• Animal Bioscience
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• v.36 no.7
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• pp.991-1002
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• 2023

Objective: This study aimed to elucidate the underlying gene regions responsible for productive, phenotypic or adaptive traits in different ecological types of Tibetan sheep and the discovery of important genes encoding valuable traits. Methods: We used whole-genome resequencing to explore the genetic relationships, phylogenetic tree, and population genetic structure analysis. In addition, we identified 28 representative Tibetan sheep single-nucleotide polymorphisms (SNPs) and genomic selective sweep regions with different traits in Tibetan sheep by fixation index (Fst) and the nucleotide diversity (θπ) ratio. Results: The genetic relationships analysis showed that each breed partitioned into its own clades and had close genetic relationships. We also identified many potential breed-specific selective sweep regions, including genes associated with hypoxic adaptability (MTOR, TRHDE, PDK1, PTPN9, TMTC2, SOX9, EPAS1, PDGFD, SOCS3, TGFBR3), coat color (MITF, MC1R, ERCC2, TCF25, ITCH, TYR, RALY, KIT), wool traits (COL4A2, ERC2, NOTCH2, ROCK1, FGF5, SOX9), and horn phenotypes (RXFP2). In particular, a horn-related gene, RXFP2, showed the four most significantly associated SNP loci (g. 29481646 A>G, g. 29469024 T>C, g. 29462010 C>T, g. 29461968 C>T) and haplotypes. Conclusion: This finding demonstrates the potential for genetic markers in future molecular breeding programs to improve selection for horn phenotypes. The results will facilitate the understanding of the genetic basis of production and adaptive unique traits in Chinese indigenous Tibetan sheep taxa and offer a reference for the molecular breeding of Tibetan sheep.

• Horticultural Science & Technology
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• v.29 no.6
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• pp.633-640
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• 2011

Brassica rapa is an A genome model species for Brassica crop genetics, genomics, and breeding. With the completion of sequencing the B. rapa genome, functional analysis of the genome is forthcoming issue. The expressed sequence tags are fundamental resources supporting annotation and functional analysis of the genome including identification of tissue-specific genes and promoters. As of July 2011, 147,217 ESTs from 39 cDNA libraries of B. rapa are reported in the public database. However, little information can be retrieved from the sequences due to lack of organized databases. To leverage the sequence information and to maximize the use of publicly-available EST collections, the Brassica rapa tissue-specific EST database (BrTED) is developed. BrTED includes sequence information of 23,962 unigenes assembled by StackPack program. The unigene set is used as a query unit for various analyses such as BLAST against TAIR gene model, functional annotation using MIPS and UniProt, gene ontology analysis, and prediction of tissue-specific unigene sets based on statistics test. The database is composed of two main units, EST sequence processing and information retrieving unit and tissue-specific expression profile analysis unit. Information and data in both units are tightly inter-connected to each other using a web based browsing system. RT-PCR evaluation of 29 selected unigene sets successfully amplified amplicons from the target tissues of B. rapa. BrTED provided here allows the user to identify and analyze the expression of genes of interest and aid efforts to interpret the B. rapa genome through functional genomics. In addition, it can be used as a public resource in providing reference information to study the genus Brassica and other closely related crop crucifer plants.

• Molecules and Cells
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• v.26 no.5
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• pp.427-435
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• 2008

In this review, we discuss the genes and the related signal pathways that regulate aging and longevity by reviewing recent findings of genetic longevity models in rodents in reference to findings with lower organisms. We also paid special attention to the genes and signals mediating the effects of calorie restriction (CR), a powerful intervention that slows the aging process and extends the lifespan in a range of organisms. An evolutionary view emphasizes the roles of nutrient-sensing and neuroendocrine adaptation to food shortage as the mechanisms underlying the effects of CR. Genetic and non-genetic interventions without CR suggest a role for single or combined hormonal signals that partly mediate the effect of CR. Longevity genes fall into two categories, genes relevant to nutrient-sensing systems and those associated with mitochondrial function or redox regulation. In mammals, disrupted or reduced growth hormone (GH)-insulin-like growth factor (IGF)-1 signaling robustly favors longevity. CR also suppresses the GH-IGF-1 axis, indicating the importance of this signal pathway. Surprisingly, there are very few longevity models to evaluate the enhanced anti-oxidative mechanism, while there is substantial evidence supporting the oxidative stress and damage theory of aging. Either increased or reduced mitochondrial function may extend the lifespan. The role of redox regulation and mitochondrial function in CR remains to be elucidated.

• Journal of Microbiology and Biotechnology
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• v.18 no.10
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• pp.1735-1740
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• 2008

Clone PERV-C (A3) env was isolated from the genomic DNA of domestic pig (Sus scrofa domesticus) in Korea to investigate the molecular properties of PERV-C. The nucleic acid homologies between the PERV-MSL (type C) reference and the PERV-C(A3) clone was 99% for env, but a single base pair deletion was found in the transmembrane (TM) region of the env open reading frame. To examine the functional characteristics of truncated PERV-C env, we constructed a replication-incompetent retroviral vector by replacing the env gene of the pCL-Eco retrovirus vector with PERV-C env. A retroviral vector bearing PERV-C/A chimeric envelopes was also created to complement the TM defect. Our results indicated that truncated PERV-C env was not infectious in human cells as expected. Interestingly, however, the vector with the PERV-C/A envelope was able to infect 293 cells. This observation suggests that recombination within PERV-C TM could render PERV-C infectious in humans. To further characterize PERV-C/A envelopes, we constructed an infectious molecular clone by using a PCR-based technique. This infectious molecular clone will be useful to examine more specific regions that are critical for human cell tropism.

• Journal of Mushroom
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• v.9 no.4
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• pp.180-185
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• 2011

Spent mushroom substrates (SMS) is a by-product remaining after a crop of mushrooms. About four surfactin-producing strains were isolated from SMS (Pleurotus eryngii). Among of them, one isolate, which designated to YJ07, potentially showed the antifungal activity against Aspergillus flavus and Aspergillus ochraceous producing mycotoxin on PDA medium. The biochemical characteristics of the strain YJ07 was similar with Bacillus subtilis and Bacillus amyloliquefaciens by Bacillus ID kit and VITEK 2 system. Comparative 16S rDNA gene sequence analysis of the strain YJ07 also showed that the strain YJ07 was most closely related to Bacillus amyloliquefaciens with sequence similarity of 99.5%. On the basis of their biochemical characteristics and phylogenetic distinctiveness, the strain YJ07 was classified within the genus Bacillus as Bacillus amyloliquefaciens YJ07. The antifungal compound from B. amyloliquefaciens YJ07 was similar to lipopeptide surfactin from Bacillus subtilis by TLC and HPLC analysis.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.2
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• pp.653-664
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• 2012

Objective: This study assessed anti-inflammatory and antioxidant activities of $E.$ $foetidum$ leaf extract on LPS-activated murine macrophages. Methods: RAW264.7 cells were pretreated with or without $E.$ $foetidum$ extract for 1 h prior to incubation with LPS for 24 h. Anti-inflammatory activity was evaluated with reference to iNOS, COX-2, TNF-${\alpha}$ and IL-6 gene expression. In addition, NO and intracellular ROS generation were determined by Griess method and fluorescence intensity and activation of MAPKs and $I{\kappa}B$ by Western blotting. Results: Prior treatment with $E.$ $foetidum$ leaf extract inhibited elevation of IL-6, TNF-${\alpha}$, iNOS and COX-2, together with their cognate mRNAs in a dose-dependent manner. NO and intracellular ROS contents were similarly reduced. These effects were due to inhibition of LPS-induced phosphorylation of JNK and p38 as well as $I{\kappa}B$. $E.$ $foetidum$ ethanol extract were shown to contain lutein, ${\beta}$-carotene, chlorogenic acid, kaempferol and caffeic acid, compounds known to exert these bioactive properties. Conclusions: $E.$ $foetidum$ leaf extract possesses suppressive effects against pro-inflammatory mediators. Thus, $E.$ $foetidum$ has a high potential to be used as a food supplement to reduce risk of cancer associated with inflammation.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.1
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• pp.41-48
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• 2012

Introduction: Breast cancer is the second leading cancer in Korean women. To assess potential genetic associations between the prostate stem cell antigen (PSCA) gene in the chromosome 8q24 locus and breast cancer risk in Korean women, 13 SNPs were selected and associations with breast cancer risk were analyzed with reference to hormone receptor (HR) and menopausal status. Methods:We analyzed DNA extracted from buffy coat from 456 patients and 461 control samples, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) based upon region-specific PCR followed by allelespecific single base primer extension reactions. Risks associated with PSCA genotypes and haplotypes were estimated with chi-square test (${\chi}^2$-test), and polytomous logistic regression models using odds ratios (OR) and 95% confidence intervals (CIs), by HR and menopausal status. Results: In case-control analysis, odds ratios (OR) of rs2294009, rs2294008, rs2978981, rs2920298, rs2976395, and rs2976396 were statistically significant only among women with estrogen receptor (ER) negative cancers, and those of rs2294008, rs2978981, rs2294010, rs2920298, rs2976394, rs10216533, and rs2976396 were statistically significant only in pre-menopausal women, and not in postmenopausal women. Risk with the TTGGCAA haplotype was significantly elevated in ER (-) status (OR= 1.48, 95% CI= 1.03~2.12, p<0.05). Especially risk of allele T of rs2294008 is significantly low in pre-menopausal breast cancer patients and AA genotype of rs2976395 in ER (-) status represents the increase of OR value. Conclusion: This report indicated for the first time that associations exist between PSCA SNPs and breast cancer susceptibility in Korean women, particularly those who are pre-menopausal with an estrogen receptor negative tumor status.

• Korean Journal of Poultry Science
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• v.45 no.3
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• pp.209-217
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• 2018

The innate immune recognition is based on the detection of microbial products. Toll-like receptors (TLRs) located on the cell surface and the endosome senses microbial components and nucleic acids, respectively. Chicken TLRs mediate immune responses by sensing ligands from pathogens, have been studied as immune adjuvants to increase the efficacy of vaccines. Single nucleotide polymorphisms (SNPs) of TLR3 and TLR4 genes in chicken were associated with resistance and susceptibility to viral infection. In this study, SNPs of chTLR3 and chTLR4 genes were retrieved from public database and annotated with chicken reference genome. Three-dimensional models of the chTLR3 and chTLR4 proteins were built using a Swiss modeler. We identified 35 and 13 nsSNPs in chTLR3 and chTLR4 genes respectively. Sorting Intolerant from Tolerant (SIFT) and Polymorphism Phenotyping v2 (Polyphen-2) analyses, suggested that, out of 35 and 13 nsSNPs, 4 and 2 SNPs were identified to be deleterious in chTLR3 and chTLR4 gene respectively. In chTLR3, 1 deleterious SNP was located in ectodomain and 3 were located in the Toll / IL-1 receptor (TIR) domain. Further structural model of chTLR3-TIR domain suggested that 1 deleterious SNP be present in the B-B loop region, which is important for TIR-TIR domain interactions in the downstream signaling. In chTLR4, the deleterious SNPs were located both in the ectodomain and TIR domain. SNPs predicted for chTLR3 and chTLR4 in this study, might be related to resistance or susceptible to viral infection in chickens. Results from this study will be useful to develop the effective measures in chicken against infectious diseases.

• The Plant Pathology Journal
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• v.36 no.5
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• pp.440-449
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• 2020

The purpose of this study was to analyze the genetic and pathogenic characteristics of Ralstonia pseudosolanacearum in roses in Korea, and to examine the similarities and differences between Korean isolates and the first-reported European strains. Between 2017 and 2019, seventeen isolates from rose plants were identified as R. pseudosolanacearum using Ralstonia-specific primers. All 17 isolates were identified as race 1 using race-specific primers, and were confirmed as biovar 3 due to their ability to utilize carbon sources. Multiplex PCR using phylotype discriminating specific primers identified the 17 isolates as phylotype I. Sequevar comparison with reference sequevars using the sequences of the egl, mutS, and fliC genes, and only the egl gene, revealed that the strains evaluated in this study corresponded to sequevar I-33. The pathogenicity in roses differed depending on the rose cultivars. The different methods used for the genetic characterization of R. pseudosolanacearum indicate that the 17 rose bacterial wilt isolates had the same genetic characteristics. The lack of genetic variation in these isolates indicates their recent introduction from other countries (likely European countries). Therefore, appropriate quarantine and control measures should be taken in order to avoid further increases in the pathogenicity and/or secondary host range of R. pseudosolanacearum through genetic mutation.

• The Journal of Pediatrics of Korean Medicine
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• v.28 no.3
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• pp.47-58
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• 2014

Objectives GyejigaChulBuTang (GCBT) is a prescription used to treat acute and chronic arthritis in Korea, China, and Japan. This study assessed the anti-inflammatory and anti-oxidant activities of GCBT on lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells. Methods Raw264.7 cells were pretreated with or without GCBT for 1 hour prior to incubation with LPS. Anti-inflammatory activity of GCBT was evaluated with reference to gene expression and production levels of proinflammatory cytokines ($TNF{\alpha}$, IL-$1{\beta}$, IL-6, GM-CSF and $INF{\gamma}$) and inflammatory mediators (iNOS, COX-2, NO and $PGE_2$). In addition, intracellular ROS generation and signal transduction of MAPK family, PI3K/Akt and $I{\kappa}B{\alpha}/NF{\kappa}B$ was investigated. Results Prior treatment with GCBT inhibited elevation of $TNF{\alpha}$, IL-$1{\beta}$, IL-6, GM-CSF, $INF{\gamma}$, NO and $PGE_2$, together with their cognate mRNAs in a dose-dependent manner. Intracellular ROS contents were similarly reduced. These effects were due to inhibition of LPS-induced phosphorylation of MAPK family, PI3K/Akt and $I{\kappa}B{\alpha}$ as well as nuclear translocation of $NF{\kappa}B$. Conclusions GCBT suppresses pro-inflammatory mediators. GCBT has potential in the treatment of juvenile rheumatoid arthritis associated with inflammation.