• Asian-Australasian Journal of Animal Sciences
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• 제24권5호
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• pp.685-695
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• 2011

Satellite cells are skeletal muscle progenitor/stem cells that reside between the basal lamina and plasma membranes of skeletal fibers in vivo. These cells can give rise to both myogenic and adipogenic cells. Given the possible role for differentiation of satellite cells into adipocytes in marbling and in some pathological disorders like sarcopenia, knowledge of the proteins involved in such process remains obscure. Using two-dimensional polyacrylamide gel electrophoresis coupled with mass spectrometry, we investigated the proteins that are differentially expressed during adipogenic differentiation of satellite cells from bovine longissimus muscle. Our proteome mapping strategy to identify the differentially expressed intracellular proteins during adipogenic differentiation revealed a total of 25 different proteins. The proteins up-regulated during adipogenic differentiation of satellite cells like Cathepsin H precursor, Retinal dehydrogenase 1, Enoyl-CoA hydratase, Ubiquinol-cytochrome-c reductase, T-complex protein 1 subunit beta and ATP synthase D chain were found to be associated with lipid metabolism. The down-regulated proteins like LIM protein, annexin proteins, cofilin-1, Rho GDP-dissociation inhibitor 1 and septin-2, identified in the present study were found to be associated with myogenesis. These results clearly demonstrate that the adipogenic conversion of muscle satellite cells is associated with the up-regulated and down-regulated proteins involved in adipogenesis and myogenesis respectively.

• Molecules and Cells
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• 제38권5호
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• pp.466-473
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• 2015

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

• Molecules and Cells
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• 제25권1호
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• pp.142-147
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• 2008

We recently used degenerate PCR and locus-specific PCR methods to identify the endogenous retroviruses (ERV) in the bovine genome. Using the ovine ERV classification system, the bovine ERVs (BERVs) could be classified into four families. Here, we searched the most recently released bovine genome database with the partial nucleotide sequence of the pro/pol region of the BERV ${\beta}3$ family. This allowed us to obtain and analyze the complete genome of BERV ${\beta}3$. The BERV ${\beta}3$ genome is 7666 nucleotides long and has the typical retroviral organization, namely, 5'-long terminal repeat (LTR)-gag-pro-pol-env-LTR-3'. The deduced open reading frames for gag, pro, pol and env of BERV ${\beta}3$ en- code 507, 271, 879 and 603 amino acids, respectively. BERV ${\beta}3$ showed little amino acid similarity to other betaretroviruses. Phylogenetic analysis showed that it clusters with HERV-K. This is the first report describing the genetic structure and sequence of an entire BERV.

• Journal of Microbiology and Biotechnology
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• 제27권9호
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• pp.1725-1725
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• 2017

• 한국축산식품학회지
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• 제38권5호
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• pp.878-888
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• 2018

In the current study, the probiotic potential of approximately 250 strains of lactic acid bacteria (LAB) isolated from piglet fecal samples were investigated; among them Lactobacillus plantarum strain JDFM LP11, which possesses significant probiotic potential, with enhanced acid/bile tolerance, attachment to porcine intestinal epithelial cells (IPEC-J2), and antimicrobial activity. The genetic characteristics of strain JDFM LP11 were explored by performing whole genome sequencing (WGS) using a PacBio system. The circular draft genome have a total length of 3,206,883 bp and a total of 3,021 coding sequences were identified. Phylogenetically, three genes, possibly related to survival and metabolic activity in the porcine host, were identified. These genes encode p60, lichenan permease IIC component, and protein TsgA, which are a putative endopeptidase, a component of the phosphotransferase system (PTS), and a major facilitator in the gut environment, respectively. Our findings suggest that understanding the functional and genetic characteristics of L. plantarum strain JDFM LP11, with its candidate genes for gut health, could provide new opportunities and insights into applications in the animal food and feed additive industries.

• 한국가금학회지
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• 제44권2호
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• pp.103-111
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• 2017

The quail (Coturnix japonica) has been used as a model animal in many research fields and its application is still expanding in other fields. Compared to the chicken, the quail is quicker to reach sexually maturity, has short generation intervals, is easy to handle, requires less space and feed, and is sturdy. In addition, it produces many eggs and the research tools developed for chicken can be applied directly to quail or with some modifications. Due to recent advances in next-generation sequencing, abundant sequence data for the quail genome and transcripts have been generated. These sequence data are valuable sources for studying functional genomics using quail, which is one of the model animal used to investigate gene function and networks. Although there are some obstacles to be removed, the quail is the best optimized model to study the functional genomics of poultry. In many research fields, functional genomics study using the quail model will provide the best opportunity to understand the phenomena and principles of life. We review why, among many other birds, the quail is the best model for studying poultry functional genomics.

• Genomics & Informatics
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• 제14권4호
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• pp.230-233
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• 2016

Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ~29,000 single nucleotide polymorphisms (SNPs) for which $r^2$ value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average $r^2$ between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on $r^2$ varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.

• Journal of Animal Science and Technology
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• 제62권6호
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• pp.960-960
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• 2020

• Journal of Animal Science and Technology
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• 제56권4호
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• pp.12.1-12.7
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• 2014

This study investigated changes in gene expression by dietary fat source, i.e., beef tallow, soybean oil, olive oil, and coconut oil (each 3% in feed), in both male and female growing-finishing pigs. Real-time PCR was conducted on seven genes (insulin receptor; INSR, insulin receptor substrate; IRS, phosphatidylinositol (3,4,5)-triphosphate; PIP3, 3-phosphoinositide-dependent protein kinase-1; PDK1, protein kinase B; Akt, forkhead box protein O1; FOXO1 and cGMP-inhibited 3', 5'-cyclic phosphodiesterase; PDE3) located upstream of the insulin signaling pathway in the longissimus dorsi muscle (LM) of pigs. The INSR, IRS, PIP3, and PDE3 genes showed significantly differential expression in barrow pigs. Expression of the PIP3 and FOXO1 genes was significantly different among the four dietary groups in gilt pigs. In particular, the PIP3 gene showed the opposite expression pattern between barrow and gilt pigs. These results show that dietary fat source affected patterns of gene expression according to animal gender. Further, the results indicate that the type of dietary fat affects insulin signaling-related gene expression in the LM of pigs. These results can be applied to livestock production by promoting the use of discriminatory feed supplies.

• Journal of Microbiology and Biotechnology
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• 제28권8호
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• pp.1352-1359
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• 2018

Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (${\text\tiny{L}}-arabinose$, ${\text\tiny{L}}-rhamnose$, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restriction-modification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered L. plantarum strains, regardless of habitats.