• BMB Reports
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• v.42 no.11
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• pp.747-751
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• 2009

Transcriptional silencing of subtelomeric genes is associated with telomere length, which is correlated with age. Long and short telomeres in young and old people, respectively, coincide with gene repression and activation in each case. In addition, differential location of genes with respect to telomeres causes telomere position effect. There is very little evidence of the manner in which age-related telomere length affects the expression of specific human subtelomeric genes. We analyzed the relationship between telomere length and gene expression levels in fibroblasts derived from human donors at ages ranging from 0-70 years. We studied three groups of genes located between 100 and 150 kb, 200 and 250 kb, and >300 kb away from telomeres. We found that the chromatin modifier-encoding genes Eu-HMTase1, ZMYND11, and RASA3 were overexpressed in adults. Our results suggest that short telomere length-related overexpression of chromatin modifiers could underlie transcriptional changes contributing to cellular senescence.

• Journal of Animal Science and Technology
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• v.57 no.3
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• pp.12.1-12.5
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• 2015

Background: The Korean native pig (KNP) is generally thought to have come from northern China to the Korean peninsula approximately 2000 years ago. KNP pigs were at the brink of extinction in the 1980s, since then efforts have been made to restore the breed by bringing together the remaining stocks in South Korea. As a result, KNP was registered as a breed in 2006. To find additional breed-specific markers that are distinct among pig breeds, variations in O-linked N-acetylglucosamine transferase (OGT) were investigated. OGT is located on chromosome X and catalyzes the post-translational addition of a single O-linked-${\beta}$-N-acetylglucosamine to target proteins. Findings: Length polymorphism in the intron 20 of OGT was identified. The intron 20 of OGT from Duroc, Landrace, and Yorkshire breeds was 281-bp longer than that from either KNP or Chinese Meishan pigs. The difference between the Western pig breeds (BB genotype) and KNP or Meishan pigs (AA genotype) was due to an inserted 276-bp element and the 5-bp ACTTG. Conclusions: The polymorphism in OGT identified in this study may be used as an additional marker for determining the breed of origin among Meishan and the Western pig breeds. The length polymorphism suggests that the locus near OGT is not fixed in KNP. This marker would be relevant in determining the breed of origin in crossbred pigs between KNP pigs with known genotypes and the Western pig breeds with BB genotypes, thus confirming the contribution of the X chromosome from each breed.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.6
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• pp.888-895
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• 2015

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost.

• The Korean Journal of Physiology and Pharmacology
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• v.25 no.6
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• pp.593-601
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• 2021

Primary cilia on kidney tubular cells play crucial roles in maintaining structure and physiological function. Emerging evidence indicates that the absence of primary cilia, and their length, are associated with kidney diseases. The length of primary cilia in kidney tubular epithelial cells depends, at least in part, on oxidative stress and extracellular signal-regulated kinase 1/2 (ERK) activation. Hydrogen sulfide (H₂S) is involved in antioxidant systems and the ERK signaling pathway. Therefore, in this study, we investigated the role of H₂S in primary cilia elongation and the downstream pathway. In cultured Madin-Darby Canine Kidney cells, the length of primary cilia gradually increased up to 4 days after the cells were grown to confluent monolayers. In addition, the expression of H₂S-producing enzyme increased concomitantly with primary cilia length. Treatment with NaHS, an exogenous H₂S donor, accelerated the elongation of primary cilia whereas DL-propargylglycine (a cystathionine γ-lyase inhibitor) and hydroxylamine (a cystathionine-β-synthase inhibitor) delayed their elongation. NaHS treatment increased ERK activation and Sec10 and Arl13b protein expression, both of which are involved in cilia formation and elongation. Treatment with U0126, an ERK inhibitor, delayed elongation of primary cilia and blocked the effect of NaHS-mediated primary cilia elongation and Sec10 and Arl13b upregulation. Finally, we also found that H₂S accelerated primary cilia elongation after ischemic kidney injury. These results indicate that H₂S lengthens primary cilia through ERK activation and a consequent increase in Sec10 and Arl13b expression, suggesting that H₂S and its downstream targets could be novel molecular targets for regulating primary cilia.

• Molecules and Cells
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• v.45 no.3
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• pp.148-157
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• 2022

Hepatitis C virus (HCV) is a major cause of chronic liver disease and is highly dependent on cellular proteins for viral propagation. Using protein microarray analysis, we identified 90 cellular proteins as HCV nonstructural 5A (NS5A) interacting partners, and selected telomere length regulation protein (TEN1) for further study. TEN1 forms a heterotrimeric complex with CTC and STN1, which is essential for telomere protection and maintenance. Telomere length decreases in patients with active HCV, chronic liver disease, and hepatocellular carcinoma. However, the molecular mechanism of telomere length shortening in HCV-associated disease is largely unknown. In the present study, protein interactions between NS5A and TEN1 were confirmed by immunoprecipitation assays. Silencing of TEN1 reduced both viral RNA and protein expression levels of HCV, while ectopic expression of the siRNA-resistant TEN1 recovered the viral protein level, suggesting that TEN1 was specifically required for HCV propagation. Importantly, we found that TEN1 is re-localized from the nucleus to the cytoplasm in HCV-infected cells. These data suggest that HCV exploits TEN1 to promote viral propagation and that telomere protection is compromised in HCV-infected cells. Overall, our findings provide mechanistic insight into the telomere shortening in HCV-infected cells.

• Bulletin of the Korean Chemical Society
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• v.31 no.7
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• pp.2019-2024
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• 2010

Insulin-like growth factor binding protein 5 (IGFBP-5) plays an important role in controlling cell survival, differentiation and apoptosis. Apoptosis can be induced by an extrinsic pathway involving the ligand-mediated activation of death receptors such as tumor necrosis factor receptor 1 (TNFR1). To determine whether IGFBP-5 and TNFR1 interact as members of the same apoptosis pathway, recombinant IGFBP-5 and TNFR1 were isolated. The expression and purification of the full-length TNFR1 and truncated IGFBP-5 proteins were successfully performed in E. coli. The binding of both IGFBP-5 and TNFR1 proteins was detected by surface plasmon resonance spectroscopy (BIAcore), fluorescence measurement, electron microscopy, and size-exclusion column (SEC) chromatography. IGFBP-5 indeed binds to TNFR1 with an apparent $K_D$ of 9 nM. After measuring the fluorescence emission spectra of purified IGFBP-5 and TNFR1, it was found that the tight interaction of these proteins is accompanied by significant conformational changes of one or both. These results indicate that IGFBP-5 acts potently as a novel ligand for TNFR1.

• International Journal of Industrial Entomology and Biomaterials
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• v.11 no.2
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• pp.119-124
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• 2005

To determine the level of heterosis, higher cocoon shell weight multivoltine congenic lines (Con. L) and bivoltine syngenic lines (Syn. L) of silkworm were used for crosses. First filial generations $(F_1s)$ expressed heterobeltiotic genetic interaction at significant magnitude (p < 0.01) for single cocoon shell weight (SCSW). The other linked characters viz., single cocoon weight (SCW) and yield by weight per 10, 000 larvae were also significantly higher (p < 0.01) than the better parental lines. All the hybrids showed significant improvement for these aforesaid characters over standard heterosis (Standard check). The reeling parameters viz., filament length, raw silk, neatness, cohesionstrokes etc, also showed improvement among the hybrids than check in congenial environment. Overall results suggested that the cross between congenic and syngenic lines provide better heterosis with good quality silk than conventional hybrids and may be used for commercial exploitation.

• The Plant Pathology Journal
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• v.30 no.4
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• pp.425-431
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• 2014

Leaf scald caused by the infection of Rhynchosporium secalis, is a worldwide crop disease resulting in significant loss of barley yield. In this study, a systematic sequencing of expressed sequence tags (ESTs) was chosen to obtain a global picture of the assembly of genes involved in pathogenesis. To identify a large number of plant ESTs, which are induced at different time points, an amplified fragment length polymorphism (AFLP) display of complementary DNA (cDNA) was utilized. Transcriptional changes of 140 ESTs were observed, of which 19 have no previously described function. Functional annotation of the transcripts revealed a variety of infection-induced host genes encoding classical pathogenesis-related (PR) or genes that play a role in the signal transduction pathway. The expression analyses by a semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) revealed that Rar1 and Rpg4 are defense inducible genes, and were consistent with the cDNA-AFLP data in their expression patterns. Hence, the here presented transcriptomic approach provides novel global catalogue of genes not currently represented in the EST databases.

• Biomedical Science Letters
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• v.19 no.3
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• pp.213-223
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• 2013

The objectives of this study are to develop a molecular diagnosis to differentiate serotypes and mating-types of C. neoformans/C. gattii complex isolates from pigeon droppings in Korea and to elucidate molecular epidemiology of the isolates. Phenotypes and genotypes of C. neoformans/C. gattii complex isolates were identified by biochemical properties and PCR using specific CNLAC1 gene, respectively. To classify serotypes and mating-types of C. neoformans/C. gattii complex isolates, the five reference strains and thirty-three isolates in Korea were investigated by restriction fragment length polymorphism (RFLP) analysis using CNLAC1 gene for varieties, by random amplified polymorphic DNA (RAPD) for serotyping, and by PCR using specific primer sets for mating typing. All isolates in Korea were belonged to C. neoformans var. grubii (serotype A) by RFLP and RAPD patterns which showed high sensitivity and specificity. Therefore, RFLP and RFLP were available to differentiate varieties and serotypes of C. neoformans. Amplification patterns of the five reference strains by specific PCR for mating typing were differentiable, and all isolates were classified into $MAT{\alpha}$. All C. neoformans environmental isolates in Korea were Cr. neoformans serotype A and $MAT{\alpha}$ which is a more virulent pathogen. This study suggests that RFLP and RAPD are rapid and correct molecular diagnosis tools for epidemiology of C. neoformans/C. gattii complex isolates.

• Journal of Plant Biotechnology
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• v.37 no.2
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• pp.133-143
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• 2010

Rice (Oryza sativa) is a major cereal crop that has been developed as a monocot model species. In past decades rice researchers have established valuable resources for functional genomics in rice, such as complete genome sequencing, high-density genetic maps, a full length cDNA database, genome-wide transcriptome data, and a large number of mutants. Of these, rice mutant lines are very important to definitively determine functions of genes associated with valuable agronomic traits. In this review we summarize the progress of functional genomics approaches in rice using T-DNA mutants.