College of Agriculture & Natural Resources
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The collections in this community comprise faculty research works, as well as graduate theses and dissertations.
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Item EFFECTS OF FOOD PROCESSING METHODS ON PHENOLIC ACIDS AND ANTIOXIDANT CAPACITY IN SWEET CORN(2024) Dong, Fangxiang; Yu, Liangli; Agricultural and Resource Economics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This thesis research was designed to evaluate the effects of different food processing methods on the phenolic acid and antioxidant properties of sweet corn. Phenolic acids, such as ferulic acid and p-coumaric acid, are known for their health benefits. The research primarily focuses on two main stages of food processing: post-harvest handling and domestic cooking (boiling and steaming. These processes are evaluated to determine their impact on the soluble free, soluble conjugated, and insoluble bound forms of phenolic acids in sweet corn.Phenolic acids were analyzed by High-Performance Liquid Chromatography (HPLC). The study found that post-harvest handling significantly reduced the phenolic acid content, particularly in the insoluble bound form. Domestic cooking also led to notable reductions in phenolic content, though antioxidant activity, as measured by DPPH and ABTS assays, showed varying responses, sometimes increasing in treated samples. It was noted that different processing methods can induce structural changes that may either preserve or enhance the antioxidant properties. Furthermore, the results of this thesis explored optimal food processing techniques to maximize the retention of bioactive compounds, providing insights for better food preservation strategies.Item ZIKA VIRUS RECRUITS CELLULAR PROTEINS TO SUPPORT ITS REPLICATION(2024) Chang, Peixi; Zhang, Yanjin YJ; Veterinary Medical Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Zika virus (ZIKV) is a mosquito-borne pathogen with a massive impact on global public health due to its association with severe neurological complications, including microcephaly in newborns and Guillain-Barré syndrome in adults. The ZIKV epidemic in the Americas in 2015-2016 and its continuing spread in tropical regions have highlighted the urgent need to understand the molecular mechanisms of viral replication to develop effective antiviral strategies. However, many aspects of how ZIKV interacts with host cells remain unclear. This study identifies and characterizes host factors contributing to ZIKV replication. First, karyopherin alpha 6 (KPNA6) contributes to ZIKV replication by interacting with the ZIKV non-structural protein NS2B. Characterization and mutational analyses identified two essential amino acid residues within NS2B that are critical for interacting with KPNA6. The substitution of these two residues of NS2B in an infectious ZIKV cDNA clone resulted in a significant reduction in viral replication, suggesting that the NS2B-KPNA6 interaction plays a vital role in the viral life cycle. Further studies found that KPNA6 contributes to ZIKV RNA synthesis. Mass spectrometry analysis of the KPNA6 interactome showed that KPNA6 interacts with proteins involved in RNA synthesis, suggesting that ZIKV recruits these factors by promoting KPNA6-binding. Second, this study developed an effective method to isolate the ZIKV replication complex, a membranous structure where viral RNA is synthesized. Proteomic analysis of the isolated complex led to identifying numerous host proteins associated with the viral replication machinery. Among these proteins, human replication factor C subunit 2 (RFC2), an accessory factor involved in DNA replication and repair, was discovered to facilitate ZIKV replication, making it a potential target for therapeutic interventions. In conclusion, this study reveals crucial host factors essential for ZIKV infection and replication and provides insights into the ZIKV-cell interactions. These findings offer new possibilities for developing novel antiviral strategies for controlling future viral outbreaks.Item DEVELOPMENT OF CHITIN NANOCRYSTALS AND THEIR APPLICATIONS IN FOOD AND AGRICULTURAL AREAS(2024) Jia, Xiaoxue; Wang, Qin; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Seafood industry generates millions of tons of waste annually, with crustacean shells being a significant component. Discarding these shells not only exacerbates environmental pollution but also represents a missed opportunity for resource recovery. This dissertation research aims to address these environmental challenges by repurposing crustacean shell waste into high-value nanomaterials, specifically chitin nanocrystals (ChNCs), and exploring their applications in the food, agricultural, and environmental sectors. The primary objective of this study is to investigate the fabrication, functionalization, and potential industrial applications of ChNCs, thereby offering a sustainable alternative to conventional synthetic materials.Traditional chitin nanocrystals ChNCs obtaining methods rely on strong acids, posing environmental risks. This research introduces a more sustainable phosphoric acid (PA) hydrolysis method, which uses significantly lower acid quantities, reduces environmental impact, and avoids corrosive waste. Moreover, the novel PA hydrolysis occurs in the solid state and can be handled by hand, simplifying operation. This method efficiently yields uniform ChNCs with positive surface charges (~+27 mV), suitable for scalable industrial applications. Additionally, 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO) oxidation was employed to produce oxidized chitin nanocrystals (O-ChNCs) with negative surface charges (~ −56 mV). ChNCs and O-ChNCs were investigated as stabilizers in Pickering emulsions. Both were able to significantly enhance the stability of oil-in-water (O/W) emulsions, particularly when pH > 9. O-ChNCs further demonstrated encapsulation efficiencies of up to 80% for bioactive compounds like quercetin, highlighting their potential in food and nutraceutical delivery systems. Additionally, ChNCs and O-ChNCs were incorporated into a colorimetric sensor array (CSA) to monitor beef freshness. The negative charged O-ChNC-based sensor exhibited sensitivity to spoilage gases, achieving 99.3% accuracy in beef freshness detection with the aid of deep learning algorithms. This innovation provides a non-invasive cost-effective method to food quality and safety monitoring. Furthermore, ChNCs were deacetylated to form chitosan nanocrystals (ChsNCs), and subsequently modified with zinc to create a ChsNCs@Zn composite for the removal of per- and polyfluoroalkyl substances (PFASs) from water. The composite achieved 50% PFAS removal within 5 minutes and ultimately achieved 68% removal, showcasing strong adsorption capabilities and offering a potential sustainable solution for PFAS remediation in contaminated water sources. In summary, this research is driven by the need to solve the environmental problem of seafood waste, while also tackling challenges in food stability and safety, as well as water purification. The findings contribute to advancing sustainable materials and practices in response to pressing environmental challenges.Item ROLE OF TRPV4 MECHANOSENSING REGULATING MACROPHAGE FUNCTIONS IN INFLAMMATORY DISEASES(2024) Dutta, Bidisha; Rahaman, Shaik O; Nutrition; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Macrophages are the most versatile cells of the hematopoietic system with roles in homeostasis, host-tissue development, innate immune response and tissue repair. Although the inflammatory activation and maintenance signals are tightly regulated, an imbalance in them results in unchecked inflammation resulting in cellular and tissue damage. Macrophages can affect most if not all phases of inflammation owing to their ability to adopt distinct functional states, secrete cytokines and phagocytose pathogens and debris. Recent evidence suggests that beyond biochemical cues, mechanical forces, like changing matrix stiffness in the tissue microenvironment, can shape immune cell functions involved in inflammation. These cells convert mechanical stimuli to biochemical signals in a process called mechanotransduction, regulating a multitude of cellular functions. However, knowledge about the molecular mediators of mechanotransduction and their functions in macrophage phenotypic and functional change is largely missing, highlighting the need for studying mechanosensory molecules such as ion channels. The present study focuses on the role of a specific mechanosensitive ion channel, Transient Receptor Potential Vanilloid 4 (TRPV4), in the regulation of macrophage mediated inflammatory responses. Given its emerging role in inflammatory diseases like fibrosis, arthritis, foreign body response (FBR), TRPV4’s contribution to macrophage behavior in inflammation is of growing interest. Employing cellular imaging and molecular biology techniques such as Ca2+ influx assays, immunohistochemistry, immunoblotting, and single nuclei RNA sequencing we delineate mechanisms by which biomechanical stimuli-mediated activation of TRPV4 affects macrophage function. We elucidate TRPV4’s role in macrophage mechanotransduction, providing a mechanistic understanding of inflammatory disease pathophysiology which could lead to the development of potential therapeutics for disease intervention.Item MEDIATION OF CORTICOSTERONE-INDUCED GROWTH HORMONE GENE EXPRESSION IN CHICKEN EMBRYONIC PITUITARY CELLS: IDENTIFICATION OF TRANS-ACTING FACTORS AND A NOVEL PITUITARY CELL TYPE(2024) Liu, Kuan Ling; Porter, Tom E.; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Growth hormone (GH) is responsible for up to 30% of growth in broiler chickens. Somatotrophs, or GH secreting cells, begin to differentiate around embryonic day (e)14, in conjunction with an increase in the primary plasma glucocorticoid (GC) corticosterone (CORT). CORT treatment of e11 chicken embryonic pituitary (CEP) cells induces premature GH secretion. This GC-induced process involves trans-acting factors because the GH gene lacks a canonical GC response element (GRE). In addition to the binding of ETS1 and the GC receptor (GR) to the GC-responsive region (GCRR; 1045/ 964), we hypothesize that there are other regulatory factors necessary for CORT responsiveness. By modifying the pGL3_-1742/+25 GH-luciferase reporter, we have constructed various other GH-luciferase reporters and analyzed them for promoter activity in response to CORT treatment. We identified a putative distal (d) ETS-Like 1 (ELK1) binding site that is necessary. The proximal (p)PIT1 site and pTATA box were also identified to be critical for CORT induction of the GH gene. Interestingly, cloning multiple copies of the extended GCRR (eGCRR; -1067/-900) further increased promoter activity in an additive manner under both basal and CORT treated conditions. Through single-cell RNA sequencing (scRNAseq), 8 members of the ETS family of transcription factors were identified in > 5% of the somatotroph population. Commercial antibodies were validated, and human (h)ETV1, hELF2, hELK3, and hETV6 antibodies were confirmed to recognize their recombinant chicken ortholog and to identify their corresponding protein in e11 CEP cells. Results from chromatin immunoprecipitation quantitative PCR suggest that multiple ETS members are involved in CORT induction of the GH gene with more evidence pointing towards ELF2 and ELK3. Identifying trans-acting factors for the GH gene inducible by CORT allows for better understanding of endogenous GH regulation in chickens. Further analysis of the scRNAseq data from e11 CEP cells revealed a cluster of cells expressing genes for more than one hormone-producing cell type (“premature nebulous” cluster). Within the premature nebulous cluster, a large population (~30%) was co-expressing proopiomelanocortin (POMC) and growth hormone (GH). We named this novel cell population the cortico-somatotrophs. Through RNA fluorescent in-situ hybridization (RNA-FISH) and dual label immunofluorescence, we verified the existence of the cortico-somatotrophs at both the mRNA and protein level, respectively. Cortico-somatotrophs were also shown to share genes for receptors normally specific to both corticotrophs (CRH-R1) and somatotrophs (GHRHR). Additionally, in response to CORT treatment, the cortico somatotrophs showed an increase in GH as well as a decrease in POMC mRNA levels. The discovery of the cortico-somatotrophs suggests a modification to the current dogma on pituitary cell lineages, where corticotrophs and somatotrophs may have overlapping developmental pathways. In conclusion, our discovery of the cortico somatotrophs has furthered our understanding of CEP development and opened the door for further exploration of the cell lineages during pituitary development.Item MACHINE LEARNING AND GENOMICS FOR IMPROVED FOOD SAFETY AND RISK ASSESSMENT OF SALMONELLA ENTERICA IN CHICKEN(2024) Benefo, Edmund Ofosu; Pradhan, Abani K; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Salmonella enterica is a leading cause of foodborne illnesses worldwide and is commonly associated with poultry. Salmonella has many closely related serovars, yet these serovars exhibit significant variability in many characteristics including host range, virulence, growth behavior, stress response, and antimicrobial resistance. In the past, this intricate and dynamic population heterogeneity of Salmonella severely hampered control efforts, but, today, this has improved through the sequencing of Salmonella genomes. Whole genome sequencing (WGS) provides a better understanding of the evolutionary and ecological adaptations that underlie the survival of Salmonella against antimicrobials, oxidative agents, non-optimal temperatures, and other stressors in the environment and their hosts. Coupling machine learning with WGS expands on these advantages by enabling the identification of genetic patterns that may not be immediately apparent. The overall goal of this research was to explore how machine learning and genomics can be integrated to improve food safety. First, a machine learning model was developed to identify stress response genes in Salmonella isolated from different poultry processing stages. It was found that beyond genes encoding for cold and heat shock proteins, other genes involved in lipopolysaccharide biosynthesis, DNA repair and replication, and biofilm formation are involved in Salmonella’s overall stress response mechanism. Additionally, a machine learning model was developed to predict antimicrobial resistance (AMR) phenotypes in Salmonella isolates using WGS data. The model predictions were comparable to existing bioinformatic methods for AMR prediction and identified AMR genes that are typically not the resistance determinants public health agencies focus on. Expanding this approach for AMR surveillance could lead to the discovery of novel AMR genes. Lastly, a quantitative microbial risk assessment for Salmonella in chicken that incorporated Salmonella heterogeneity in growth and virulence was developed. The findings revealed that variations in virulence have a greater impact on the risk of salmonellosis than variations in growth rate. Overall, this research contributes to efforts to enhance food safety measures and reduce chicken-associated Salmonella illnesses.Item SMALL MAMMAL POPULATIONS, TICKS, AND TICK-BORNE DISEASES IN URBAN PARKS(2024) Coriell, Carson; Mullinax, Jennifer; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)As urban environments expand, the distribution of wildlife, particularly white-footed mice, influences public health through zoonotic pathogen transmission, such as Lyme disease. This study examined pathogen risk in urban green spaces, focusing on interactions among small mammal communities, black-legged ticks, and the bacterium Borreliella (Borrelia) burgdorferi. Over two years, small mammal trapping was conducted across six urban park sites in Maryland to 1) quantify small mammal densities in six unique urban sites and 2) identify correlations between small mammal community and habitat structure related to pathogen prevalence. Findings revealed significant differences in pathogen risk between parks, driven by elevation and landscape features, with open shrub-scrub, and upland habitats, such as powerline corridors, linked to increased transmission risk. These results underscore the importance of habitat-level management strategies for urban green spaces to mitigate pathogen risk, rather than focusing solely on white-footed mice.Item Managing Cover Crops for Better N Efficiency and Soil Health(2024) Stefun, Melissa; Weil, Ray; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Winter cover cropping is a major tool that agriculture can use to protect soil and water quality and mitigate climate change. Unlike farmland in the world at large, most Maryland cropland has seen little tillage disturbance and some level of cover cropping for decades. With that background, field experiments on two soils with contrasting textures at the Beltsville Facility of Central Maryland Research and Education Center tested the effects of cover crop management enhancements on nitrogen (N) leaching, soil health indicators, and cover crop N uptake over three years. Two cover crops (sole rye and a mixture of forage radish, crimson clover, and rye) were compared to a control where cover cropping was ceased. The cash crops were corn and soybean grown in rotation. With best nutrient management practices applied, suction lysimeter sampling at 90 cm depth from October through April showed low levels of N leaching in general, but NO3-N concentrations were significantly lower under cover crops. Overall mean concentrations of NO3-N were 2.20 mg N/L in the control but 0.43 mg N/L under cover crops. Additionally, soil water samples were digested to determine dissolved organic N (DON) which was found to make up between 44-60% of the total dissolved N in the leaching water. In additional experiments, a small fertilizer N application was made to cover crops to stimulate rapid deep rooting with the goal of accessing soluble N deep in the profile to increase N capture by more than the amount of N applied. The response to fall N fertilization failed to accomplish this goal and was not related to the surface soil NO3-N concentration as expected. In spring, cover crops were terminated on three dates from mid-April to mid-May and rye biomass doubled with each extra two weeks it was allowed to grow whether it was in the mix or alone. The effect of cover crops on soil health indicators was evident with increased soil permanganate oxidizable carbon, total soil carbon, lower bulk density, and greater aggregation. These experiments demonstrated that cover crops with enhanced management can have marked effects on an agricultural system already using sustainable practices.Item ANTHROPOGENIC INFLUENCES ON BOTTOM-UP AND TOP-DOWN REGULATION OF ANIMAL DISTRIBUTIONS, POPULATIONS, AND BEHAVIORS IN URBAN ENVIRONMENTS(2024) Herrera, Daniel Joseph; Gallo, Travis; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Animal populations are simultaneously governed by both bottom-up (e.g., habitat availability) and top-down (e.g., predation) regulation. While ecologists historically sought to differentiate the roles of bottom-up and top-down regulation on ecosystems, the two are not so easily defined in urban ecosystems due to the immense influence humans have on ecological processes in cities. In Chapter One, I present this argument from a philosophical perspective and comment on how this philosophy has shaped my worldview. In Chapter Two, I examine the legacy of historical park planning on urban bird assemblages using archived municipal maps and historical bird data. My analysis found a positive correlation between percent park area and both species richness and functional richness of birds. Additionally, I found the effect size of park area was larger than the effect of certain life history traits thought to facilitate urban exploitation. These results indicate that landscape features and life history traits are equally responsible for the success of synurbic species. Chapter Three explores the effect of urbanization on animal behavior by analyzing anti-predator behavior of white-tailed deer (Odocoileus virginianus) in relation to ambient light, noise, and human activity. Despite negligible predation risk in my study area, deer expressed higher vigilance behavior in dark and noisy conditions, and increased their foraging group size during noisy conditions. These results suggest that anti-predator behaviors are a response to the perception of predation risk rather than a response to the actual presence of predators. Although predation of deer is rare in urban ecosystems, predation of smaller wildlife species by mesopredators, such as non-native domestic cats (Felis catus) is common. Chapter Four examines the potential for predation and zoonotic disease transmission between cats and eight native mammals by estimating the spatial and temporal overlap between species. I found that cat distribution was largely driven by anthropogenic features, whereas native wildlife was generally deterred by anthropogenic features and instead occupied forested areas. I also found that cats, as a species, were active on the landscape during the full 24-hour cycle. As a result, while spatial overlap between cats and wildlife varied across the study area, temporal overlap was possible anywhere cats and wildlife co-occurred. Chapter Five expands on Chapter Four and investigates predation directly by using observations of cats carrying prey documented by motion-activated cameras. I found that predation by cats was higher in areas where supplemental cat food was prevalent, but declined near forested areas. Additionally, my results indicate that cats within 250 meters of a forest edge predominantly preyed on native wildlife, whereas cats generally preyed on non-native rats (Rattus norvegicus) when greater than 250 meters from a forest edge. Each chapter provides applied recommendations to the management and conservation of urban wildlife, but together, my work demonstrates the entanglement of bottom-up, top-down, and anthropogenic forces in urban ecosystems. In light of these findings, I advocate for a more nuanced understanding of ecosystem regulation through a socio-ecological lens.Item Phenotypic and Genetic Analysis of Reasons for Disposal in Dairy Cattle(2024) Iqbal, Victoria Audrey; Ma, Li; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Reasons for disposal are defined as why a cow has left the herd during lactation and are documented as termination codes. Dairy cattle termination codes were collected by Dairy Records Processing Centers and stored in the National Cooperator Database maintained by the Council on Dairy Cattle Breeding for analysis. The list of possible termination codes is as follows: code 0 is cow lactation that ended typically without an abortion, code 1 is locomotion problems, code 2 is female transferred or sold, code 3 is low milk yield, code 4 is reproductive problems, code 5 is unspecified reasons, code 6 is death, code 7 is the presence of mastitis, code 8 is abortion, code 9 is udder problems, code A is an unfavorable phenotype, and lastly code B is undesirable temperament. Understanding termination codes is the key to understanding and improving farm management. Unfortunately, the secondary termination codes are not utilized, despite studies saying one reason is too limited. Heifer termination codes should be more utilized, and studies show that this could improve heifer management. The four processing centers' principal termination codes deviated a little from year to year, but processing center D had the most variation in principal termination codes. There were few records with termination codes 9, A, and B. There was low lameness found for Jersey cattle but more fluctuations for their termination codes 6, 7, and 8. Jersey's main reason for disposal was sold and low milk yield. As for Holstein, the main reasons for disposal were low milk production and death. Recommendations include removing termination code 5 (other reasons) and enforcing a secondary termination code for code 2 (sold). Also, including the percentage of animal records used in traits developed at the CDCB was recommended to encourage farmers to add more records to improve breeding selections. Overall, the top main reasons for disposal were low milk yield, death, and reproduction across breeds from 2011 to 2022. To determine whether health traits correlate to termination codes and how health traits change the probability of survival, a multinomial logistic regression was developed, where twelve health traits, breeds, and other factors were used as an independent variable for the termination code, the dependent variable. The output is a regression coefficient list that conveys the effect of each health trait for each termination code. The results show the apparent impacts of animal breeds on different termination codes, such as dairy crossbreeds negatively affecting termination due to reproductive advantages that follow the literature. Lastly, using termination codes as phenotype, this study focuses on developing a genome-wide association study (GWAS) using the Weighted single-step Genomic Best Linear unbiased prediction (WssGBLUP) model to find significant SNPs related to survival in Holstein cows. In summary, this study provided an understanding of reasons for disposal trends, modeled the reasons for disposal, determined the likelihood of termination post-incidence, and found the heritability and important SNPs of each termination code.