitives to fit our reduced mesh data. With this tagging tool, we can enable more people without modeling expertise to tag objects. Data generated with this tool can support future research that studies object affordances with learning, as well as improve applications in robotics, product design, and assembly design like FabHacks.

Mobile genes are commonly found in bacteria, and they are capable of being transferred between unrelated bacterial cells via a process termed horizontal gene transfer (HGT). Mobile genes that undergo HGT can evolve in various “host” bacteria and thereby evolve in several different genomic backgrounds. In a recent publication, my lab constructed a mathematical model to assess the effects of HGT (i.e “host-switching”) on mobile gene evolution. I have built upon this work by probing additional factors that may influence mobile gene evolution. In phase one of my project, I compared the original evolutionary model used in the publication to a newly expanded, more ecologically realistic model in which growth rates of the bacteria depend on resource availability. To compare the models, I ran simulations with both models on a set of bacterial-host pairs and compared the resulting evolutionary outcomes from both models. I found that the categorical effect of HGT occurring (i.e. HGT confers a higher, lower, or neutral change in host fitness) was the same across both models, indicating that ecological factors are less predictive of mobile gene evolutionary outcomes. For the second phase of my experiment, I assessed the effect of variable HGT rate on mobile gene evolutionary outcomes. I ran simulations using a set of bacterial host-pairs while varying the HGT rate along a biologically relevant range, and found a positive correlation between HGT rate and the magnitude of positive fitness effects conferred by a mobile gene that has undergone HGT. This indicates that HGT rates play an important role in governing the evolutionary outcomes of mobile genes. Using evolutionary simulations has allowed us to gain insight into the predictive factors governing mobile gene evolution and thereby mobile gene-containing bacterial evolution. This is especially important, as many genes conferring antibiotic resistance are mobile.

The expected launch of the Nancy Grace Roman Space Telescope (Roman), a next-generation space-based infrared observatory, will soon allow us to observe fields in minutes that would previously have taken months to cover. As such, it will advance our knowledge of galactic structure and evolution at a rapid rate. To better leverage the influx of science that will come out of the launch and commissioning of Roman, we are developing a pipeline that simulates observational images taken by Roman and then performs photometry on the images. As a first step, we are testing methods for recovering dwarf galaxies from photometry catalogs that contain both a dwarf and a surrounding stellar halo. In order to produce mock Roman observations, we use the Space Telescope Science Institute's Space Telescope Image Product Simulator (STScI-STIPS) software tools, which are able to add background galaxies, realistic background levels, and noise along with source catalogs to produce simulated images. Our early testing uses input catalogs designed to simulate typical dwarf galaxy characteristics added to stellar catalogs generated from numerical simulations that mimic the nearby spiral galaxy M81. The ultimate goal of this pipeline software is to determine the observational strategy to resolve structures in extended stellar halos of nearby galaxies. Such measurements would allow us to distinguish between formation and evolution scenarios for these halos. This work is part of the Roman Infrared Nearby Galaxies Survey (RINGS), a large Roman Wide-Field Science (WFS) program funded by NASA under grant 80NSSC24K0084.

Local Group galaxies are the closest ones we can study in detail to decipher the processes that shape the universe around us. An interesting property of these galaxies is their star formation history (SFH), which provides a fossil record of when stars were formed in a galaxy. The process by which this occurs is a complex interplay between the gas, the interstellar medium (ISM), and the energy from newly formed stars. By pairing SFH measurements with data on the galaxy’s gas content, we can investigate the timescales on which young massive stars affect the structure of the surrounding gas in the (ISM) as well as its ability to form more stars. Furthermore, since star formation is closely linked to the properties of the gas in a galaxy, such as metallicity and extinction, the SFH also probes these properties. By utilizing resolved stellar photometry from the Hubble Space Telescope (HST), I measured the SFH for four Local Group galaxies (IC10, IC1613, WLM, and NGC 6822) that already have detailed imaging of their gas content from radio observations. First I measured the colors and brightnesses of resolved stars in each galaxy from the HST imaging. Next, I generated and processed a set of artificial stars using the same photometry pipeline as the real observations to provide statistical measures of our data quality. With the processed artificial stars and the original photometry, I then fitted a series of model Hess diagrams for a range of ages and metallicities to obtain each galaxy’s SFH. These measurements allow us to pair this SFH with other observational data. For example, we can map star formation and compare it with observations such as supernovae locations, and we can explore links between the star formation and the ISM as measured through emission from neutral and ionized hydrogen.