• Journal of Life Science
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• v.20 no.4
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• pp.614-617
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• 2010

We sequenced a 522 bp fragment including the $tRNA^{Thr}$, $tRNA^{Pro}$ gene and the first half of the control region from 29 wild and cultured olive flounder specimens from Korea. Out of 522 nucleotide sites, 49 (9.4%) were variable, 23 haplotypes being found. Most haplotypes are unique in the wild population and only four were shared by cultured specimins. The nucleotide diversity and differences between wild and cultured populations were $0.025{\pm}0.013$ and $0.015{\pm}0.008$, and $12.94{\pm}6.00$ and $7.83{\pm}3.75$, respectively. Haplotype diversity was $0.98{\pm}0.02$ and $0.49{\pm}0.09$ in the wild and cultured populations, respectively. These results show that marked reductions of genetic variability in the hatchery strains were observed in the number of mitochondrial DNA haplotypes and haplotype diversity when compared to the wild populations. Furthermore, we detected significant population differentiation between both populations. The mtDNA sequencing technique used to evaluate the genetic variability of hatchery strains compared to that of the wild population is potential for genetic monitoring of olive flounder hatchery stocks.

• BMB Reports
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• v.57 no.1
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• pp.60-65
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• 2024

The CRISPR-Cas9 system has significantly advanced regenerative medicine research by enabling genome editing in stem cells. Due to their desirable properties, mesenchymal stem cells (MSCs) have recently emerged as highly promising therapeutic agents, which properties include differentiation ability and cytokine production. While CRISPR-Cas9 technology is applied to develop MSC-based therapeutics, MSCs exhibit inefficient genome editing, and susceptibility to plasmid DNA. In this study, we compared and optimized plasmid DNA and RNP approaches for efficient genome engineering in MSCs. The RNP-mediated approach enabled genome editing with high indel frequency and low cytotoxicity in MSCs. By utilizing Cas9 RNPs, we successfully generated B2M-knockout MSCs, which reduced T-cell differentiation, and improved MSC survival. Furthermore, this approach enhanced the immunomodulatory effect of IFN-r priming. These findings indicate that the RNP-mediated engineering of MSC genomes can achieve high efficiency, and engineered MSCs offer potential as a promising therapeutic strategy.

• Journal of Plant Biotechnology
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• v.6 no.1
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• pp.55-61
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• 2004

Callus induction and somatic embryogenesis are fundamental to cotton tissue culture biotechnology. An efficient protocol for callus induction, somatic embryogenesis and their maturation have been developed to regenerate plantlets from cotton (Gossypium hirsutum L.) variety coker 312. Embryogenic callus was initiated from hypo-cotyl region that was used as an explant at seedling stage when it was about 7-8 days old. Callus induction was achieved through culturing hypocotyls (5-7mm) on $MS_{1a} medium supplemented with 2,4-D (0.1 mg/L) and KT (0.5 mg/L) for six weeks. A friable, colorless, bulky and well proliferating callus becomes greenish with the addition of NAA (2.0 mg/L), ZT (0.1 mg/L) and removal of 2,4-D (M $S_{1b}$) cultured for two weeks then again transferred to $MS_{1a}. 2,4-dichlorophenoxyacetic acid (2,4-D) promoted the proliferation of embryogenic callus, but had a negative effect on the differentiation and germination of somatic embryos. ZT (0.1mg/L) and activated charcoal (2g/L), both hormones play an important role in differentiation and germination of somatic embryos in hypocotyls derived embryogenic callus but in case of cotton, such a capability have been observed on MS medium with 1.92 g/L $KNO_3$, but it is considered to attain somewhat more improvement. High embryogenesis frequency was achieved through nutrient deficient stress treatment. The frequency of globular embryogenesis (two-three folds) was achieved when well proliferating callus was (from $MS_{1a}$ media) cultured on MS (1/5 strength) medium for four weeks. Here the development of anthocyanins is the best indicator for somatic embryogenesis. However, when embryoid callus was cultured on MS (full strength) medium, the globular embryos were developed into normal plantlets immediately. In this procedure 27.49% cotyledenary embryos were developed. Of that 70% cotyledenary embryos were developed not only into normal plantlets but rooted simultaneously, when cultured on MS (with 0.05 mgg/L giberrelic acid) medium. So complete plants could be regenerated through somatic embryogenesis from hypocotyl explants within 6 months.s.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.9
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• pp.1137-1144
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• 2010

In this study, to examine genetic variability within a breed and genetic relationships between populations/breeds, we genotyped 606 birds from seven Japanese native chicken breeds at seven polymorphic loci of egg white proteins and compared those with Asian native chicken populations and commercial breeds. Genotyping of the Japanese native breeds showed that ovalbumin, two ovoglobulins and ovotransferrin were polymorphic, but ovomacroglobulin, ovoflavoprotein and lysozyme were monomorphic. The proportion of polymorphic loci ($P_{poly}$) and average heterozygosity ($\bar{H}$) within a population ranged from 0.286 to 0.429 and from 0.085 to 0.158, respectively. The coefficient of gene differentiation ($G_{ST}$) was 0.250 in the Japanese native chicken breeds. This estimate was higher than that of Asian native chicken populations ($G_{ST}$ = 0.083) and of commercial breeds ($G_{ST}$ = 0.169). Dendrogram and PCA plot showed that Satsuma-dori, Jitokko, Amakusa-daio and Hinai-dori were closely related to each other and grouped into Asian native chickens and that Tsushima-jidori, Nagoya and Chan (Utaichan) were ramified far from other Japanese native chicken breeds. The egg white protein polymorphisms demonstrated that the population differentiation of the seven Japanese native chicken breeds was relatively large.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.16 no.3
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• pp.237-250
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• 2003

Since an orthotropic steel deck bridge has large number of design variables and shows complex structural behavior, it would be very difficult and impractical to directly use a Conventional Single Level (CSL) optimization algorithm for its optimum design. Thus, in this paper, an Improved Multi Level Design Synthesis (IMLDS) optimization algorithm is proposed to improve the computational efficiency. In the proposed IMLDS algorithm, a coordination method is introduced to divide the bridge into main girders and orthotropic steel deck with preserving the characteristics of the structural behavior. For an efficient optimization of the bridge, the IMLDS algorithm incorporates the various crucial approximation techniques such as constraints deletion, Automatic Differentiation (AD), stress reanalysis, and etc. In the case of orthotropic steel deck system, optimum design problems are characterized by mixed continuous discrete variables and discontinuous design space. Thus, a modified Genetic Algorithm (GA) is also applied to optimize discrete member design for orthotropic steel deck. From the numerical example, the efficiency and convergency of the IMLDS algorithm proposed in this paper is investigated. It may be positively stated that the IMLDS algorithm will lead to more effective and practical design compared with previous algorithms.

• Animal cells and systems
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• v.2 no.2
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• pp.249-258
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• 1998

Obesity, one of the most common metabolic diseases in industrial countries is characterized by an increase in the number or size of adipocytes. In an effort to create transgenic mouse models for the study of obesity we developed a novel technique in which adipose tissue can be ablated genetically at will, at any specific developmental stage and/or physiological condition, by the treatment of ganciclovir. We made a series of adipocytespecific expression vectors using minimal regulatory regions of brown adipocyte-specific uncoupling protein (UCP-1) gene and adipocyte-specific aP2 gene, and then analyzed their expression characteristics in cultured cell lines. When both constructs pUCP-LacZ and paP2-LacZ were transfected transiently into differentiating 3T3-L1 (pre-while adipocytes) and HIB-1B (pre-brown adipocytes) cell lines in vitro and then monitored by X-gal staining of cells, these regulatory regions were sufficient to show proper differentiation stage-specific expression in adipocvtes. To confirm that adipocytes expressing HSV-TK controlled by these minimal requlatory elements are sufficient to kill themselves with ganciclovir treatment pUCP-TK and paP2-TK expression constructs were transfected stably into HIB-1B and 3T3-L1 cells, respectively, and their ganciclovir sensitivities were tested during in vitro differentiation of cells. As expected more than 80% of cells were dead by the 7th day of treatment with ganciclovir while negative control cells were not affected at all. The data suqqest that the constructed vectors are suitable for obtaining novel obese transqenic models based on a conditional genetic tissue ablation method.

• Journal of Animal Science and Technology
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• v.65 no.6
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• pp.1194-1204
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• 2023

Meat quality comprises a set of key traits such as pH, meat color, water-holding capacity, tenderness and marbling. These traits are complex because they are affected by multiple genetic and environmental factors. The aim of this study was to investigate the molecular genetic basis underlying nine meat quality-related traits in a Yorkshire pig population using a genome-wide association study (GWAS) and subsequent biological pathway analysis. In total, 45,926 single nucleotide polymorphism (SNP) markers from 543 pigs were selected for the GWAS after quality control. Data were analyzed using a genome-wide efficient mixed model association (GEMMA) method. This linear mixed model-based approach identified two quantitative trait loci (QTLs) for meat color (b^*) on chromosome 2 (SSC2) and one QTL for shear force on chromosome 8 (SSC8). These QTLs acted additively on the two phenotypes and explained 3.92%-4.57% of the phenotypic variance of the traits of interest. The genes encoding HAUS8 on SSC2 and an lncRNA on SSC8 were identified as positional candidate genes for these QTLs. The results of the biological pathway analysis revealed that positional candidate genes for meat color (b^*) were enriched in pathways related to muscle development, muscle growth, intramuscular adipocyte differentiation, and lipid accumulation in muscle, whereas positional candidate genes for shear force were overrepresented in pathways related to cell growth, cell differentiation, and fatty acids synthesis. Further verification of these identified SNPs and genes in other independent populations could provide valuable information for understanding the variations in pork quality-related traits.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.11
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• pp.1691-1699
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• 2018

Objective: In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods: Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results: Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average $r^2$ value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, interpopulation, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion: Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.

• Proceedings of the KSAR Conference
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• 2003.06a
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• pp.27-27
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• 2003

A diversified and concentrative approach of methylation player can be one of the most powerful studies in the understanding of global epigenetic modifications. Previous studies have suggested that DNA methylation contributes to transcriptional silencing through the several DNA methylation-mediated repression systems by hypermethylation, including methyltransferases (DNMTs), DNA methyltransferase association protein 1 (DMAPl), methyl-CpG binding domain (MBD), and histone deacetylases (HDACs). Assembly of these regulatory protein complexes act sequentially, reciprocally, and interdependently on the newly composed DNA strand through S phase. Therefore, these protein complexes have a role in coupling DNA replication to the designed turn-off system in genome. In this study, we attempted to address the role of DNA methylation by the functional analysis of the methyltransferase molecule, we described the involvement of DMAP1 and DNMTs in cell divistion and the effect of their loss. We also described distinct patterns that DMAP1 and DNMTs are spatially reorganized and displaced from condensing chromosomes as cells progress through mitosis in HeLa cell, COS7, and HIH3T3 cell cycle progressions. DNMT1, DNMT3b, and DMAP1 do not stably contact the genetic material during chromosome compaction and repressive expression. These finding show that the loss of activities of DNMTs and DMAP1 occure stage specifically during the cell cycle, may contribute to the integral balance of global DNA methylation. This is consistent with previous studies resulted in decreased histone acetyltransferases and HDACs, and differs from studies resulted in increased histone methyltransferases. Our results suggest that DNA methylation by DNMTs and DMAP1 during mitosis acts to antagonize hypermethylation by which this mark is epigenetical mitotic-specific methylation.

• Development and Reproduction
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• v.10 no.3
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• pp.197-202
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• 2006

Sex steroids are generally considered as natural sex inducers in fish, and aromatase (cytochrome P450 aromatase) that catalyzes androgens into estrogens in the steroidogenic pathway is also known to be involved in sex differentiation. The timing of aromatase action is, thus, of central importance in the study of fish sex differentiation. We treated sexually undifferentiated tilapia (Oreochromis niloticus) larvae with $Fadrozole^{TM}$, a non-steroidal aromatase inhibitor (AI), by immersing the fish in a solution containing AI during the sex differentiation period to narrow down the critical period of aromatase action. Fish were treated once at 11 or 13 days post fertilization (dpf), or twice at 11 and 13 dpf. The concentrations of AI at each time of the treatment were 0 mg/L (control), 50 mg/L or 100 mg/L. Survival rate was not statistically associated with AI immersion treatment (p>0.25). However, sex ratio was significantly altered by the treatment, with higher concentration and double immersion being more effective in masculinizing genetic females (p<0.05). These results suggest that aromatase action for sex differentiation in this fish species would begin at least from 11 dpf which is much earlier than previously expected, and that only 3 hours of brief immersion in AI solution is powerful enough to alter genetically programed sex.