College of Agriculture and Life Sciences Honors Theses
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Undergraduate Honors theses for the College of Agriculture and Life Sciences.
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Item Aigamo alongside Nouminren: Situating Japanese Integrated Rice-Duck Farming in the Food Sovereignty MovementLeiber, 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.Item Customizing Deep Neural Networks for Call-Type Distinction in Eastern Meadowlark (Sturnella magna): Investigating links with Land Use, Behavioral Ecology, and ConservationCheeley, 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.Item Heart Rate Variability over the Lifespan and its Potential as a Peripheral Biomarker for Cognitive Decline in Long-Evans RatsSutter, 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.Item Assessing Retrotransposition of Keno, a Site-specific Transposable Element in ZebrafishVictoria 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.Item AGO Argonautes in spermatogenesisJohnstone, 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.Item Effect of 5HT-modulated bulbar processing on cortical odor responses in awake-behaving ratsSugita, 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.Item Potential Impacts of New York State’s Food Donation and Food Scraps Recycling Law on Diet Composition, Milk Production, and Emissions in the New York Dairy IndustrySteele, Jacqueline (2023-05-24)Food waste accumulating in landfills has become an increasing issue in the face of global warming. Over 30% of food collects in landfills where it will decompose into methane. New York State recently passed the Food Donation and Food Scraps Recycling Law, which mandates that businesses creating over two tons of food waste per week find an alternative way to dispose of food waste to prevent it from entering landfills. Feeding food waste to livestock is one way to accomplish this. Food waste donated to dairy farms is a heterogeneous mixture consisting of fruits, vegetables, and bakery-related goods. In this study, I first aimed to examine the nutrient variability of this type of food waste. I studied key nutrients for dairy cattle nutrition including fats, sugar, starch, fiber, and crude protein. Second, I estimated milk production for diets with a 1 to 5% inclusion rate of food waste. Lastly, I evaluated the potential emission reductions when food waste was included from 1 to 5%. To determine the variability in nutritional quality of food waste, I collected three independent samples of food waste with duplicate subsamples biweekly for seven weeks and sent them to DairyOne for composition analysis. Sugar and starch were the most variable nutrients. Using CNCPS, I determined that the diet with a 5% inclusion rate was best for milk production, which produced a predicted 45.9 kg milk / day. I evaluated the potential emissions reduction of 60,000 kilograms of CH4 for every 5 million kilograms of food waste used.Item Exploring Color-Physiology Relationships Across Two Populations of Tree Swallows, Tachycineta bicolorRodriguez, Alyssa (2018-03)Signal traits often evolve to communicate information about individual differences in physiological state, especially those important for fitness. As the ability to cope with stressors is an essential aspect of an animal’s fitness, it may be beneficial to advertise to conspecifics. When facing stressors, vertebrates mount a glucocorticoid stress response. However, mounting a stress response is energetically demanding and can be especially costly when breeding. Because regulation of the stress response is important to fitness, and because glucocorticoids (CORT) shares biochemical pathways with many condition-dependent ornaments, I investigated whether ventral plumage color in tree swallows—an apparent social signal—predicts CORT regulation across populations of tree swallows, Tachycineta bicolor. Specifically, I examined whether the brightness of white ventral plumage predicts three aspects of CORT regulation: baseline levels,the CORT response to a standardized stressor, and the ability to down-regulate the CORT response through negative feedback. For a population in Alaska (AK), facing harsher breeding conditions than one in New York (NY), I expected brighter ventral plumage to positively correlate with negative feedback efficacy. My results showed that in NY, birds with brighter breast feathers had significantly stronger negative feedback, but that in AK, there was no relationship between feedback efficacy and breast brightness. Neither baseline nor stress-induced CORT levels predicted color in either population. Mean negative feedback strength was weaker in NY for the favorable year of 2016 than in 2017, despite both populations facing challenging environmental conditions that year. These results suggest that bright white breast plumage in tree swallows could serve as signal trait to communicate strong negative feedback to potential mates or aggressors.Item Acoustic Variation in Ictalurid CatfishesLecorchick, Jessica (2022-05)There are more than 35,000 ray-finned fishes (Actinopterygii) species potentially using acoustic communication. However, of the approximately 1200 known soniferous fish species, few include North American freshwater fish. To help fill this knowledge gap in fish acoustic communication, which holds great promise for conservation monitoring, I document acoustic measurements (duration 90%, bandwidth 90%, number of pulses, center frequency, and peak time) across 4 species (Ameiurus nebulosus, Ameiurus natalis, Noturus flavus, Ictalurus punctatus) from 3 genera of the North American catfish family, Ictaluridae. This was done by recording 10 trials of disturbance calls from 28 individuals and analyzing a total of 1294 sounds using Raven Pro 1.6 software. I hypothesized that: 1) more phylogenetically/morphologically related species would have more similar acoustic features, 2) acoustic features would correlate with one another, and 3) acoustic features would correlate with standard length (cm). For hypothesis 1, I instead found that Ameriurus nebulosus were the most acoustically dissimilar, despite having the highest level of phylogenetic/morphological similarity with Ameirus natalis. However, only Ameriurus nebulosus' number of pulses were significantly different from other species. For hypothesis 2, it was found that many acoustic measurements were correlated with one another as predicted. For hypothesis 3, only the number of pulses was found to be significantly correlated with standard length, but minimally so. These findings further support the notion that pulsation measurements may contain a high level of phylogenetic signal given it being the most important characteristic to differentiate species.Item Coronavirus Emergence and Evolution: 6+In vitro Analysis of Spike Protein Cleavage of SARS-CoV-2, AcCoV-JC34, and Murine Hepatitis VirusSingleton, Deanndria T. (2022-05)Members of the Coronaviridae family of viruses represents a highly diverse group that emerges from a wide range of animal reservoirs. Animal reservoirs may vary, from bats and birds to mammals and rodents. Interestingly, some members of Coronaviridae contain a distinct furin cleavage site (FCS) (RXR/KR) at the S1/S2 domain of the spike glycoprotein. The FCS is recognized by the prototypical proprotein convertase, furin, and previous studies show that SARS-CoV-2 contains an FCS, which happens to be atypical in terms of the positioning of the basic (R) residues (RRAR). The FCS can often be found in human, avian and rodent coronaviruses, but are not typically present in SARS-like viruses, including in bat reservoirs. AcCoV-JC34 is a little understood coronavirus (sub-genus Luchacovirus) isolated from Apodemus chevrieri (Chevrier’s field mouse) in Yunnan, China, and is predicted to contain a putative FCS. In this study, first we determined whether the presence of the FCS on AcCoV-JC34 allows for furin cleavage, as it does for SARS-CoV-2. Next, we analyzed the spike protein cleavage of murine hepatitis virus (MHV) strains using furin, and compared our data to prior studies with the goal of understanding disease pathology in mice. To examine these cleavage events, we generated predicted furin cleavage scores using ProP computer software for the S1/S2 domain of selected coronaviruses. We then utilized a fluorogenic peptide cleavage assay in which linear peptide mimics of the S1/S2 domain of selected coronaviruses were mixed with furin protease and buffwe. From the data, we obtained the comparative activity of the protease. We found that although AcCoV-JC34 appears to have an appropriate series of amino acid residues for furin cleavage, our data suggests that it is not cleaved by furin. Further, for MHV, furin cleavage is strain-dependent and can vary across pH values. Overall, this work informs a study of coronavirus evolution, emergence, and pathogenesis with respect to the S protein.