Animal & Avian Sciences
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Item Identification of QTL controlling meat quality traits in an F2 cross between two chicken lines selected for either low or high growth rate(Springer Nature, 2007-06-08) Nadaf, Javad; Gilbert, Hélène; Pitel, Frédérique; Berri, Cécile M; Feve, Katia; Beaumont, Catherine; Duclos, Michel J; Vignal, Alain; Porter, Tom E; Simon, Jean; Aggrey, Samuel E; Cogburn, Larry A; Le Bihan-Duval, ElisabethMeat technological traits (i.e. meat pH, water retention and color) are important considerations for improving further processing of chicken meat. These quality traits were originally characterized in experimental lines selected for high (HG) and low (LG) growth. Presently, quantitative trait loci (QTL) for these traits were analyzed in an F2 population issued from the HG × LG cross. A total of 698 animals in 50 full-sib families were genotyped for 108 microsatellite markers covering 21 linkage groups. The HG and LG birds exhibit large differences in body weight and abdominal fat content. Several meat quality traits [pH at 15 min post-slaughter (pH15) and ultimate pH (pHu), breast color-redness (BCo-R) and breast color-yellowness (BCo-Y)] were lower in HG chickens. In contrast, meat color-lightness (BCo-L) was higher in HG chickens, whereas meat drip loss (DL) was similar in both lines. HG birds were more active on the shackle line. Association analyses were performed using maximum-likelihood interval mapping in QTLMAP. Five genome-wide significant QTLs were revealed: two for pH15 on GGA1 and GGA2, one for DL on GGA1, one for BCo-R and one for BCo-Y both on GGA11. In addition, four suggestive QTLs were identified by QTLMAP for BCo-Y, pHu, pH15 and DL on GGA1, GGA4, GGA12 and GGA14, respectively. The QTL effects, averaged on heterozygous families, ranged from 12 to 31% of the phenotypic variance. Further analyses with QTLExpress confirmed the two genome-wide QTLs for meat color on GGA11, failed to identify the genome-wide QTL for pH15 on GGA2, and revealed only suggestive QTLs for pH15 and DL on GGA1. However, QTLExpress qualified the QTL for pHu on GGA4 as genome-wide. The present study identified genome-wide significant QTLs for all meat technological traits presently assessed in these chickens, except for meat lightness. This study highlights the effects of divergent selection for growth rate on some behavioral traits, muscle biochemistry and ultimately meat quality traits. Several QTL regions were identified that are worthy of further characterization. Some QTLs may in fact co-localize, suggesting pleiotropic effects for some chromosomal regions.Item Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster(Springer Nature, 2008-02-28) Zhang, Wensheng; Zou, Sige; Song, JiuzhouPredictive classification on the base of gene expression profiles appeared recently as an attractive strategy for identifying the biological functions of genes. Gene Ontology (GO) provides a valuable source of knowledge for model training and validation. The increasing collection of microarray data represents a valuable source for generating functional hypotheses of uncharacterized genes. This study focused on using support vector machines (SVM) to predict GO biological processes from individual or multiple-tissue transcriptional profiles of aging in Drosophila melanogaster. Ten-fold cross validation was implemented to evaluate the prediction. One-tail Fisher's exact test was conducted on each cross validation and multiple testing was addressed using BH FDR procedure. The results showed that, of the 148 pursued GO biological processes, fifteen terms each had at least one model with FDR-adjusted p-value (Adj.p) <0.05 and six had the values between 0.05 and 0.25. Furthermore, all these models had the prediction sensitivity (SN) over 30% and specificity (SP) over 80%. We proposed the concept of term-tissue specific models indicating the fact that the major part of the optimized prediction models was trained from individual tissue data. Furthermore, we observed that the memberships of the genes involved in all the three pursued children biological processes on mitochondrial electron transport could be predicted from the transcriptional profiles of aging (Adj.p < 0.01). This finding may be important in biology because the genes of mitochondria play a critical role in the longevity of C. elegans and D. melanogaster.Item Principal component tests: applied to temporal gene expression data(Springer Nature, 2009-01-30) Zhang, Wensheng; Fang, Hong-Bin; Song, JiuzhouClustering analysis is a common statistical tool for knowledge discovery. It is mainly conducted when a project still is in the exploratory phase without any priori hypotheses. However, the statistical significance testing between the clusters can be meaningful in helping the researchers to assess if the classification results from implementing a clustering algorithm need to be improved, even after the cluster number has been determined by a well-established criterion. This is important when we want to identify highly-specific patterns through classification. We proposed to use a principal component (PC) test, which is an implementation of an exact F statistic for the measures at multiple endpoints based on elliptical distribution theory, to assess the statistical significance between clusters. A challenge in the implementation is the choice of the number (q) of principal components to be considered, which can severely influence the statistical power of the method. We optimized the determination via validation according to a permutation test based on the clustering to be evaluated. The method was applied to a public dataset in classifying genes according to their temporal gene expression profiles. The results demonstrated that the PC testing were useful for determining the optimal number of clusters.Item Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen(Springer Nature, 2009-07-13) Garcia-Reyero, Natàlia; Kroll, Kevin J; Liu, Li; Orlando, Edward F; Watanabe, Karen H; Sepúlveda, María S; Villeneuve, Daniel L; Perkins, Edward J; Ankley, Gerald T; Denslow, Nancy DAquatic organisms are continuously exposed to complex mixtures of chemicals, many of which can interfere with their endocrine system, resulting in impaired reproduction, development or survival, among others. In order to analyze the effects and mechanisms of action of estrogen/anti-estrogen mixtures, we exposed male fathead minnows (Pimephales promelas) for 48 hours via the water to 2, 5, 10, and 50 ng 17α-ethinylestradiol (EE2)/L, 100 ng ZM 189,154/L (a potent antiestrogen known to block activity of estrogen receptors) or mixtures of 5 or 50 ng EE2/L with 100 ng ZM 189,154/L. We analyzed gene expression changes in the gonad, as well as hormone and vitellogenin plasma levels. Steroidogenesis was down-regulated by EE2 as reflected by the reduced plasma levels of testosterone in the exposed fish and down-regulation of genes in the steroidogenic pathway. Microarray analysis of testis of fathead minnows treated with 5 ng EE2/L or with the mixture of 5 ng EE2/L and 100 ng ZM 189,154/L indicated that some of the genes whose expression was changed by EE2 were blocked by ZM 189,154, while others were either not blocked or enhanced by the mixture, generating two distinct expression patterns. Gene ontology and pathway analysis programs were used to determine categories of genes for each expression pattern. Our results suggest that response to estrogens occurs via multiple mechanisms, including canonical binding to soluble estrogen receptors, membrane estrogen receptors, and other mechanisms that are not blocked by pure antiestrogens.Item Analysis of recent segmental duplications in the bovine genome(Springer Nature, 2009-12-01) Liu, George E; Ventura, Mario; Cellamare, Angelo; Chen, Lin; Cheng, Ze; Zhu, Bin; Li, Congjun; Song, Jiuzhou; Eichler, Evan EDuplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimated that 3.1% (94.4 Mb) of the bovine genome consists of recently duplicated sequences (≥ 1 kb in length, ≥ 90% sequence identity). Similar to other mammalian draft assemblies, almost half (47% of 94.4 Mb) of these sequences have not been assigned to cattle chromosomes. In this study, we provide the first experimental validation large duplications and briefly compared their distribution on two independent bovine genome assemblies using fluorescent in situ hybridization (FISH). Our analyses suggest that the (75-90%) of segmental duplications are organized into local tandem duplication clusters. Along with rodents and carnivores, these results now confidently establish tandem duplications as the most likely mammalian archetypical organization, in contrast to humans and great ape species which show a preponderance of interspersed duplications. A cross-species survey of duplicated genes and gene families indicated that duplication, positive selection and gene conversion have shaped primates, rodents, carnivores and ruminants to different degrees for their speciation and adaptation. We identified that bovine segmental duplications corresponding to genes are significantly enriched for specific biological functions such as immunity, digestion, lactation and reproduction. Our results suggest that in most mammalian lineages segmental duplications are organized in a tandem configuration. Segmental duplications remain problematic for genome and assembly and we highlight genic regions that require higher quality sequence characterization. This study provides insights into mammalian genome evolution and generates a valuable resource for cattle genomics research.Item Quantification of fatty acids over the gametogenic cycle of striped bass (Morone saxatilis) with varying dietary levels of DHA, EPA and AA(2000) Dickey, Lisa Ann; Woods, L. Curry III; Animal and Avian Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)The purpose of this thesis was to investigate the effects of dietary treatments on the fatty acid composition of striped bass (Marone saxatilis) blood, liver and ovary over the course of the gametogenic cycle. Striped bass were fed experimental diets in which docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA) and arachidonic acid (AA) were increased in a stepwise fashion progressing from diets 1-4 respectively. A significant difference was seen in the tissues between fish from dietary treatment group 1 when compared to those fish from dietary treatment group 4 suggesting a direct impact on the tissues by the fatty acid composition of the diet. The second purpose of this thesis was to explore the use of a novel method of fatty acid extraction from fish tissues. This method was compared (UMD method) was compared to the well-known Bligh and Dyer method commonly used for fatty acid extraction. The UMD method proved to be superior quantitatively in terms of fatty acid extraction when compared to the Bligh and Dyer method. The UMD is also more cost affective and leaves less room for human error.Item NUTRITIONAL AND ENVIRONMENTAL IMPLICATIONS OF STARCH DEGRADABILITY AND NITROGEN FERTILIZATION OF ORCHARDGRASS SILAGE IN TOTAL MIXED RATIONS FED TO LACTATING COWS(2003) Woodward-Greene, Mary Jennifer; Erdman, Richard; Animal & Avian Sciences; University of Maryland, College Park, Md.; Digital Repository at the University of MarylandThe objectives of this research were to determine the effect of starch and nitrogen (N) availability on microbial protein production and N efficiency, ruminal N efficiency and ammonia, and to assess forage fertilization and grain selection decisions. Diets were incubated in vitro batch culture, and fed in a 6 x 6 Latin square in vivo digestion trial. Total mixed rations (TMR) contained 50:50 forage:concentrate (dry matter (DM) basis) of second-cutting orchardgrass silage fertilized with 200 (OG200) or 400 (OG400) pounds per acre N, plus concentrate mixes using high to low rumen available starches: barley, corn, and milo. TMR crude protein (CP) was 17% and 18% for in vivo, and 20% and 21% for in vitro OG200 and OG400 diets, respectively. Synchronous diets were low:low or high:high rumen starch availability:diet N (corn or milo withOG200, and barley with OG400). No effects on ruminal microbial protein synthesis and flow, N flow, or milk production were observed. DM, organic matter (OM) (P<0.01), N, and neutral detergent fiber (NDF) (P<0.02) total digestibilities increased with synchronous diets. N digestibility was depressed in diets of low:high rumen starch availability:diet N, due to increased hindgut fermentation adding microbial protein to the feces (P<0.001). All OG400 diets had higher fecal N percentage (P<0.001). OG400 had higher ruminal ammonia both in vitro and in vivo (P<0.05), and higher total in vivo volatile fatty acid (VFA) concentration (P<0.001), but rumen pH was stable due to increased recycling of urea. Orchardgrass fertilized at high N can be digested as well as lower N fertilized forages when combined with a rapidly available ruminal starch such as barley, and decrease outputs of fecal DM by up to 401.5 and N by nearly 22 kilograms per year per cow. Crop fertilization and grain selection decisions affect forage composition, rumen fermentation, ration digestibility, and fecal DM and N output.Item DELINEATING THE ROLES OF C. ELEGANS HEME RESPONSIVE GENES HRG-2 AND HRG-3 IN HEME HOMEOSTASIS(2009) Chen, Caiyong; Hamza, Iqbal; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Heme is an essential cofactor for diverse biological processes such as oxygen transport, xenobiotic detoxification, and circadian clock control. Since free heme is hydrophobic and cytotoxic, we hypothesize that within eukaryotic cells, specific trafficking pathways exist for the delivery of heme to different subcellular destinations where hemoproteins reside. To identify molecules that may be involved in heme homeostasis, we conducted a C. elegans microarray experiment on RNA extracted from worms grown at different concentrations of heme in axenic liquid medium. Analysis of the microarrays revealed that the mRNA levels of heme-responsive gene-2 (hrg-2) and hrg-3 increased more than 70 fold when worms were grown at 4 µM compared to 20 µM heme. hrg-2 is expressed in hypodermal tissues in the worm, and the protein localizes to the endoplasmic reticulum and the apical plasma membrane. In vitro hemin agarose pull-down experiments indicate that HRG-2 binds heme. Deletion of hrg-2 in C. elegans leads to reduced growth rate at low heme. Moreover, expression of HRG-2 in hem1δ, a heme-deficient yeast strain, results in growth rescue at submicromolar concentrations of exogenous heme. These results indicate that HRG-2 may either directly participate in heme uptake or facilitate heme delivery to another protein. Unlike hrg-2, hrg-3 is exclusively expressed in the worm intestine under heme deficiency. Following its synthesis, HRG-3 is secreted into the body cavity pseudocoelom. Deletion of hrg-3 results in increased heme levels in the worm intestine, suggesting that HRG-3 may function in intercellular heme transport in C. elegans. To identify the functional network or pathways for HRG-2 and HRG-3, we performed a genome-wide microarray analysis using RNA samples prepared from the worms grown at different concentrations of heme and oxygen. The results showed that a total of 446 genes were transcriptionally altered by heme and/or oxygen. Among them, 41 and 29 genes exhibited similar expression profiles to hrg-2 and hrg-3, respectively. We postulate that these genes may function in conjunction with hrg-2 and hrg-3. Taken together, we have identified two novel heme-responsive genes in metazoa that may play critical roles in modulating organismal heme homeostasis in C. elegans.Item Proteomic Profiling and Label-Free Quantification of Bovine Milk Proteins during Experimentally Induced Escherichia coli Mastitis(2009) Boehmer, Jamie Layne; Peters, Robert R; Bannerman, Douglas D; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Coliform mastitis has been a primary focus of dairy cattle disease research due to staggering affiliated losses, severe systemic complications arising from host inflammatory response to lipopolysaccharide, and the poor response of coliform pathogens to antimicrobials. Reliable biomarkers are needed to evaluate the efficacy of adjunctive therapies for the treatment of inflammation associated with coliform mastitis, and to aid in the approval of new veterinary drugs. The aims of the current analyses were to utilize proteomic methodologies to evaluate protein expression in whey from cows with experimentally induced coliform mastitis, and to employ label-free quantification strategies to estimate changes in relative abundance of proteins identified in milk over the course of clinical infection. Two-dimensional gel electrophoresis followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI- TOF) mass spectrometry (MS) resulted in the identification of complement factors, antimicrobial proteins, and acute phase proteins in mastitic milk. Analysis using liquid chromatography (LC) inline with electrospray ionization - quadrupole TOF tandem mass spectrometry (MS/MS) resulted primarily in the identification of abundant whey and casein proteins, and the transient detection of proteins related to host response. Nano-LC- nanospray-MS/MS using a linear ion trap, however, led to the robust discovery of over fifty inflammatory proteins in whey from mastitic milk, including the novel markers kininogen-2 and inter-alpha trypsin inhibitor heavy chain-4. Normalized spectral counts were compared to enzyme-linked immunosorbant assay (ELISA) for select proteins to assess the accuracy of the spectral count data. Similar expression patterns were detected using spectral counts and ELISA. Results indicate that proteomic methodologies can detect biomarkers of coliform mastitis in bovine milk during clinical infections, and that spectral counts are a viable means of evaluating relative changes in protein biomarkers of mastitis, including those for which no antibody currently exists.Item Identification and characterization of a heme responsive element in the hrg-1 promoter(2008) Sinclair, Jason; Hamza, Iqbal; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Despite its biological significance, little is known about how animals sense and respond to heme to maintain homeostasis. C. elegans is a heme auxotroph, which makes it an excellent model to identify and dissect heme homeostasis pathways. Using C. elegans we have identified HRG-1, a vesicular heme transporter that is transcriptionally upregulated when environmental heme is low. The current study seeks to address how hrg-1 is regulated by heme. Here, we show that a putative 23 base pair (bp) heme-responsive element (HRE) and GATA-binding motifs are necessary for heme-dependent regulation of hrg-1. The HRE comprises both enhancer and repressor elements and works in conjunction with ELT-2 to regulate hrg-1 expression. We propose that the HRE could be used as a molecular tool in C. elegans to tightly regulate internal gene expression by modulating environmental heme. Our ultimate goal is to identify the trans-acting factor to eventually create a whole animal sensor for monitoring organismal heme homeostasis.