• Journal of Embryo Transfer
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• v.23 no.3
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• pp.203-209
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• 2008

To estimate the genetic characteristics and cumulative power of discrimination (CPD) existing among Hanwoo (Korean cattle) and exotic foreign population (Angus, Herford, Charolais, Holstein) we used a total of 414 genomic DNAs from five breeds population (Hanwoo, Angus, Hereford, Charolais, Holstein). Genetic characteristics indices including mean allele number among loci, unbiased heterozygosity ($h_i$) within locus and polymorphic information content (PIC) and unbiased average heterozygosity (H) among loci in four breeds were calculated using the generated allele frequencies by each marker. The mean allele numbers for all loci ranged between 5 and 7 while heterozygosity (H) ranged from 0.75 (HW) to 0.64 (HF) among loci and across breeds heterozygosity (H) was 0.69. The generated unbiased average heterozygosity among loci in each breed was integrated to the global formula of CPD resulting in 99.71 % within the populations. The genetic variation of HW (Hanwoo) showed highest estimates among the analyzed breeds.

• BMB Reports
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• v.39 no.4
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• pp.464-467
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• 2006

Recently, the nucleotide sequences of entire genomes became available. This information combined with older sequencing data discloses the exact chromosomal location of millions of nucleotide markers stored in the databases at NCBI, EMBO or DDBJ. Despite having resolved the intron/exon structures of all described genes within these genomes with a stroke of a pen, the sequencing data opens up other interesting possibilities. For example, the genomic mapping of the end sequences of the human, murine and rat BAC libraries generated at The Institute for Genomic Research (TIGR), reveals now the entire encompassed sequence of the inserts for more than a million of these clones. Since these clones are individually stored, they are now an invaluable source for experiments which depend on genomic DNA. Isolation of smaller fragments from such clones with standard methods is a time consuming process. We describe here a reliable one-step cloning technique to obtain a DNA fragment with a defined size and sequence from larger genomic clones in less than 48 hours using a standard vector with a multiple cloning site, and common restriction enzymes and equipment. The only prerequisites are the sequences of ends of the insert and of the underlying genome.

• Korean Journal of Agricultural Science
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• v.42 no.4
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• pp.397-406
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• 2015

Quantitative traits are mostly controlled by a large number of genes. Some of these genes tend to have a large effect on quantitative traits in cattle and are known as major genes primarily located at quantitative trait loci (QTL). The genetic merit of animals can be estimated by genomic selection, which uses genome-wide SNP panels and statistical methods that capture the effects of large numbers of SNPs simultaneously. In practice, the accuracy of genomic predictions will depend on the size and structure of reference and training population, the effective population size, the density of marker and the genetic architecture of the traits such as number of loci affecting the traits and distribution of their effects. In this review, we focus on the structure of Hanwoo reference and training population in terms of accuracy of genomic prediction and we then discuss of genetic architecture of intramuscular fat(IMF) and marbling score(MS) to estimate genomic breeding value in real small size of reference population.

• Proceedings of the KSAR Conference
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• 2003.06a
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• pp.47-47
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• 2003

The present study was conducted to determine the expression of the antioxidant enzyme(CuZn-SOD, Mn-SOD and GPX and apoptosis gene(caspase-3) for in vitro culture in in vitro maturation and in vitro fertilization(IVM/IVF) embryos in porcine. Porcine embryos derived from IVM/IVF were cultured in NCSU23 medium under 5% $CO_2$ in air at 38.5$^{\circ}C$. The patterns of gene expression for several antioxidant enzyme and apoptosis genes during preimplantion porcine embryo development were examined by the modified semi-quantitative single cell reverse transcriptase- polymerase chain reaction (RT-PCR). Preimplantation porcine embryos produced by IVM/IVF have expressed mRNAs for CuZn-SOD and GPX, whereas transcripts for Mn-SOD have not detected at any developmental stages. Expression of caspase-3 mRNA was detected at 2 cell, 8 cell, 16 cell and morula stages. The fas ligand transcripts were detected in porcine blastocyst. These results suggest that various antioxidant enzymes and apoptosis genes play crucial roles in in vitro culture of porcine IVM/IVF embryos.

• Genomics & Informatics
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• v.21 no.3
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• pp.37.1-37.11
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• 2023

Systemic lupus erythematosus (SLE) is an inflammatory-autoimmune disease with a complex multi-organ pathogenesis, and it is known to be associated with significant morbidity and mortality. Various genetic, immunological, endocrine, and environmental factors contribute to SLE. Genomic variants have been identified as potential contributors to SLE susceptibility across multiple continents. However, the specific pathogenic variants that drive SLE remain largely undefined. In this study, we sought to identify these pathogenic variants across various continents using genomic and bioinformatic-based methodologies. We found that the variants rs35677470, rs34536443, rs17849502, and rs13306575 are likely damaging in SLE. Furthermore, these four variants appear to affect the gene expression of NCF2, TYK2, and DNASE1L3 in whole blood tissue. Our findings suggest that these genomic variants warrant further research for validation in functional studies and clinical trials involving SLE patients. We conclude that the integration of genomic and bioinformatic-based databases could enhance our understanding of disease susceptibility, including that of SLE.

• The Journal of the Korean Society for Microbiology
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• v.34 no.6
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• pp.519-532
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• 1999

Helicobacter pylori is a causative agent of type B gastritis and plays a central role in the pathogenesis of gastroduodenal ulcer and gastric cancer. To elucidate the host-parasite relationship of the H. pylori infection on the basis of molecular biology, we tried to evaluate the genomic diversity of H. pylori. An ordered overlapping bacterial artificial chromosome (BAC) library of a Korean isolate, H. pylori 51 was constructed to set up a genomic map. A circular physical map was constructed by aligning ApaI, NotI and SfiI-digested chromosomal DNA. When the physical map of H. pylori 51 was compared to that of unrelated strain, H. pylori 26695, completely different restriction patterns were shown. Fifteen known genes were mapped on the chromosome of H. pylori 51 and the genetic map was compared with those of strain 26695 and J99, of which the entire genomic sequences were reported. There were some variability in the gene location as well as gene order among three strains. For further analysis on the genomic diversity of H. pylori, when comparing the genomic structure of 150 H. pylori Korean isolates with one another, genomic macrodiversity of H. pylori was characterized by several features: whether or not susceptible to restriction digestion of the chromsome, variation in chromosomal restriction fingerprint and/or high frequency of gene rearrangement. We also examined the extent of allelic variation in nucleotide or deduced amino acid sequences at the individual gene level. fucT, cagA and vacA were confirmed to carry regions of high variation in nucleotide sequence among strains. The plasticity zone and strain-specific genes of H. pylori 51 were analyzed and compared with the former two genomic sequences. It should be noted that the H. pylori 51-specific sequences were dispersed on the chromosome, not congregated in the plasticity zone unlike J99- or 26695-specific genes, suggesting the high frequency of gene rearrangement in H. pylori genome. The genome of H. pylori 51 shows differences in the overall genomic organization, gene order, and even in the nucleotide sequences among the H. pylori strains, which are far greater than the differences reported on the genomic diversity of H. pylori.

• Development and Reproduction
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• v.10 no.2
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• pp.85-92
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• 2006

Progesterone(P4) is an important intermediate in the synthesis of androgens and estrogens. Furthermore, P4 itself plays a crucial role in ovulation, atresia and luteinization, and is essential for the continuation of early pregnancy in all mammalian species. In spite of the hormone's physiological importance, the exact action mechanism(s) of P4 in mammalian ovary has not been fully understood yet. In this context, a decades-long controversy regarding the identity of receptors that mediate non-genomic, transcription-independent cellular responses to P4 is presently attracting huge scientific interests. P4 may exert its action in mammalian ovary by several ways: 1) the well-documented genomic pathway, involving hormone binding to so-called classic cytosolic receptor(PGR) and subsequent modulation of gene expression by the ligand-receptor complex as transcription factor. 2) pathways are operating that do not act on the genome, therefore refered to as non-genomic actions. The prominent characteristics of the non-genomic P4 actions are: (i) rapid, (ii) insensitive to transcription inhibitors, (iii) transduced by membrane associated molecules. In particular, the non-genomic P4 actions could be mediated by: (a) classic genomic P4 receptor(PGR) that localizes at or near the plasma membrane, (b) a family of membrane progestin receptors(MPR $\alpha$, MPR $\beta$ and MPR $\gamma$), (c) progesterone receptor membrane component I(PGRMC1), and (d) a membrane complex composed of serpine I mRNA binding protein(SERBP1). The present review summarized these rapid signaling pathways of P4 in the mammalian ovary.

• The Korean Journal of Physiology and Pharmacology
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• v.24 no.4
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• pp.339-348
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• 2020

We aimed to characterize the participation of rapid non-genomic and delayed non-genomic/genomic or genomic mechanisms in vasoactive effects to triiodothyronine (T3), emphasizing functional analysis of the involvement of these mechanisms in the genesis of nitric oxide (NO) of endothelial or muscular origin. Influences of in vitro and in vivo T3 treatments on contractile and relaxant responsiveness of isolated rat aortas were studied. In vivo T3-treatment was 500 ㎍·kg^-1·d^-1, subcutaneous injection, for 1 (T3_1d) and 3 (T3_3d) days. In experiments with endothelium-intact aortic rings contracted with phenylephrine, increasing concentrations of T3 did not alter contractility. Likewise, in vitro T3 did not modify relaxant responses induced by acetylcholine or sodium nitroprusside (SNP) nor contractile responses elicited by phenylephrine or angiotensin II in endothelium-intact aortas. Concentration-response curves (CRCs) to acetylcholine and SNP in endothelium-intact aortic rings from T3_1d and T3_3d rats were unmodified. T3_3d, but not T3_1d, treatment diminished CRCs to phenylephrine in endothelium-intact aortic rings. CRCs to phenylephrine remained significantly depressed in both endothelium-denuded and endothelium-intact, nitric oxide synthase inhibitor-treated, aortas of T3_3d rats. In endothelium-denuded aortas of T3_3d rats, CRCs to angiotensin II, and high K⁺ contractures, were decreased. Thus, in vitro T3 neither modified phenylephrine-induced active tonus nor CRCs to relaxant and contractile agonists in endothelium-intact aortas, discarding rapid non-genomic actions of this hormone in smooth muscle and endothelial cells. Otherwise, T3_3d-treatment inhibited aortic smooth muscle capacity to contract, but not to relax, in an endothelium- and NO-independent manner. This effect may be mediated by delayed non-genomic/genomic or genomic mechanisms.

• Genomics & Informatics
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• v.2 no.3
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• pp.126-130
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• 2004

T helper-type 2 cytokines, such as IL-4 and IL-13, may play a central role in allergic diseases. The protein known as signal transducers and activators of transcription 6 (STAT6) is a key transcription factor involved in both IL-4- and -13-mediated biological responses. Two polymorphisms of the STAT 6 gene (exon 1 and G2964A variant) have been found. We investigated whether these STAT6 gene polymorph isms were associated with allergic rhinitis. Blood samples for genetic analysis were obtained from 285 individuals with allergic rhinitis and from 271 healthy subjects without atopic disease. The G2964A variant of the STAT6 gene was genotyped using PCR-RFLP analysis. The GT repeat polymorphism in exon 1 of the STAT6 gene was genotyped by fragment analysis. There was no association between the 2964A variant and GT repeat polymorphism in exon 1 of the STAT6 and allergic rhinitis in a Korean population (both p > 0.05). Our results suggest that a combination of STAT6 gene polymorphisms is not a useful marker for predicting allergic rhinitis.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.12
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• pp.1691-1695
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• 2006

The identification method that inflects real time ultrasound (RUT) and the potential application of marker assisted selection (MAS) for improvement of a cow population of Hanwoo (Korean Native cattle) was studied. The averages of RUT longissimus muscle area, RUT fat thickness, and RUT marbling score scanned at the 13th rib were 55.78 $cm^2$, 3.70 mm and 3.83 scores, respectively. We investigated the effects of the two SNPs (Kpn2 I and Msp I) in the leptin gene on carcass traits for Hanwoo cows by using ultrasound measurements. Genotype CC of the Kpn2 I had a significantly higher effect on back fat thickness (4.23 mm) and longissimus muscle area (57.57 $cm^2$) than genotype TT (3.14 mm, 53.93 $cm^2$, respectively, p<0.05). Genotype AA of the Msp I had a significantly higher effect only on marbling score (5.37) than genotype AB (3.57, p<0.05) and BB (3.37, p<0.05). Significant effects of SNPs in the leptin gene were found for the ultrasound measures of body composition in live cattle.