An essential component of functional genomics studies is the sequence of DNA expressed in tissues of interest. To provide a resource of bovine-specific expressed sequence data and facilitate this powerful approach in cattle research, four normalized cDNA libraries were produced and arrayed for high-throughput sequencing. The libraries were made with RNA pooled from multiple tissues to increase efficiency of normalization and maximize the number of independent genes for which sequence data were obtained. Target tissues included those with highest likelihood to have impact on production parameters of animal health, growth, reproductive efficiency, and carcass merit. Success of normalization and inter-and intralibrary redundancy were assessed by collecting 6000-23,000 sequences from each of the libraries (68,520 total sequences deposited in GenBank). Sequence comparison and assembly of these sequences was performed in combination with 56,500 other bovine EST sequences present in the GenBank dbEST database to construct a cattle Gene Index (available from The Institute for Genomic Research at http://www.tigr.org/tdb/tgi.shtml). The 124,381 bovine ESTs present in GenBank at the time of the analysis form 16,740 assemblies that are listed and annotated on the Web site. Analysis of individual library sequence data indicates that the pooled-tissue approach was highly effective in preparing libraries for efficient deep sequencing.The rapid progress of genomic research in diverse organisms such as yeast, fruit flies, nematodes, mice, and humans has been driven by a combination of mapping, sequencing, and identification of expressed portions of each genome. Progress in these areas has lagged in the livestock species, limiting the use of functional genomics approaches to current problems in production-animal agriculture. Resources for a public effort to sequence the genomes of livestock species are not currently available. However, more modest sequencing efforts aimed at cDNA libraries have substantial value to the research community, especially when combined with mapping efforts to produce comparative maps with other mammalian species. Comparative maps make use of the general conservation of synteny between mammals and allow the livestock community to tap into the wealth of information generated in the human genome effort.To provide a resource of livestock-specific expressed sequence data to facilitate proteomics and functional genomics approaches in animal science, an EST-sequencing program was initiated with the aim to maximize the efficiency of obtaining sequence from the highest possible number of independent genes. Four normalized bovine cDNA libraries specifically designed for this task were produced and arrayed for high-throughput sequencing. To make the data more accessible and useful, assembly and annotation analyses were performed and an interactive Web site constructed by The Institute for Genomic Research (TIGR) to view and analyze bovine genes. We report the construction of this Cattle Gene Index and assessment ...
Functional genomic studies of the mammary gland require an appropriate collection of cDNA sequences to assess gene expression patterns from the different developmental and operational states of underlying cell types. To better capture the range of gene expression, a normalized cDNA library was constructed from pooled bovine mammary tissues, and 23,202 expressed sequence tags (EST) were produced and deposited into GenBank. Assembly of these EST with sequences in the Bos taurus Gene Index (BtGI) helped to form 5751 of the current 23,883 tentative consensus (TC) sequences. The majority (87%) of these 5751 assemblies contained only one to three mammary-derived EST. In contrast, 18% of the mammary EST assembled with TC sequences corresponding to 12 genes. These results suggest library normalization was only partially effective, because the reduction in EST for genes abundantly transcribed during lactation could be attributed to pooling. For better assessment of novel content in the mammary library and to add to existing annotation of all bovine sequence elements, gene ontology assignments, and comparative sequence analyses against human genome sequence, human and rodent gene indices, and an index of orthologous alignments of genes across eukaryotes (TOGA) were performed, and results were added to existing BtGI annotation. Over 35,000 of the bovine elements significantly matched human genome sequence, and the positions of some alignments (3%) were unique relative to those using human expressed sequences. Because 3445 TC sequences had no significant match with any data set, mammary-derived cDNA clones representing 23 of these elements were analyzed further for expression and novelty. Only one clone met criteria suggesting the corresponding gene was a divergent ortholog or expressed sequence unique to cattle. These results demonstrate that bovine sequence expression data serve as a resource for characterizing mammalian transcriptomes and identifying those genes potentially unique to ruminants.
Lag and generation times for the growth of SalmoneUla typhimurium on sterile lean beef were modeled as functions of cooling time under various carcass-chilling scenarios. Gompertz growth models were fit to the log1o colony counts over time at each of six temperatures in the range of 15 to 40°C. Lag and generation times were defined as the points at which the second and first derivatives, respectively, of each growth curve attained a
The purpose of this study was to classify organs/tissues into clusters according to their association with fasting heat production (FHP) by multivariate cluster analysis and to identify primary tissues. A data set consisting of 47 variables and 2256 data points was collected from 48 growing male pigs. Variance was perturbed by varying the daily feed allowance. Cluster analysis was conducted at each of six levels of body dissections, and a final analysis was conducted with all 47 variables. Small intestine, pancreas, liver, and kidneys were consistently assigned to the FHP-cluster; stomach, cecum, and colon to clusters correlated, r greater than 0.5, to the FHP-cluster; carcass, thoracic and offal variables to unrelated clusters. In the final analysis with all 47 variables represented, only variables from the small intestine and jejunum were assigned to the FHP-cluster. It is concluded that the small intestine, which accounts for only 2% of the body weight, is a primal organ system in swine and that pancreas, liver, and kidneys are of similar importance.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
customersupport@researchsolutions.com
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.