• Proceedings of the PSK Conference
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• 2003.10b
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• pp.70.2-71
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• 2003

Quinolone resistance in Streptococcus pneumoniae is related to mutations in the DNA gyrase and topoisomerase IV genes. DW-286a displayed potent activity against S. pneumoniae C9211 (MIC, 0.015 ${\mu}$g/ml) compared with gemifloxacin (MIC, 0.06 ${\mu}$g/ml). This study was performed to analyze the ability of DW-286a to cause resistance development in S. pneumoniae and to establish whether DNA gyrase or topoisomerase IV is primary target. DW-286a resistant mutants of S. pneumoniae C9211 were generated by stepwise selection at increasing drug concentration. (omitted)

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.180.1-180.1
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• 2003

Eukaryotic DNA topoisomerase I (top I) is an essential enzyme that act to relax supercoiled DNA during the transcription, replication and mitosis. Intracellular levels of top I are elevated in a number of human solid tumors, relative to the respective normal tissues, suggesting that controlling the topI level is important to treat cancer. Top I poisons show their antitumor activities by stabilizing the cleavable ternary complex consisting of top I enzyme, DNA, and drug. Thus, top I is a promising target for the development of new cancer chemotherapeutics against a number of solid tumors. (omitted)

• International Journal of Stem Cells
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• v.17 no.1
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• pp.1-14
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• 2024

The clustered regularly interspaced short palindromic repeats (CRISPR) system, a rapidly advancing genome editing technology, allows DNA alterations into the genome of organisms. Gene editing using the CRISPR system enables more precise and diverse editing, such as single nucleotide conversion, precise knock-in of target sequences or genes, chromosomal rearrangement, or gene disruption by simple cutting. Moreover, CRISPR systems comprising transcriptional activators/repressors can be used for epigenetic regulation without DNA damage. Stem cell DNA engineering based on gene editing tools has enormous potential to provide clues regarding the pathogenesis of diseases and to study the mechanisms and treatments of incurable diseases. Here, we review the latest trends in stem cell research using various CRISPR/Cas technologies and discuss their future prospects in treating various diseases.

• Maxillofacial Plastic and Reconstructive Surgery
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• v.30 no.3
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• pp.302-309
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• 2008

Epigenetic is usually referring to heritable traits that do not involve changes to the underlying DNA sequence. DNA methylation is known to serve as cellular memory. and is one of the most important mechanism of epigenetic. DNA methylation is a covalent modification in which the target molecules for methylation in mammalian DNA are cytosine bases in CpG dinucleotides. The 5' position of cytosine is methylated in a reaction catalyzed by DNA methyltransferases; DNMTl, DNMT3a, and DNMT3b. There are two different regions in the context of DNA methylation: CpG poor regions and CpG islands. The intergenic and the intronic region is considered to be CpG poor, and CpG islands are discrete CpG-rich regions which are often found in promoter regions. Normally, CpG poor regions are usually methylated whereas CpG islands are generally hypomethylated. DNA methylation is involved in various biological processes such as tissue-specific gene expression, genomic imprinting, and X chromosome inactivation. In general. cancer cells are characterized by global genomic hypomethylation and focal hypermethylation of CpG islands, which are generally unmethylated in normal cells. Gene silencing by CpG hypermethylation at the promotors of tumor suppressor genes is probably the most common mechanism of tumor suppressor inactivation in cancer.

• Mycobiology
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• v.42 no.1
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• pp.46-51
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• 2014

A degenerated strain of Pleurotus eryngii KNR2312 was isolated from a commercial farm. Random amplified polymorphic DNA analysis performed on the genomic DNA of the normal and degenerated strains of this species revealed differences in the DNA banding pattern. A unique DNA fragment (1.7 kbp), which appeared only in the degenerated strain, was isolated and sequenced. Comparing this sequence with the KNR2312 genomic sequence showed that the sequence of the degenerated strain comprised three DNA regions that originated from nine distinct scaffolds of the genomic sequence, suggesting that chromosome-level changes had occurred in the degenerated strain. Using the unique sequence, three sets of PCR primers were designed that targeted the full length, the 5' half, and the 3' half of the DNA. The primer sets P2-1 and P2-2 yielded 1.76 and 0.97 kbp PCR products, respectively, only in the case of the degenerated strain, whereas P2-3 generated a 0.8 kbp product in both the normal and the degenerated strains because its target region was intact in the normal strain as well. In the case of the P2-1 and P2-2 sets, the priming regions of the forward and reverse primers were located at distinct genomic scaffolds in the normal strain. These two primer sets specifically detected the degenerate strain of KNR2312 isolated from various mushrooms including 10 different strains of P. eryngii, four strains of P. ostreatus, and 11 other wild mushrooms.

• Journal of Food Hygiene and Safety
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• v.15 no.3
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• pp.262-266
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• 2000

The polymerase chain reaction was used to selectively detect sequences within the fimbrial antigen of Salmonella enteritidis. Sterile milk was artificially inoculated with known amount of S. enteritidis and then DNA was extracted with guanidine thiocyanate/phenol/chloroform, followed by PCR. A detection limit of as few as 100 colony forming unit (cfu) per 0.5 ml milk was obtained with this method. For the whole procedure, it took only 5 h. A semi-quantitative polymerase chain reaction assay which allows an estimation of colony forming unit of S. enteritidis was developed. Known amount of standard plasmid pGem-4Z-Sef B(-) containing cloned S. enteritidis fimbrial antigen gene was co-amplified with Salmonella genomic DNA isolated from artificially inoculated milk. The same set of primers were used for the amplification and the products were cleaved with Bam HI. The concentration of the target DNA could be estimated by comparing the intensity of the two bands after electrophoresis. The PCR-based protocol described in this paper provides a rapid, simple, and sensitive method for detecting S. enteritidis in milk.

• YAKHAK HOEJI
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• v.53 no.4
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• pp.222-227
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• 2009

Human topoisomerase I (Topo I) plays a pivotal role in cell replication, transcription and repair and, therefore, is an important anti-cancer target. 20S-camptothecin (CPT) is a representative Topo I inhibitor. Compounds belonging to CPT family inhibit the religation step of Topo I-DNA by binding to the DNA cleavage site. Computational docking studies with Surflex-Dock were carried out to investigate the binding modes between Topo I-DNA binary complex structure and the ligand such as 20S-CPT and 9,10-substituted 20S-CPT analogues. The docking results demonstrated that most of the compounds with $IC_{50}$ value under $0.5{\mu}M$ intercalated exactly between the -1 and +1 DNA bases, deeply toward the cleavage site. The complex was stabilized by hydrogen-bonding and hydrophobic interactions with both the enzyme and the DNA. The compounds with $IC_{50}$ value above $0.5{\mu}M$ were poorly docked and did not intercalate. In addition, the docking results confirmed the overall correlation between the $IC_{50}$ values and docking scores, indicating the possible use of the modeling for the prediction of biological activity and design of potential inhibitors.

• Food Science of Animal Resources
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• v.30 no.3
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• pp.403-409
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• 2010

Accurate methods for the identification of closely related species or breeds in raw and processed meats must be developed in order to protect both consumers and producers from mislabeling and fraud. This paper describes the development of DNA markers for the discrimination and improvement of Korean native pig (KNP) meat. The KIT gene is related to pig coat color and is often used as a candidate marker. A 538 bp fragment comprising intron 19 of the pig KIT gene was amplified by PCR using specific primers, after which the PCR amplicons of a number of meat samples from KNP and three major improved breeds (Landrace, Duroc and Yorkshire) were sequenced in order to find a nucleotide region suitable for PCR-RFLP analysis. Sequence data showed the presence of two nucleotide substitutions, g.276G>A and g.295A>C, between KNP and the improved pig breeds. Digestion of KIT amplicons with AccII enzyme generated characteristic PCR-RFLP profiles that allowed discrimination between meats from KNP and improved pig. KNP showed three visible DNA bands of 264/249, 199, and 75 bp, whereas DNA bands of 249, 199, and 90 bp were detected in the three improved pig breeds. Therefore, the 75 bp DNA fragment was specific only to KNP, whereas the 90 bp DNA fragment was specific to the improved breeds. The breed-specific DNA markers reported here that target the KIT gene could be useful for the identification of KNP meat from improved pig meats, thus contributing to the prevention of falsified breed labeling.

• Proceedings of the PSK Conference
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• 2000.04a
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• pp.82-85
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• 2000

• Genomics & Informatics
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• v.6 no.2
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• pp.84-86
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• 2008

The Tetrahymena group I intron has been shown to employ a trans-splicing reaction and has been modified to specifically target and replace human telomerase reverse transcriptase (hTERT) RNA with a suicide gene transcript, resulting in the induction of selective cytotoxicity in cancer cells that express the target RNA, in animal models as well as in cell cultures. In this study, we evaluated the target RNA specificity of trans-splicing phenomena by the group I intron in mice that were intraperitoneally inoculated with hTERT-expressing human cancer cells to validate the anti-cancer therapeutic applicability of the group I intron. To this end, an adenoviral vector that encoded for the hTERT-targeting group I intron was constructed and systemically injected into the animal. 5'-end RACE-PCR and sequencing analyses of the trans-spliced cDNA clones revealed that all of the analyzed products in the tumor tissue of the virus-infected mice resulted from reactions that were generated only with the targeted hTERT RNA. This study implies the in vivo target specificity of the trans-splicing group I intron and hence suggests that RNA replacement via a trans-splicing reaction by the group I intron is a potent anti-cancer genetic approach.