• Korean Journal of Veterinary Research
• /
• v.50 no.1
• /
• pp.55-57
• /
• 2010

Torque teno virus (TTV), a species of Anellovirus, is a non-enveloped single stranded DNA virus with a wide range of animal hosts. The incidence of TTV is quite ubiquitous throughout the world. A total of 235 serum samples obtained from 137 pigs and 98 cattle at slaughterhouses in Korea during April 2005 to May 2005 were tested by TTV-specific PCR as to monitor prevalence of TTV among swine and cattle. As a result, the prevalent rates of TTVs in pigs and cattle were 43.1% and 4.1%, respectively. It seems that TTV infection is quite prevalent in swine population.

• Archives of Pharmacal Research
• /
• v.29 no.5
• /
• pp.363-368
• /
• 2006

EGCG [(-)-epigallocatechin-3-gallate], a major component of green tea has been considered as a major antioxidant constituent. In addition to having been considered for cancer treatment as a chemopreventive and chemotherapeutic agent, EGCG has recently been attributed an anti-proliferative effect. We re-examined the latter finding in this study and added specific focus on the ability of EGCG to induce apoptosis in human osteogenic sarcoma (HOS) cells. Antiproliferative action of EGCG $(IC_{50}=35.3{\pm}6.0{\mu}g/mL)$ appeared to be linked to apoptotic cell death based on morphological changes, chromosomal DNA degradation, and an increase in the $sub-G_1$ apoptotic cell population. Treatment of HOS cells with EGCG gradually activated caspase-3, an established inducer of apoptotic cell death.

• The Plant Pathology Journal
• /
• v.19 no.4
• /
• pp.210-216
• /
• 2003

This study examined the existence of genetically diverse population of Cucumber mosaic virus (CMV), known as quasispecies, from lily, Nicotiana benthamiana and from purified virions. Based on the conserved sequences of CMV lily isolates in intergenic region (IR) on RNA3, the genetic variation of IR from three different sources was investigated by a specific restriction endonuclease hydrolysis of amplified reverse transcription-polymerase chain reaction (RT-PCR) products using virus-specific primers, and was compared with IR sequences. The IR nucleotide sequences of CMV lily isolates were highly conserved, however, quasispecies was detected from all three sources in low level, containing sub-populations of RNA3. These subpopulations of RNA3 were inoculated onto zucchini squash by in vitro transcripts from corresponding full-length cDNA clones together with Eny RNA1 and 2 transcripts. The systemic symptom of zucchini plants infected by these quasispecies was chlorotic spotting, which was milder than severe mosaic and stunt symptom caused by Eny-CMV. The severity of symptom was correlated with RNA accumulation of viruses. These results suggest that the genome of CMV lily isolates consists of quasispecies populations.

• Genomics & Informatics
• /
• v.10 no.2
• /
• pp.81-87
• /
• 2012

Large-scale copy number variants (CNVs) in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered. Although the examination of relatively large numbers of specific ethnic groups has recently started in regard to inter-ethnic group differences in CNVs, identifying and understanding particular instances of natural selection have not been performed. The traditional $F_{ST}$ measure, obtained from differences in allele frequencies between populations, has been used to identify CNVs loci subject to geographically varying selection. Here, we review advances and the application of multinomial-Dirichlet likelihood methods of inference for identifying genome regions that have been subject to natural selection with the $F_{ST}$ estimates. The contents of presentation are not new; however, this review clarifies how the application of the methods to CNV data, which remains largely unexplored, is possible. A hierarchical Bayesian method, which is implemented via Markov Chain Monte Carlo, estimates locus-specific $F_{ST}$ and can identify outlying CNVs loci with large values of FST. By applying this Bayesian method to the publicly available CNV data, we identified the CNV loci that show signals of natural selection, which may elucidate the genetic basis of human disease and diversity.

• IMMUNE NETWORK
• /
• v.11 no.1
• /
• pp.50-58
• /
• 2011

Background: Epstein-Barr virus associated gastric lymphoepithelioma-like carcinoma (LELC) is characterized by the intensive infiltration of lymphoid cells, the presence of EBV, and the better prognosis over typical adenocarcinoma. Thus, it was assumable that viral latent proteins may be responsible for the recruitment of a certain T cell repertoire to EBV-associated gastric carcinoma. Methods: To examine above possibility, EBV gene expression in gastric carcinoma tissues and usage of TCR among the tumor infiltrating lymphocytes were analyzed. Results: EBV specific DNA and EBERs RNA were detected in 4 out of 30 patients. RT-PCR analysis revealed that all 4 of EBV-positive tumor tissues expressed EBNA1 mRNA and BARTs and LMP2a was detected only one sample out of 4. However, the EBNA2 and LMP-1 transcripts were not detected in these tissues. $CD8^+$ T cells were the predominant population of infiltrating lymphocytes in the EBV-positive gastric carcinoma. According to spectra type analysis of infiltrating T cells, 10 predominant bands were detected by TCR $V{\beta}$ CDR3 specific RT-PCR from 4 EBV-positive tumor tissues. Sequence analysis of these bands revealed oligoclonal expansion of T cells. Conclusion: These findings suggest that clonally expanded T cells in vivo might be a population of cytotoxic T cells reactive to EBV-associated gastric carcinoma.

• Korean Journal of Plant Taxonomy
• /
• v.43 no.1
• /
• pp.34-45
• /
• 2013

The Polygonum amphibium complex (Poygonaceae) is a highly polymorphic taxon that can grow in aquatic environments as well as in moist terrestrial habitats. Aquatic and terrestrial plants of the P. amphibium complex vary significantly in morphology and exhibit very complicated patterns of morphological variation, resulting in the description of numerous infra-specific taxa. Principal components analysis of 107 individuals of the P. amphibium complex from Asia and North America using 11 morphological characters showed that the aquatic plants can be discerned from the terrestrial plants by leaf size, shape, and petiole length. In contrast, both aquatic and terrestrial plants collected from the same population or locality shared identical sequences in the matK, psbA-trnH IGS, rbcL-accD IGS and trnL-trnF regions of the chloroplast DNA (cpDNA), suggesting that aquatic and terrestrial forms of the P. amphibium complex are not genetically diverged; morphological differences between the two forms are probably due to the differences in environmental conditions of the habitats. In addition, results from the morphological analysis and the maximum parsimony analysis of the cpDNA data set revealed that the plants from Asia including Korea, Japan, China, Mongolia and Russia Far East are diverged from those in North America and Europe, suggesting that the Asian populations should be recognized as a distinct variety, P. amphibium var. amurense Korsh.

• Journal of Sericultural and Entomological Science
• /
• v.51 no.2
• /
• pp.185-190
• /
• 2013

The superworm, as known the larva of Zophobas morio, has been officially imported from 2011 and bred commercially in Korea. But it is named as the corrected scientific name, Zophobas atratus by junior synonym throughout traditional taxonomy in this study and newly designated Korean name as 'a-me-ri-ca-wang-geo-jeo-ri' in terms of resource management. Z. atratus was compared with wild native tenebrionids, Promethis valgipes and a commercial reared Tenebrio molitor on the basis of DNA barcode analysis. As the results, the average genetic divergence was 21.4% between Z. atratus and P. valgipes, and 20.9% between Z. atratus and T. molitor. These large divergences imply these tenebrionids species can be easily identified by DNA barcodes. The results of genetic divergences within species also suggest that Korean populations of Z. atratus, having the same haplotype, might be introduced from the same area of foreign country. On the other hand, a population of T. molitor was separated into two distinct intra-specific groups with DNA barcoding gaps ranged from 1.17- 2.19%. We suppose that domestic breeding entities of T. molitor might be introduced and mixed from two different local groups. Through this study, we expect that classification for two tenebrionid introduced from foreign countries can be used for the management of insect resources in Korea.

• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.4
• /
• pp.2185-2193
• /
• 2016

Background: The pathogenesis of sporadic colorectal cancer (CRC) is influenced by the patient genetic background and environmental factors. Based on prior understanding, these are classified in two major pathways of genetic instability. Microsatellite instability (MSI) and CPG island methylator phenotype (CIMP) are categorized as features of the hypermethylated prototype, and chromosomal instability (CIN) is known to be indicative of the non-hypermethylated category. Secreted frizzled related protein 2 (SFRP2), APC1A in WNT signaling pathway and the DNA repair gene, O6-methylguanine-DNA methyltransferase (MGMT), are frequently hypermethylated in colorectal cancer. Detection of methylated DNA as a biomarker by easy and inexpensive methods might improve the quality of life of patients with CRC via early detection of cancer or a precancerous condition. Aim: To evaluate the rate of SFRP2 and MGMT hypermethylation in both polyp tissue and serum of patients in south Iran as compared with matched control normal population corresponding samples. Materials and Methods: Methylation-specific PCR was used to detect hypermethylation in DNA extracted from 48 polypoid tissue samples and 25 healthy individuals. Results: Of total polyp samples, 89.5% had at least one promoter gene hypermethylation. The most frequent methylated locus was SFRP2 followed by MGMT-B (81.2 and 66.6 percent respectively). Serologic detection of hypermethylation was 95% sensitive as compared with polyp tissue. No hypermethylation was detected in normal tissue and serum and its detection in patients with polyps, especially of serrated type, was specific. Conclusions: Serologic investigation for detection of MGMT-B, SFRP2 hypermethylation could facilitate prioritization of high risk patients for colonoscopic polyp detection and excision.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.2
• /
• pp.283-294
• /
• 2007

Conventional culture-based methods of enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) are being rapidly replaced by nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation. The foundation of these techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The next step in functional analysis of the ecosystem is to measure how specific and, or, predominant members of the ecosystem are operating and interacting with other groups. It is also apparent that techniques which optimise the analysis of complex microbial communities rather than the detection of single organisms will need to address the issues of high throughput analysis using many primers/probes in a single sample. Nearly all the molecular ecological techniques are dependant upon the efficient extraction of high quality DNA/RNA representing the diversity of ruminal microbial communities. Recent reviews and technical manuals written on the subject of molecular microbial ecology of animals provide a broad perspective of the variety of techniques available and their potential application in the field of animal science which is beyond the scope of this treatise. This paper will focus on nucleic acid based molecular methods which have recently been developed for studying major functional groups (cellulolytic bacteria, protozoa, fungi and methanogens) of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective.

• Korean Journal of Plant Taxonomy
• /
• v.34 no.1
• /
• pp.63-74
• /
• 2004

The genus Suaeda is one of the most popular plants on salt marsh areas in Korean Peninsular. The entities that comprise taxa in Korea exhibit widely overlapping ranges in all morphological attributes. Ramdom amplified polimorphic DNA (RAPD) markers were used to clarify taxonomic delimitation among the Korean taxa of Suaeda and to analyse genetic variations among the populations of S. japoniro in western and southern coastal regions. Six decamer primers amplified a total of 65 scorable bands, of which 61 were polymorphic. In all primers investigated, S. glauro of sect. Schanginia is the most distinctive species, compared with others of sect. Heterosperma. S. japonica, S. maritima, and S. malacosperma, which have been hardly distinguished each other by external morphology, were readily recognized by its specific DNA bands. The characteristic RAPD markers were identified local populations of S. japonica, but this feature was not revealed within population.