Animal & Avian Sciences Theses and Dissertations

Permanent URI for this collectionhttp://hdl.handle.net/1903/2741

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    Identification of the molecular networks governing ovulation frequency in low and high egg producing turkey hens
    (2019) Brady, Kristen Marie; Porter, Tom E; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Selection for carcass traits has negatively impacted and varied the reproductive efficiency of the commercial turkey hen, creating overall lowered egg production as well as distinct groups of low egg producing hens (LEPH) and high egg producing hens (HEPH). Ovulation frequency correlates with egg production and differs between LEPH and HEPH. Ovulation is governed primarily by the hypothalamo-pituitary-gonadal (HPG) axis through a preovulatory surge (PS) of luteinizing hormone (LH) and progesterone (P4) but ovulation can be influenced by the hypothalamo-pituitary-thyroid (HPT) axis. Dysregulation of the thyroid and reproductive axes, disrupting the PS, leads to lowered egg production, leaving the poultry industry to compensate with larger breeding flocks. LEPH exhibited hypothalamic and pituitary expression consistent with decreased ovulation stimulation and increased ovulation inhibition as well as decreased steroid synthesis in follicle cells. Neuroendocrine and ovarian tissues from HEPH showed a higher sensitivity and response to in vitro HPG axis stimulation. Moreover, cells from HEPH responded positively to HPG axis inhibition while cells from LEPH responded negatively, indicating functional differences in HPG axis regulation. RNA sequencing results reinforced the higher expression of HPG axis genes in HEPH and showed higher expression of HPT axis genes in LEPH. Estradiol (E2) was identified as an upstream regulator activated in HEPH. Hens with average egg production (AEPH) also showed upregulation of E2 receptors during the PS, suggesting involvement in positive feedback loops. Supporting the role of E2 in neuroendocrine feedback, higher plasma concentrations of E2 were seen during the PS in HEPH. Looking into the HPT axis, LEPH displayed lower plasma concentrations of triiodothyronine (T3) and higher levels of thyroxine (T4) outside of the PS while HEPH displayed lower levels of T3 and higher levels of T4 inside of the PS. The T3 and T4 levels surrounding the PS in HEPH were consistent with levels seen in AEPH. At a molecular, cellular, and endocrine level, the reproductive physiology of LEPH and HEPH differs, ultimately leading to egg production differences. Studies tying the noted differences to egg production rates will allow for identification of genetic markers to increase the reproductive efficiency of commercial breeding hens.
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    ANTIBIOTIC ALTERNATIVES FOR TREATMENT OF MASTITIS IN DAIRY CATTLE
    (2019) Scholte, Cynthia Madeleine; Moyes, Kasey M; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Mastitis is one of the most costly diseases to the dairy cow industry. Implementation of management protocols have decreased the incidence rate of contagious mastitis pathogens, while the incidence of cases caused by environmental pathogens, such as Escherichia coli (E. coli) and Streptococcus uberis (Strep. uberis), remains unchanged. Currently, antibiotics are the primary therapy utilized to control mastitis. However, growing concern for antibiotic overuse, improper use and bacterial resistance have led to the examination of alternative strategies. Two promising alternative mitigation strategies were explored in the research leading to this dissertation. The first is a potent endolysin, PlyC, which has demonstrated bactericidal activity against several streptococcal species in a variety of applications. However, it is unknown how PlyC interacts with the bovine immune system. Varying doses of PlyC were non-toxic and did not alter the oxidative burst response of bovine neutrophils, the first immune cells recruited to the intramammary infection. The second alternative to an antimicrobial drug explored was citrus oil dissolved in ethanol. This was tested against E. coli strain P4. Prior antimicrobial investigations with citrus oil utilized dimethylsulfoxide as a carrier solvent, which is currently prohibited in the dairy industry. Citrus oil and its primary components were tested to determine minimum inhibitory, bactericidal and biofilm eradication concentrations. Citrus oil components, citral and linalool, demonstrated better antimicrobial activity than the native oil in vitro. In addition, citral and linalool were minimally toxic to bovine neutrophils and did not hinder their oxidative burst response in vitro. Because citral demonstrated greater antimicrobial activity than linalool, it was the logical candidate to test for the efficacy as an intramammary therapy against experimentally-induced E. coli mastitis. Unfortunately, citral treatment did not differ from a common intramammary antibiotic therapy or sterile buffered solution. In conclusion, the use of PlyC as an alternative therapy for Strep. uberis mastitis is promising as PlyC may not interfere with immune response during mastitis. The antimicrobial effects of citral may better serve as a disinfectant than a therapy for E. coli mastitis.
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    ESTIMATION OF DRY MATTER INTAKE AND IDENTIFICATION OF DIETARY AND PRODUCTION PARAMETERS THAT INFLUENCE FEED EFFICIENCY OF INDIVIDUAL DAIRY COWS
    (2019) Iwaniuk, Marie Elizabeth; Erdman, Richard A.; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The objectives of this dissertation were to: 1) develop and validate equations used to estimate individual cow dry matter intake (DMI; kg/d) based on a nitrogen (N) balance approach, 2) determine the discriminatory power of several biological, production, and dietary variables on dairy feed efficiency (FE) as defined as energy-corrected milk (ECM; kg/d) per unit of DMI, 3) repeat the second objective using residual feed intake (RFI) to indicate FE status, and 4) determine if RFI values are dependent on the equation utilized to estimate DMI. Results from the first experiment (Chapter 3) indicated that DMI could be successfully estimated on an individual cow basis using the following commonly measured parameters: milk yield, milk protein concentration, body weight (BW; kg), and dietary N concentration. These inputs are relatively simple to measure; therefore, this equation may be used in the dairy industry as a practical method to estimate individual cow DMI when cows are fed in a group setting. The results of the second experiment (Chapter 4) suggested that days in milk (DIM), milk fat yield (g/d), and BW had the most discriminatory power (89% success rate) to discriminate between cows based on their FE status when FE was defined as ECM per unit of DMI. Therefore, dairy producers can use these 3 variables to select for cows with high FE without requiring the measurement of DMI which can be costly and difficult to obtain. Observations from the third experiment (Chapter 5) suggested that RFI is indicative of differences in metabolic efficiency between cows independent of most biological, production, and dietary variables, except DIM. These results are consistent with other studies that have suggested that RFI is indicative of true differences in metabolic efficiency between cows regardless of production parameters. Lastly, the results of the fourth experiment (Chapter 6) suggest that RFI values generated from different DMI equations are strongly correlated such that RFI values are independent of the DMI equation utilized in the calculation. Thus, dairy producers can select the equation to estimate DMI that is most suitable for their operation without causing an “equation bias” on the RFI calculation.
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    Effect of grazing muzzles on grazing miniature horse behavior and physiological stress
    (2019) Davis, Kristina; Burk, Amy O; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Grazing muzzles are highly effective at reducing forage intake in horses and are a popular tool to control horse weight. However, grazing muzzle design may cause horses stress. The objective of these studies was to determine how grazing muzzles impact behavior and physiological stress in grazing horses. Two groups of 6 miniature horses, housed individually or in a herd, wore grazing muzzles for 0, 10, and 24 h/d. Over 9 weeks, body weight, heart rate parameters, salivary cortisol concentrations, and observations of behavior were collected. Results indicate muzzling did not seem to cause physiological stress as measured by cardiac and salivary cortisol parameters but did alter grazing and locomotive patterns. Muzzling for 24 h/d was necessary for weight loss and was associated with lower heart rate and higher heart rate variability. These findings suggest that muzzles do not cause stress in horses, even if left on for 24 h/d.
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    COMMUNITY STRUCTURES OF GUT MICROBIOME UNDER DIFFERENT DIETS IN ANGUS BEEF CATTLE
    (2019) Liu, Jianan; Song, Jiuzhou; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The microbiota of animals’ digestive tract plays important roles in health, nutrient utilization, and performance. For ruminants, the digestive tract, including rumen and other gastro-intestinal regions, hosts a unique and diverse microbiome that aids feed fermentation, digestion, and absorption. We hypothesize that compositions of diets can influence microbiomes and further affect the production of VFA and the composition of bile acids in beef cattle. We used rectum microbiota as a baseline and examined the microbiome in rumen and jejunum by16S-seq, together with quantifications of VFAs, lactate, and bile acids under grass-feeding and grain-feeding. We found that microbial communities displayed significant differences in microbiome structure and VFA production. Moreover, increased VFAs in grain-fed group may trigger lactate-associated bacteria growth. Bile acids could promote the growth of bacteria that had abilities of secondary bile acids conversion. These results provided deep insights into differences in beef quality and bovine biology under different diets.
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    SUPPLEMENTAL CHOLINE AND METHIONINE FOR DAIRY CATTLE: EFFECTS ON PERFORMANCE, LIVER FAT CONTENT AND GENE EXPRESSION, AND PLASMA AMINO ACID AND CHOLINE METABOLITE CONCENTRATIONS
    (2019) Potts, Sarah B; Erdman, Richard A; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The objectives of this dissertation were to 1) determine markers of post-ruminal choline supply so that bioavailability of rumen-protected choline (RPC) sources can be calculated in lactating cows and 2) investigate the production performance and metabolic effects of supplemental choline, methionine, or both on periparturient dairy cows. Observations from Experiment 1 indicated that of the 26 choline metabolites investigated, including 16 species of phosphatidylcholine (PC) and 4 species of lysophosphatidylcholine, free choline and betaine in blood and milk were most responsive to post-ruminal choline supplied via abomasal infusion. However, RPC did not elicit changes in blood or milk choline metabolites, even at the very high doses tested in Experiment 2. These results suggest that choline supplied as RPC is absorbed differently than choline supplied via abomasal infusion, that RPC is over-protected such that choline supplied in this form is not available to the cow, or that responses to RPC vary depending physiological state of the cow. Results from Experiment 2 indicated that primi- and multiparous cows respond differently to supplemental choline and methionine fed during the periparturient period. Feeding RPC to primiparous cows increased milk yield, while feeding rumen-protected methionine (RPM) had minimal effects on production. In contrast, RPM improved milk components and fat-corrected milk yield for multiparous cows. These observations suggest that primi- and multiparous cows have different methionine and choline requirements in the periparturient period. Investigation into the specific metabolic effects of choline and methionine fed to periparturient cows in Experiment 3 suggested that both RPC and RPM modify choline metabolism. The milk and blood PC profile was altered by both RPC and RPM. In line with this observation, RPC increased hepatic expression of the gene that encodes the enzyme responsible for catalyzing the rate-limiting step of PC synthesis via the CDP-choline pathway. The RPC-induced increase in hepatic betaine-homocysteine methyltransferase expression provided additional support for the connection between choline and methionine metabolism via one-carbon metabolism. Modification of postpartum plasma lactate concentrations by RPC for both primi- and multiparous cows, in conjunction with alterations in pre- or postpartum body condition, also suggest a choline-induced modification of tissue mobilization.
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    EVALUATION OF A METHOD TO MEASURE VOLATILE FATTY ACIDS AND GASES IN VITRO WITH MATHEMATICAL MODELING
    (2018) Judd, Latisha Marquita; Kohn, Richard A; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Methane emissions from ruminants have become an issue over the last 50 years. Previous research has shown that methane emissions are stoichiometrically linked with volatile fatty acid (VFA) profiles in ruminant animals. For example, a shift from acetate to propionate may decrease carbon dioxide (CO2) and hydrogen (H2) production, and in turn, decrease conversion of CO2 and H2 to methane. In vitro methods have been developed to measure the digestibility of feeds, but such methods may not accurately estimate methane or volatile fatty acid (VFA) profile. The development of in vitro methods to accurately estimate gas production and VFA profile in rumen fermentation would enable isolation of fermentation effects from various animal interactions. Therefore, the focus of this dissertation was to develop an in vitro method that will have the same VFA and gas profiles as in the rumen. The objectives of this project are: to develop an in vitro technique that mimics an in vivo rumen environment in order to study VFA profiles and gas production during fermentation, to examine and evaluate the efficacy of selected feed additives (e.g. probiotics) on VFA profiles and gas production, and to develop a mechanistic model of the in vitro fermentation system and the effects of feed supplements on the system. The results indicate that gas profile, VFA profile, and gas production were affected by differing in vitro fermentation conditions (buffering capacity, headspace gas composition, acetate concentration). A review of the literature was conducted to establish the effect of probiotics such as lactic acid bacteria on in vitro and in vivo systems. These findings indicated Enterococcus and Lactobacillus species tended to affect ruminal fermentation parameters. Further in vitro analysis of these probiotics indicated these bacteria tended to affect ruminal fermentation, such as gas and VFA production. A developmental mechanistic model was built to predict whether the effect of probiotics was thermodynamically or kinetically limiting. Future studies will further development of this simple model by using published literature for a meta-analysis that may aid in further interpretation of rumen fermentation regarding thermodynamic limits and maximal efficiency of key rumen fermentation reactions.
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    Genetic Architecture of Complex Traits and Accuracy of Genomic Selection in Dairy Cattle
    (2018) Jiang, Jicai; Ma, Li; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Genomic selection has emerged as an effective approach in dairy cattle breeding, in which the key is prediction of genetic merit using dense SNP genotypes, i.e., genomic prediction. To improve the accuracy of genomic prediction, we need better understanding of the genetic architecture of complex traits and more sophisticated statistical modeling. In this dissertation, I developed several computing tools and performed a series of studies to investigate the genetic architecture of complex traits in dairy cattle and to improve genomic prediction models. First, we dissected additive, dominance, and imprinting effects for production, reproduction and health traits in dairy cattle. We found that non-additive effects contributed a non-negligible amount (more for reproduction traits) to the total genetic variance of complex traits in cattle. We also identified a dominant quantitative trait locus (QTL) for milk yield, revealing that detection of QTLs with non-additive effect is possible in genome-wide association studies (GWAS) using a large dataset. Second, we developed a powerful Bayesian method and a fast software tool (BFMAP) for SNP-set association and fine-mapping. We demonstrated that BFMAP achieves a power similar to or higher than existing software tools but is at least a few times faster for association tests. We also showed that BFMAP performs well for fine-mapping and can efficiently integrate fine-mapping with functional enrichment analysis. Third, we performed large-scale GWAS and fine-mapped 35 production, reproduction, and body conformation traits to single-gene resolution. We identified many novel association signals and many promising candidate genes. We also characterized causal effect enrichment patterns for a few functional annotations in dairy cattle genome and showed that our fine-mapping result can be readily used for future functional studies. Fourth, we developed an efficient Bayesian method and a fast computing tool (SSGP) for using functional annotations in genomic prediction. We demonstrated that the method and software have great potential to increase accuracy in genomic prediction and the capability to handle very large data. Collectively, these studies advance our understanding of the genetic architecture of complex traits in dairy cattle and provide fast computing tools for analyzing complex traits and improving genomic prediction.
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    Derivation of pluripotent stem cells from blastocysts and somatic cells in the domestic cat (Felis Catus)
    (2018) Zhou, Ran; Keefer, Carol L; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Pluripotent stem cells in the domestic cat model represent a huge potential for disease modeling, drug screening and regenerative medical treatments for feline species as well as for humans. However, current knowledge on deriving and maintaining stem cells has been obtained primarily from studies in mouse, rat, and human. Difficulties in attaining similar results in cats indicate the necessity to better understand pluripotency in this species. The hypothesis was that inadequate cytokine supplementation results in pluripotency loss along with declining transcription factors expression. The main goal of this project was to assess the effects of selected growth factors and inhibitors, in maintaining pluripotency in embryonic cells, and to attain pluripotency from fibroblasts by controlling expression of exogenous transcription factors. In the first study, conventional cytokine cocktails, leukemia inhibitory factor coupling with glycogen synthase inhibitor 3, and mitogen-activated protein kinase inhibitor (LIF and 2i) could partially maintain pluripotency regulatory circuitry in the cat. In this condition, embryonic cells reached a state that was not fully defined (neither naive nor primed). Overall, cell characterizations revealed a trend of pluripotency loss over time. In the second study, pluripotency was attained by forced expression of inducible exogenous transcription factors (NANOG, POU5F1, CMYC, and SOX2) and cultured in medium supplemented with the same cytokine combination identified in the first study. Notably, unlike previous reports in the cat, colonies with partial pluripotent features could be maintained after the transgenes were silenced. In addition to the protein and transcript markers for pluripotency, lineage marker dynamics were examined in pluripotent cells and embryoid bodies. The outcome suggested the cells generated with LIF and 2i had developed beyond the undifferentiated stage of ICM in expanded blastocyst. Collective results not only challenged the efficacy of the cytokines combinations LIF and 2i in maintaining feline pluripotency, but also suggest direction of research towards the species-specific signaling requirement in embryonic progression and stem cell derivation.
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    DYNAMIC ANALYSIS OF CD4+ T CELL EPIGENETIC STATUS IN CHICKENS FOLLOWING MDV INFECTION AND DURING DIFFERENTIATION IN MICE
    (2018) Ding, Yi; Song, Jiuzhou; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Epigenetic modifications constitute a complicated regulatory network controlling various biological processes from cell development to immune responses. The mechanisms through which CD4+ T cells react to environmental stimuli, including virus intrusion and differentiation signals, represent the fundamental cell biological question of how the external microenvironment influences intrinsic transcriptional networks. This dissertation investigates the epigenetic status changes in CD4+ T cells induced by Marek’s disease virus (MDV) infection in chickens and during differentiation in mice. First, a genome-wide gene expression analysis in the immune organs from resistant line 63 and susceptible line 72 chickens was performed to explore Marek’s disease (MD) resistance mechanisms. MDV infection influences both cytokine-cytokine receptor interaction and cellular development in resistant and susceptible chickens. Second, we examined the epigenetic status of CD4+ T cells induced by MDV infection, including chromatin accessibility and chromosome organization. Our results revealed extensive epigenetic modification changes caused by MDV infection. Only resistant line 63 chickens could initiate robust adaptive immune responses at the transcription level, and the increase in chromatin accessibility and chromosome reorganization represented by A/B compartment flipping were related to up-regulated genes induced by MDV infection at 10 days post-infection in line 63 chickens. Finally, we investigated CD4+ T cells plasticity during Th1 helper cell differentiation. We showed “early” (48 hours) CD4+ T cells were plastic for cellular reprogramming while “late” (72 hours) cells lost reprogram plasticity and became committed to Th1 cell fate. T-bet, the Th1 cell master regulator, was not the direct determinant of Th1 cell plasticity. Our integrative analysis of multiple “omics” datasets revealed dynamic and genome-wide changes of chromatin accessibility associated with the process of cellular differentiation and commitment. We predicted that several candidate regulators could contribute to cellular plasticity, including Mxi1, JunB, BATF, IRF4, and Hif-1α. We observed that substantial alterations of chromatin interactions occurred at the IRF4 locus across differentiation time. Conditional deletion of IRF4 in CD4+ T cells impacted the expression of T cell activation and differentiation genes, including T-bet, and extended Th1 cell plasticity during the differentiation process. Our findings provided deeper understanding of CD4+ T cell commitment and responses toward viral infection.