Animal & Avian Sciences
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Item A WIDE SCALE INVESTIGATION INTO LNCRNA IN BOS TAURUS(2023) Marceau, Alexis; Ma, Li; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Although the history of genetic research has focused on genes and gene products, there is an interesting emerging subclass of genetic elements: long noncoding RNAs (lncRNAs). These are portions of the genome that are longer than 200 base pairs in length and are transcribed from DNA to RNA but do not yield a protein. The function of lncRNA is wide reaching and difficult to define; however, they are predominantly linked to the regulation of gene expression. This is done via transcriptional control, translation control, pre- and post- transcriptional and translational control, epigenetic modifications, RNA processing,as well as other methods. In this dissertation, multiple Bos taurus tissues across various life conditions were investigated in order to identify lncRNA and to begin making predictions about the role and function of identified transcripts. First, lncRNA were identified and analyzed in Bos taurus rumen tissue in pre-weaning and post-weaning cattle. lncRNA were implicated in the weaning process and demonstrated enrichment in complex traits, indicating the continued impact rumen-associated lncRNA have on dairy cattle. Following this study, mammary tissues from dry and lactating cattle were used for lncRNA analysis, in relation to the lacta-tion processes. This study revealed both the presence and impact of mammary lncRNA, and identified lncRNA associated with genes and biological processes that are strongly linked to lactation and mammary tissue function. Subsequently, immune system related tissues were analyzed for lncRNA and their roles. This investigation demonstrated lncRNA to be present in all investigated tissues, including transcripts being repeatedly present. Further analysis into identified lncRNA associated transcripts with genes and functions that are crucial to immune response. Finally, a tutorial was created to make lncRNA identification research more easily accessible to future researchers. The findings and creations of this dissertation increase the knowledge base of lncRNA and their role, allowing for further research endeavors and improvements in Bos taurus husbandry.Item REDUCED CAMPYLOBACTER INFECTION AND ENHANCED PERFORMANCE IN POULTRY WITH BIOACTIVE PHENOLICS THROUGH EPIGENETIC MODULATION OF THE GUT MICROBIOME(2017) Salaheen, Serajus; Biswas, Debabrata; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Campylobacter jejuni, a major enteric pathogen and a natural resident in the poultry gut, causes gastrointestinal illness followed by severe post-infection complications, including Guillain-Barré syndrome, reactive arthritis, myocarditis, and ulcerative colitis in humans. Risk assessment studies have projected a 30-fold reduction in human campylobacteriosis cases with only a 100-fold reduction in the number of C. jejuni colonizing the poultry gut. Current commercial poultry production practices involve use of antibiotic growth promoters (AGP); modulation of gut microbiota with AGPs for food safety and enhanced performance in poultry can be justified until acquisition of antibiotic resistance in zoonoses through inter-bacterial transfer of antibiotic resistance genes (ARGs) in a complex microbial community is considered. As an alternative, natural phenolics extracted from by-products of berry juice industry, with antimicrobial, anti-inflammatory, anticarcinogenic, antioxidant and vasodilatory activities, demonstrate promising prospects. In this study, we adopted mass-spectrometry, microbiological, phylogenetic, and metagenomic approaches to evaluate bioactive phenolic extracts (BPE) from blueberry (Vaccinium corymbosum) and blackberry (Rubus fruticosus) pomaces as AGP alternative. We detected that major phenolics in BPE included, but were not limited to, apigenin, catechol, chlorogenic acid, cinnamic acid, coumarin, ellagic acid, eugenols, flavan, gallic acid, gingerol, glucosides, glucuronides, myricetin, phenols, quercetin, quinones, rhamnosides, stilbenol, tannins, triamcinolone, and xanthine. BPE reduced C. jejuni growth and motility in vitro, resulting in lower adherence and invasiveness to chicken fibroblast cells. Anti-inflammatory effects of BPE significantly reduced the expression of pro-inflammatory cytokine genes in chick macrophage cell line ex vivo. Furthermore, BPE reduced the colonization of C. jejuni in broiler cecum by 1 to 5 logs while increasing broiler weight by 6% compared to 9.5% with commercial AGPs. Metagenomic analysis of broiler gut indicated that BPE caused an AGP-like pattern in bacterial communities with a comparative increase of Firmicutes and a concomitant reduction of Bacteroidetes in broiler ceca. AGP supplementation clearly caused phage induction and a richer resistome profile in the cecal microbiome compared to BPE. Functional characterization of cecal microbiomes revealed a significant variation in the abundance of genes involved in energy and carbohydrate metabolism. Our findings established a baseline upon which mechanisms of plant based antimicrobial performance-enhancers in regulation of animal growth can be investigated.Item Integrative genomic, epigenetic and metabolomic characterization of beef from grass-fed Angus steers(2016) Carrillo Tabakman, Jose Adrian; Song, Jiuzhou; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Beef constitutes a main component of the American diet and still represent the principal source of protein in many parts of the world. Currently, the meat market is experiencing an important transformation; consumers are increasingly switching from consuming traditional beef to grass-fed beef. People recognized products obtained from grass-fed animals as more natural and healthy. However, the true variations between these two production systems regarding various aspects remain unclear. This dissertation provides information from closely genetically related animals, in order to decrease confounding factors, to explain several confused divergences between grain-fed and grass-fed beef. First, we examined the growth curve, important economic traits and quality carcass characteristics over four consecutive years in grain-fed and grass-fed animals, generating valuable information for management decisions and economic evaluation for grass-fed cattle operations. Second, we performed the first integrated transcriptomic and metabolomic analysis in grass-fed beef, detecting alterations in glucose metabolism, divergences in free fatty acids and carnitine conjugated lipid levels, and altered β-oxidation. Results suggest that grass finished beef could possibly benefit consumer health from having lower total fat content and better lipid profile than grain-fed beef. Regarding animal welfare, grass-fed animals may experience less stress than grain-fed individuals as well. Finally, we contrasted the genome-wide DNA methylation of grass-fed beef against grain-fed beef using the methyl-CpG binding domain sequencing (MBD-Seq) method, identifying 60 differentially methylated regions (DMRs). Most of DMRs were located inside or upstream of genes and displayed increased levels of methylation in grass-fed individuals, implying a global DNA methylation increment in this group. Interestingly, chromosome 14, which has been associated with large effects on ADG, marbling, back fat, ribeye area and hot carcass weight in beef cattle, allocated the largest number of DMRs (12/60). The pathway analysis identified skeletal and muscular system as the preeminent physiological system and function, and recognized carbohydrates metabolism, lipid metabolism and tissue morphology among the highest ranked networks. Therefore, although we recognize some limitations and assume that additional examination is still required, this project provides the first integrative genomic, epigenetic and metabolomics characterization of beef produced under grass-fed regimen.Item Identification and characterization of long intergenic noncoding RNAs associated with Marek's disease resistance in chicken(2013) Zhan, Fei; Song, Jiuzhou; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Marek's disease (MD) is a highly contagious lymphomatous disease of chicken caused by Marek's disease virus (MDV). MDV has steadily evolved toward increased resistance and virulence over the past decades. A promising strategy for MD prevention and control would be the enhancement of genetic resistance. This study aimed to investigate the roles of long intergenic noncoding RNAs (lincRNAs) in MD resistance and susceptibility in chickens. We reported more than 1000 lincRNA loci in chicken. Computational functional annotation suggested that lincRNAs were involved in a wide range of biological processes. Moreover, distinct lincRNA expression signatures were observed between MD resistance and susceptible chickens. Additionally, a candidate lincRNA termed linc-stab1 was identified and it may play an important role in MD immune response by regulating a nearby protein-coding gene STAB1. In summary, our results demonstrated that lincRNAs also play an important role in MD resistance and provide good candidates for hypothesis-driven functional studies.Item Genome-Wide Analysis of Histone Modification Enrichments Induced by Marek's Disease Virus in Inbred Chicken Lines(2013) Mitra, Apratim; Song, Jiuzhou; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Covalent histone modifications constitute a complex network of transcriptional regulation involved in diverse biological processes ranging from stem cell differentiation to immune response. The advent of modern sequencing technologies enables one to query the locations of histone modifications across the genome in an efficient manner. However, inherent biases in the technology and diverse enrichment patterns complicate data analysis. Marek's disease (MD) is an acute, lymphoma-inducing disease of chickens with disease outcomes affected by multiple host and environmental factors. Inbred chicken lines 63 and 72 share the same major histocompatibility complex haplotype, but have contrasting responses to MD. This dissertation presents novel methods for analysis of genome-wide histone modification data and application of new and existing methods to the investigation of epigenetic effects of MD on these lines. First, we present WaveSeq, a novel algorithm for detection of significant enrichments in ChIP-Seq data. WaveSeq implements a distribution-free approach by combining the continuous wavelet transform with Monte Carlo sampling techniques for effective peak detection. WaveSeq outperformed existing tools particularly for diffuse histone modification peaks demonstrating that restrictive distributional assumptions are not necessary for accurate ChIP-Seq peak detection. Second, we investigated latent MD in thymus tissues by profiling H3K4me3 and H3K27me3 in infected and control birds from lines 63 and 72. Several genes associated with MD, e.g. MX1 and CTLA–4, along with those linked with human cancers, showed line-specific and condition-specific enrichments. One of the first studies of histone modifications in chickens, our work demonstrated that MD induced widespread epigenetic variations. Finally, we analyzed the temporal evolution of histone modifications at distinct phases of MD progression in the bursa of Fabricius. Genes involved in several important pathways, e.g. apoptosis and MAPK signaling, and various immune-related miRNAs showed differential histone modifications in the promoter region. Our results indicated heightened inflammation in the susceptible line during early cytolytic MD, while resistant birds showed recuperative symptoms during early MD and epigenetic silencing during latent infection. Thus, although further elucidation of underlying mechanisms is necessary, this work provided the first definitive evidence of the epigenetic effects of MD.