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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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 Industry
Steele, 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.
Exploring Color-Physiology Relationships Across Two Populations of Tree Swallows, Tachycineta bicolor
Rodriguez, 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.
Acoustic Variation in Ictalurid Catfishes
Lecorchick, 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.
Coronavirus Emergence and Evolution: 6+In vitro Analysis of Spike Protein Cleavage of SARS-CoV-2, AcCoV-JC34, and Murine Hepatitis Virus
Singleton, 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.
Understanding T-cell dependence in the mouse immune response to glycosylated outer membrane vesicles
Tyagi, Srishti (2022-05)
While engineered Escherichia coli outer membrane vesicles expressing glycans have been previously characterized as efficient vaccine delivery platforms capable of producing a glycan-specific immune response, the mechanisms behind this immune response are largely unknown. Furthermore, the modification of the native structure of lipid A on the OMVs from a hexa- to a penta-acylated form has been routinely used to decrease the toxicity of OMVs under the assumption that it does not have an effect on the adaptive immune response to the antigen displayed on the OMV. Here, we immunized C57BL/6 and T-cell deficient mice with hexa- and penta-acylated OMVs expressing polysialic acid (polySia), a repeating glyco-polymer of sialic acid. Results demonstrate that the immune response to penta-acylated polySia-OMVs relies on the presence of T cells, is driven by B2 cells in the peritoneal cavity, and fails to activate or create a polySia-specific memory B cell response. Alternatively, the response to hexa-acylated polySia-OMVs has a T-independent component that is driven by B1 cells in the spleen and peritoneal cavity, and generates a class-switched, polySia-specific memory B cell population. These results raise key insights for the use of glycosylated outer membrane vesicles (glycOMVs) in vaccination, as considering induction of a T-dependent or T-independent immune response may be beneficial for patients with differing immune competencies.
Equine Synovial Sepsis -A Systematic Review of the Literature
Peek, Michael (2022-05)
For my thesis I performed a systematic review of the literature on equine synovial sepsis covering 1990-July 2021 using appropriate PICOS criteria. Of the 541 studies initially screened, 110 were retained in the final review. These were first reviewed from the perspective of the etiology of synovial sepsis, the frequency with which specific synovial structures were involved, and survival rates to discharge for foals and adults. Return to soundness and athletic performance were also analyzed for adults. The microorganisms most commonly identified and the prevalence of antimicrobial susceptibility were also reviewed. The most common cause of synovial sepsis in adults was trauma (70%) compared to hematogenous infection in foals (96%). Overall the most common form of synovial sepsis was septic arthritis, with the tarsus being the most affected joint in adults. The digital flexor tendon sheath and navicular bursa were the most commonly affected tendon sheath and bursa respectively. Survival rates to discharge (p=0.03) were higher in adults (83%) than foals (63%), but did not change over time (p=0.17). Rates of survival, return to soundness, and return to athletic performance did not differ for adults with septic arthritis, tenosynovitis, or bursitis. In adults the most common organisms isolated were Staphylococci, Streptococci, and E.coli, compared to E.coli, Rhodococcus equi, and Actinobacillus spp, in foals. Although antimicrobial data was limited, the prevalence of antimicrobial resistant coagulase-positive Staphylococci increased over the duration of the study. Prevalence of antimicrobial resistant coagulase-negative Staphylococci and beta-hemolytic Streptococci varied between antimicrobials.
Quantification of bacteriain Xanthomonas citripv.malvacearuminfection and identification of virulence factors in the emergent strain Xcm4
Bauer, Taran (2022-05)
The pathogen Xanthomonas citripv. Malvacearum (Xcm) is widely known as the causal agent of Cotton Bacterial Blight (CBB), which causes millions of dollars of crop loss in the United States annually. Understanding the molecular mechanism underlying this disease is vital for engineering resistant cotton varieties and preventing crop failures worldwide. In 2011, novel virulent strains of Xcm appeared in the southwestern United States which lacked previously identified key virulence factors but could infect varieties of cotton which were resistant to historical strains of Xcm, suggesting that the pathogen had evolved a new mechanism for effecting virulence. This thesis describes an efficient method of quantifying this bacteria’s proliferation in planta in a laboratory setting and utilizes this method to test this pathogen for a primary mode of virulence through systematic gene knockouts. The data from this study suggests that light emission can be used to efficiently track bacterial populations in planta, and that novel strains of Xcm may be using a new type III effector named Tal7b as a primary virulence factor. Development of a method to track bacterial infections enables a more precise understanding of how bacteria proliferate during the infection process, which can be used to understand with more depth how this pathogen causes disease. Additionally, laboratory studies of Tal7b may yield potential routes for future crop editing and resistance to these emergent strains.
Computational Modeling and Optimization Applied to Controlled Environment Agriculture Lighting Systems
Santander, Daniel; Mattson, Neil; Harbick, Kale (2021-11-09)
Supplemental lighting is integral to year-round production of greenhouse crops; however, the location of lights within the greenhouse and its effects on lighting uniformity in the growing space is often not considered. This research was conducted to assist Controlled Environment Agriculture (CEA) producers and researchers in identifying the optimum lighting layout for improved lighting uniformity. The methodology outlines the development of an algorithm for modelling supplemental lighting, based on standardized goniophotometric data, and optimizing the location of lighting fixtures within the CEA environment. This resulted in the production of a software package in the Python Programming Language that could model and optimize lighting uniformity for unique CEA environments based on their physical dimensions and specified lighting fixture. Through the implementation of this novel software, the lighting uniformity for hypothetical CEA environments with a small number of supplemental lighting fixtures were optimized.
CRISPRi Knockdown and Sequence Analysis of the BHIKHARI Family of Endogenous Retroviruses in Zebrafish
Schofield, Phillip (2021-07)
Transposable Elements (TEs) are mobile, selfish genes that have, in some cases, been shown to provide functions for the host. A poorly characterized family of LTR retrotransposons, BHIKHARI (bik), has unusual early embryonic, cell-specific expression patterns in the zebrafish (Danio rerio). This led me to investigate their possible role in the development of the zebrafish embryo and their evolutionary history in related species. I present a successful CRISPRi knockdown experiment of bik-1, one of five subfamilies of bik, that shows evidence of the involvement of bik-1 in cell differentiation. Polymorphism analysis gave evidence that bik-1 may still be active in zebrafish while the other bik subfamilies may not be. Sequence analysis of the subfamilies suggests that all five may have arisen from a common element sometime after the divergence of the Danionella and Danio genera. Additionally, I characterize bik elements as members of the recently described Lokiretrovirus clade of retroelements.
Investigating the Diversity of Latex Metabolites in Species of the Euphorbia Genus
Park, Se Jin (2021-07)
The Euphorbiaceae family is one of the largest angiosperm families with its largest genus Euphorbia, containing about 2000 species. This genus is characterized by the presence of laticifers and latex. Latex is a milky fluid with diverse secondary metabolites but especially enriched with terpenes. Many of these metabolites, especially diverse terpenes, are used by the Euphorbias as a defense mechanism against herbivores. Although Euphorbia is a large genus, it is relatively understudied at the metabolomic and genomic level compared to other Euphorbiaceae genera. The goal of this research was to establish a foundation for further investigation into latex, laticifers and their contribution to species diversity in the Euphorbia genus. Towards this goal, first, I performed a metabolomics study of 18 Euphorbia species. Next, two model Euphorbias – Euphorbia peplus and Euphorbia lathyris – were selected for further analysis based on previous biochemical studies.We confirmed their identity and estimated their genome size using maturase K (matK) and flow cytometry analysis, respectively. Further, a latex metabolite extraction protocol was standardized and used for assessing the diversity of metabolites from the latex of the two Euphorbia model species using a machine learning approach. The metabolite networking analysis suggested that the Euphorbia latex has a diverse network of secondary metabolites, from which we identified 13 unique terpenes. Finally, to understand the genetic causes of the metabolic diversity, de novo assembled transcriptomes were used to identify terpene synthase genes. Phylogenetic analysis revealed that the Euphorbiaceae family and the Euphorbia genus have conserved terpene synthase subfamilies in relation to other plant families that were studied. The results indicate that the Euphorbia latex is highly diversified while having relatively conserved proteins that are responsible for producing the latex metabolic diversity.

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