College of Agriculture and Life Sciences Honors Theses

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https://hdl.handle.net/1813/2937

Undergraduate Honors theses for the College of Agriculture and Life Sciences.

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Diversity in Dosage: How Minority Inclusion Shapes Adverse Outcomes in GLP-1 Clinical Trials
Kanvar, Maaya (2025-05-04)
The thesis determines the relationship between racial minority representation and the reporting of non-fatal adverse events in clinical trials for Glucagon-like Peptide-1 (GLP-1) interventions. Using data extracted from ClinicalTrials.gov, the study utilizes three modeling approaches to conduct a meta-analysis on how different compositions of minority participants correlate with reported rates of five common side-effects in GLP-1 usage: nausea, vomiting, diarrhea, dizziness, and upper respiratory infection. Contrary to the initial hypothesis that minority inclusion would correlate with higher reported rates of adverse events, based on prior literature, the current findings reveal a consistent inverse relationship. A higher proportion of racial and ethnic minority participants was associated with lower reported incidence rates of the five adverse events analyzed. When this trend is interpreted through a sociomedical context, it reflects issues with underreporting. Contributing factors include cultural traditions and perceptions, reduced health literacy rates, and medical mistrust. This study is further supported by qualitative interviews with experts in clinical trials and health ethics, as well as by the application of sociological frameworks. Collectively, the findings from the qualitative and quantitative data underscore the pressing need to make clinical trials more inclusive, transparent, and culturally responsive.
Sex differences in LDL-C control and race-specific genetic heritability in the All of Us Research Program
Liquori, Jaclyn (2025-09-03)
Cardiovascular diseases (CVDs) have been the primary source of mortality among women and men in the United States since 1921. Despite prior research demonstrating sexually dimorphic symptom presentation of CVD, women remain underdiagnosed and undertreated for CVDs. Low-density lipoprotein cholesterol (LDL-C) is a well-established and modifiable risk factor for CVDs. Here, I use genotype and phenotype data from the All of Us Research Program (AoU) to examine (a) if LDL-C measurements differ between cisgender women and cisgender men, (b) if the efficacy of statin treatment differs between these groups, (c) if there is a sex-specific difference in LDL-C measurements over age, (d) if there is a sex-specific difference in genetic variants associated with LDL-C measurements, (e) if there is a sex-specific difference in genetic effect, and (f) if heritability differs among or between groups. Based on my analysis of AoU data, I found that the median LDL-C measurements of women are consistently higher than men's and that this difference persists across all age strata and becomes most apparent in middle age. In addition, women are treated with statins at a lower rate than their male counterparts, and they are less effective. Genetic variants associated with LDL-C measurements differ between women and men, as do their effect size. Finally, I found that heritability differs between sex, age, racial identity, and treatment groups. My findings indicate that current clinical intervals of LDL-C and pharmaceutical-based LDL-C modification approaches may not be equally appropriate for cisgender women and cisgender men.
Oxidative costs and constraints of territory quality and reproductive effort in male black-throated blue warblers (Setophaga caerulescens)
Thomson, Braeden (2024)
Life-history evolution is constrained by reproductive costs, as indicated by trade-offs between investing in current reproduction and future reproduction and survival. The physiological mechanisms driving these trade-offs, however, are not well understood. Oxidative stress is a candidate physiological mechanism for mediating costs that drive breeding season tradeoffs in migratory songbirds. Yet, few studies have focused on links between oxidative stress and reproductive effort. I hypothesized that reproductive effort generates oxidative stress (oxidative-cost hypothesis) and that oxidative stress shapes reproductive effort to mitigate the costs of reproduction (oxidative-constraints hypothesis). I examined whether variation in three oxidative measures (oxidative damage, antioxidant capacity, and oxidative stress) were associated with measures of breeding territory size and quality, parental effort, and reproductive success in male black-throated blue warblers at Hubbard Brook Experimental Forest, NH, USA. I found that oxidative stress functions as both a cost of and a constraint on reproduction. Across the breeding season, oxidative damage and oxidative stress decreased. Males with higher oxidative damage and oxidative stress had larger and higher quality territories, and males with higher antioxidant capacity delivered more prey biomass to nestlings. Males with higher-quality territories had lower oxidative stress and greater reproductive success. My results suggest that oxidative stress mediates the costs of reproduction in male black-throated blue warblers and, therefore, is an important driver of life-history tradeoffs in this migratory songbird. Delineating further relationships between oxidative stress and reproductive costs is critical to understanding life-history evolution in migratory songbirds.
Early acquisition and intestinal colonization by E. coli of infants born to mothers with Inflammatory Bowel Disease
Lastras-Castrejon, Daniela (2025-07-10)
The early life environment, when the microbiome is established, may dictate Inflammatory Bowel Disease (IBD) risk later in life. E. coli has emerged as a neonatal colonizer across species. To investigate E. coli colonization, phylogeny and virulence in response to different exposures, we analyzed metagenomic data and characterized E. coli isolates from mothers and their children. Taxa and alpha diversity for control mothers was higher than IBD mothers, and the opposite was true for E. coli abundance. An increase in taxa and alpha diversity is seen as infants age from 7 days to 4 years old with a concurrent decrease in E. coli abundance. In control mothers, E. coli were predominantly phylogroups B2 and D, whereas B1 isolates were more common in IBD mothers. In contrast, most infants were colonized by B2 isolates, independent of maternal IBD status. Furthermore, the phylogroup distribution of toddlers resembled that of control mothers. Cytotoxin and genotoxin genes were rare in maternal E. coli but common in infants of IBD mothers and absent in infants of control mothers. Conversely, AIEC-associated genes were more common in maternal E. coli particularly IBD mothers than infant E. coli. The E. coli isolates from toddler’s were similar to the maternal cohort in rarity of genes encoding cytotoxins and genotoxins, but had more genes associated with AIEC. Our findings reveal that mothers and their babies are colonized by a diverse group of non-diarrheagenic E. coli that vary in phylogeny, genotype and virulence, refuting clonal transmission of maternal isolates.
Aigamo alongside Nouminren: Situating Japanese Integrated Rice-Duck Farming in the Food Sovereignty Movement
Leiber, Oscar (2025-05)
Japanese integrated rice-duck farming (aigamo) emerged in the late 20th century as an alternative method for growing rice avoiding the standard practice of applying synthetic fertilizers, pesticides, and herbicides. In the current agricultural moment of de-agriculturalization and farmland abandonment in Japan, the aigamo method offers an alternative approach for farmers that promotes farmer innovation and self-sufficiency, new markets, a diversified agroecosystem, and food sovereignty. Zooming further out, the aigamo method exists in a global food economy where smallholder agriculture is increasingly overshadowed by free-trade agreements threatening foodways worldwide. By situating the aigamo method in conversation with agroecology and food sovereignty, this paper reveals how the aigamo method is a localized endeavor at addressing a global agrarian crisis. By incorporating fieldwork conducted in 2024 in Japan, this paper aims to update the English literature on aigamo today and present it alongside the Japanese food sovereignty organization Nouminren.
Customizing Deep Neural Networks for Call-Type Distinction in Eastern Meadowlark (Sturnella magna): Investigating links with Land Use, Behavioral Ecology, and Conservation
Cheeley, Lucy (2025-04)
Grassland birds are experiencing steep population declines across North America due to habitat loss, agricultural intensification, and land-use change. The Eastern Meadowlark (Sturnella magna) has declined by over 75% since 1966 and serves as an important indicator of grassland ecosystem health. We utilized passive acoustic monitoring (PAM) and a custom BirdNET classifier to examine the spatial and temporal variation in Eastern Meadowlark vocalizations, songs, and calls across 45 grassland sites in New York State. We analyzed how vocalization frequency varied across management regimes, land-use types, regions, and the breeding season. A total of 143,305 songs and 11,489 calls were detected and analyzed using generalized additive models (GAMs). Results showed that song was significantly influenced by geographic region and date, and call was significantly influenced by date. Song rates increased in later parts of the season and were significantly higher in the Eastern region, while call frequency remained relatively stable with a slight increase at the end of the season. No significant effects were found for land cover, management regime, or protected versus working land status. These results show how PAM and call-type classification can provide insights into the differential roles of vocalization types in avian behavioral ecology. Future work should explore multi-year trends, additional sites, and juvenile versus adult vocalization patterns, and additional local and regional landscape variables.
Heart Rate Variability over the Lifespan and its Potential as a Peripheral Biomarker for Cognitive Decline in Long-Evans Rats
Sutter, Olivia (2025-04-10)
This study investigates the effects of pharmacological cholinergic manipulation and aging on heart rate variability (HRV) and performance during an odor discrimination task in Long-Evans rats. Rats from distinct age cohorts (“Adult,” “Older Adult,” and “Elderly”) completed proactive interference (PI) odor-detection tasks using an olfactometer. Proactive interference refers to the phenomenon where previously learned information impedes the acquisition of new, related material. Pharmacological interventions involved systemic intraperitoneal (IP) injections of normal saline (0.9% sterile medical grade), methylscopolamine (0.25 mg/kg), or scopolamine (0.25 mg/kg). The ability to overcome PI was evaluated for each injection type. HRV data were collected via surgically implanted telemeters recording electrocardiogram (ECG) data. Results revealed no significant age-related differences in HRV between the “Elderly” and “Adult” cohorts. Pharmacological manipulation affected PI resolution differently between age cohorts, with adult rats showing impaired PI resolution under scopolamine and methylscopolamine compared to saline controls, while older adult rats behaved comparably across each injection type. These data suggest that cholinergic drugs may affect the body differently in naturally aged subjects. Unexpectedly, rats also experienced declines in baseline and new learning accuracy from cholinergic manipulation, which may be due to learning odor discriminations at an older age compared to previous studies that used younger animals. Rats experienced a drop in HRV after injection, suggesting a reduction in vagal tone due to reduced cardiac parasympathetic regulation.
Assessing Retrotransposition of Keno, a Site-specific Transposable Element in Zebrafish
Victoria Capobianco (2025-03-14)
Transposable elements (TEs) constitute a significant portion of eukaryotic genomes, yet their roles in genome function, disease and evolution remains understudied. Keno is a site-specific non-LTR retrotransposon that inserts into a conserved region of the U2 small nuclear RNA (U2 snRNA), which is an essential component of the spliceosomal machinery. Intrigued by these properties, we set out to investigate whether Keno is transpositionally active and what cellular properties affect its transposition in zebrafish. By observing GFP expression, marking insertion of a copy from injected RNA in zebrafish embryos, I reveal no detectable activity of the cloned Keno element. By whole plasmid sequencing of the cloned Keno element, I discovered that it was significantly (10.8%) diverged from the consensus sequence. I attempted to isolate Keno copies that were potentially more likely to be active by cloning from zebrafish cDNA separately, but this method was unsuccessful in isolating more recent Keno copies. We also assayed transposition with Keno ORF1 and ORF2 RNAs introduced with the reporter RNA, but observed no transposition. To assess if the synthesized Keno ORF2 RNA was being translated into protein during development, we monitored translation through a split luciferase tag (HiBiT epitope tag). I observed low levels of luminescence, suggesting low levels of translation of the injected Keno ORF2 HiBiT RNA. Taken together, these results suggest that the copies of Keno we isolated thus far are not capable of transposition. We discuss future directions including the possibility that other Keno copies not yet isolated are transpositionally active.
AGO Argonautes in spermatogenesis
Johnstone, Jessica P (2023-05-25)
Of the four different Argonaute proteins from the AGO family (AGO) present in mice, previous work from the Cohen Lab has identified that AGO3 and AGO4 are found in the nucleus of male germline cells during spermatogenesis and that knockout(KO) Ago4 male mice have a subfertility phenotype along with the upregulation of AGO3 protein localization. This upregulation suggests that AGO4 and AGO3 might have overlapping function(s) in the germline. The main goal of this study is to investigate the role of AGO proteins during spermatogenesis, specifically their function in prophase I of meiosis. Two mutant mouse lines were utilized: a triple knockout mouse line (Ago413 KO) and a single knockout mouse line, Ago3 KO. Prophase I spreads were performed on homozygous mutant Ago413 KO males, to investigate if meiotic sex chromosome inactivation (MSCI), a characteristic feature of meiotic prophase I, occurs properly since our previous studies indicated a requirement for AGO4 in these events. Spreads revealed the mislocalization of BRCA1, TOPBP1, and γH2AX, known sex-body markers, supporting a role for one or more of these AGOs in MSCI and meiotic prophase I. To narrow down a specific role for AGO3, I investigated the fertility of Ago3 KO males. Spermatozoa numbers and function were assessed with computer assisted sperm analysis (CASA). Surprisingly, homozygous mutant Ago3 KO mice had both normal sperm counts and testis weight when compared to wild-type (WT) mice. However, the Ago3 KO mice show abnormal testis architecture, supporting that there may be a role for AGO3 in spermatogenesis.
Effect of 5HT-modulated bulbar processing on cortical odor responses in awake-behaving rats
Sugita, Kyle (2024-09-18)
The sense of smell is important for survival of many species with respect to finding food and shelter, avoiding danger and interacting with conspecifics. Neuromodulators such as acetylcholine, dopamine, noradrenaline and serotonin can act broadly on brain networks to adjust processing to diverse situations and behavioral needs. In this respect, the present study investigates the impact of serotonin (5HT) manipulation within the olfactory bulb (OB) on neural activity in response to odor stimuli in adult Long Evans Hooded rats. 5HT modulation of olfactory processing has not been studied extensively. We ask to what extend 5HT modulation of early olfactory processing in the olfactory bulb affects cortical responses to odorants. Towards this goal, we manipulated 5HT action in the olfactory bulb via intracerebral infusions of 5HT in rats Our results demonstrate that 5HT significantly increased spontaneous firing rates in both the OB and PC as well as enhanced odor sensitivity of cortical neurons. These findings underscore the importance of 5HT in modulating neural activity within the olfactory pathway, shedding light on the mechanisms underlying odor processing and sensitivity.

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