• Proceedings of the Korean Society of Toxicology Conference
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• 2002.11b
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• pp.116-116
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• 2002

It is believed that cell and/or tissue toxicity is resulted from alterations in expression of many genes in response to environmental stresses or toxicants. New technology, such as DNA microarray analysis, can measure the expression of thousands of genes at a time providing the potential to accelerate discovery of toxicant pathways and specific gene targets.(omitted)

• Journal of Microbiology
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• v.43 no.3
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• pp.313-318
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• 2005

In this study, we demonstrate the use of a PCR-based method for the detection of the specific genes involved in natural-product biosynthesis. This method was applied, using specifically designed PCR primers, to the amplification of a gene segment encoding for sedo-heptulose 7-phosphate cyclase, which appears to be involved in the biosynthetic pathways of $C_7N$ aminoacyclitol or its keto analogue-containing metabolites, in a variety of actinomycetes species. The sequences of DNA fragments (about 540 bp) obtained from three out of 39 actinomycete strains exhibited a high degree of homology with the sedo-heptulose 7-phosphate cyclase gene, which has been implicated in acarbose biosynthesis. The selective cultivation conditions of this experiment induced the expression of these loci, indicating that the range of $C_7N$ aminoacyclitol or its keto analogue-group natural products might be far greater than was previously imagined. Considering that a total of approximately 20 $C_7N$ aminoacyclitol metabolites, or its keto analogue-containing metabolites, have been described to date, it appears likely that some of the unknown loci described herein might constitute new classes of $C_7N$ aminoacyclitol, or of its keto analogue-containing metabolites. As these metabolites, some of which contain valienamine, are among the most potent antidiabetic agents thus far discovered, the molecular detection of specific metabolite-producing actinomycetes may prove a crucial step in current attempts to expand the scope and diversity of natural-product discovery.

• Journal of Sericultural and Entomological Science
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• v.38 no.1
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• pp.13-18
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• 1996

To secure the genetic resources of silkworm, Bomyx mori, the cDNA library was constructed with mRNA isolated from fifth instar larvae. Titer of the cDNA library was about 1.3 X 106 plaques in total. We presumed that the titer covered all transcripts existed in Bombyx mori. Meanwhile, it is knowen that partial cDNA sequences, Expressed Sequence Tags(ESTs), have a good value for the discovery of novel genes and the elucidation of their structures. For this purpose, partial cDNA sequencing was carried out from randomly selected cDNA clones in the library. Partial cDNA sequences of 37 clones were determined and an average of 212 nucleotides of sequence can be read from the clone. The ESTs were searched in GenBAnk database and fifteen ESTs showed significant similarities to enlisted sequences. They included the genes of storage protein, heat shock protein, actin, catalase and so forth. We presumed that the 22 unmatched ESTs were novel genes.

• Journal of Ecology and Environment
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• v.46 no.2
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• pp.126-135
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• 2022

Background: Pollinators are important ecological elements due to their role in the maintenance of ecosystem health, wild plant reproduction, crop production and food security. The pollinator-plant interaction supports the preservation of plant and animal populations and it also improves the yield in pollination dependent crops. Having knowledge about the plant-pollinator interaction is necessary for development of pesticide risk assessment of pollinators and conservation of endangering species. Results: Traditional methods to discover the relatedness of insects and plants are based on tracing the visiting pollinators by field observations as well as palynology. These methods are time-consuming and needs expert taxonomists to identify different groups of pollinators such as insects or identify flowering plants through palynology. With pace of technology, using molecular methods become popular in identification and classification of organisms. DNA metabarcoding, which is the combination of DNA barcoding and high throughput sequencing, can be applied as an alternative method in identification of mixed origin environmental samples such as pollen loads attached to the body of insects and has been used in DNA-based discovery of plant-pollinator relationship. Conclusions: DNA metabarcoding is practical for plant-pollinator studies, however, lack of reference sequence in online databases, taxonomic resolution, universality of primers are the most crucial limitations. Using multiple molecular markers is preferable due to the limitations of developed universal primers, which improves taxa richness and taxonomic resolution of the studied community.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4597-4606
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• 2012

Cholangiocarcinoma (CCA) is an uncommon adenocarcinoma which arises from the epithelial cells of the bile ducts. The aim of the study was to investigate the cytotoxicity, toxicity, and anticancer activity of a crude ethanolic extract of ginger (Zingiber officinale Roscoe) against CCA. Cytotoxic activity against a CCA cell line (CL-6) was assessed by calcein-AM and Hoechst 33342 assays and anti-oxidant activity was evaluated using the DPPH assay. Investigation of apoptotic activity was performed by DNA fragmentation assay and induction of genes that may be involved in the resistance of CCA to anticancer drugs (MDR1, MRP1, MRP2, and MRP3) was examined by real-time PCR. To investigate anti-CCA activity in vivo, a total of 80 OV and nitrosamine (OV/DMN)-induced CCA hamsters were fed with the ginger extract at doses of 1000, 3000, and 5000 mg/kg body weight daily or every alternate day for 30 days. Control groups consisting of 10 hamsters for each group were fed with 5-fluorouracil (positive control) or distilled water (untreated control). Median $IC_{50}$ (concentration that inhibits cell growth by 50%) values for cytotoxicity and anti-oxidant activities of the crude ethanolic extract of ginger were 10.95, 53.15, and $27.86{\mu}g/ml$, respectively. More than ten DNA fragments were visualized and up to 7-9 fold up-regulation of MDR1 and MRP3 genes was observed following exposure to the ethanolic extract of ginger. Acute and subacute toxicity tests indicated absence of any significant toxicity at the maximum dose of 5,000 mg/kg body weight given by intragastric gavage. The survival time and survival rate of the CCA-bearing hamsters were significantly prolonged compared to the control group (median of 54 vs 17 weeks). Results from these in vitro and in vivo studies thus indicate promising anticancer activity of the crude ethanolic extract of ginger against CCA with the absence of any significant toxicity. Moreover, MDR1 and MRP3 may be involved in conferring resistance of CCA to the ginger extract.

• Research in Plant Disease
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• v.25 no.4
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• pp.205-212
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• 2019

Analysis of differentially expressed genes has assisted discovery of gene sets involved in particular biological processes. The purpose of this study was to identify genes involved in appressorium formation in the rice blast fungus Magnaporthe oryzae via analysis of cDNA-amplified fragment length polymorphisms. Amplification of appressorial and vegetative mycelial cDNAs using 28 primer combinations generated over 200 differentially expressed transcript-derived fragments (TDFs). TDFs were excised from gels, re-amplified by PCR, cloned, and sequenced. Forty-four of 52 clones analyzed corresponded to 42 genes. Quantitative real-time PCR showed that expression of 23 genes was up-regulated during appressorium formation, one of which was the MCK1 gene that had been shown to be involved in appressorium formation. This study will be providing valuable resources for identifying the genes such as pathogenicity-related genes in M. oryzae.

• Journal of Microbiology and Biotechnology
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• v.25 no.3
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• pp.307-316
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• 2015

Beginning from the recognition of FtsZ as a bacterial tubulin homolog in the early 1990s, many bacterial cytoskeletal elements have been identified, including homologs to the major eukaryotic cytoskeletal elements (tubulin, actin, and intermediate filament) and the elements unique in prokaryotes (ParA/MinD family and bactofilins). The discovery and functional characterization of the bacterial cytoskeleton have revolutionized our understanding of bacterial cells, revealing their elaborate and dynamic subcellular organization. As in eukaryotic systems, the bacterial cytoskeleton participates in cell division, cell morphogenesis, DNA segregation, and other important cellular processes. However, in accordance with the vast difference between bacterial and eukaryotic cells, many bacterial cytoskeletal proteins play distinct roles from their eukaryotic counterparts; for example, control of cell wall synthesis for cell division and morphogenesis. This review is aimed at providing an overview of the bacterial cytoskeleton, and discussing the roles and assembly dynamics of bacterial cytoskeletal proteins in more detail in relation to their most widely conserved functions, DNA segregation and coordination of cell wall synthesis.

• Korean Journal of Biological Psychiatry
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• v.8 no.2
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• pp.203-207
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• 2001

The genome sequencing project has generated and will continue to generate enormous amounts of sequence data including 5 eukaryotic and about 60 prokaryotic genomes. Given this ever-increasing amounts of sequence information, new strategies are necessary to efficiently pursue the next phase of the genome project-the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip(or gene microarray) technology was developed to efficiently identify the differential expression pattern of independent biological samples. DNA chip provides a new tool for genome expression analysis that may revolutionize many aspects of biotechnology including new drug discovery and disease diagnostics.

• Molecules and Cells
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• v.21 no.3
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• pp.376-380
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• 2006

Gene expression is regulated in large part at the level of transcription under the control of sequence-specific transcriptional regulatory proteins. Therefore, the ability to affect gene expression at will using sequencespecific artificial transcription factors would provide researchers with a powerful tool for biotechnology research and drug discovery. Previously, we isolated 56 novel sequence-specific DNA-binding domains from the human genome by in vivo selection. We hypothesized that these domains might be more useful for regulating gene expression in higher eukaryotic cells than those selected in vitro using phage display. However, an unpredictable factor, termed the "context effect", is associated with the construction of novel zinc finger transcription factors--- DNA-binding proteins that bind specifically to 9-base pair target sequences. In this study, we directly selected active artificial zinc finger proteins from a zinc finger protein library. Direct in vivo selection of constituents of a zinc finger protein library may be an efficient method for isolating multi-finger DNA binding proteins while avoiding the context effect.

• Korean Journal of Plant Resources
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• v.18 no.1
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• pp.169-178
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• 2005

Effects of heavy-ion beam$(^{20}Ne)$ irradiation on growth and DNA alteration of tobacco plants were investigated. Seed germination and plant height were decresed as the ion-beam intensity was increased. However, the bolting and flowering were promoted by the low intensities of 5 Gy to 10 Gy treatment. Out of the 100 primers screened, 59 primers generated 336 DNA fragments by RAPD analysis, and one specific DNA fragment that amplified in control but not in the ion-beam irradiated plants was observed. By AFLP analysis, DNA fragment difference related to the ion-beam treatment was not detected but observed among the plant bodys.