• Mycobiology
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• 제37권3호
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• pp.183-188
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• 2009

The molecular phylogeny in nine different commercial cultivated strains of Pleurotus nebrodensis was studied based on their internal transcribed spacer (ITS) region and RAPD. In the sequence of ITS region of selected strains, it was revealed that the total length ranged from 592 to 614 bp. The size of ITS1 and ITS2 regions varied among the strains from 219 to 228 bp and 211 to 229 bp, respectively. The sequence of ITS2 was more variable than ITS1 and the region of 5.8S sequences were identical. Phylogenetic tree of the ITS region sequences indicated that selected strains were classified into five clusters. The reciprocal homologies of the ITS region sequences ranged from 99 to 100%. The strains were also analyzed by RAPD with 20 arbitrary primers. Twelve primers were efficient to applying amplification of the genomic DNA. The sizes of the polymorphic fragments obtained were in the range of 200 to 2000 bp. RAPD and ITS analysis techniques were able to detect genetic variation among the tested strains. Experimental results suggested that IUM-1381, IUM-3914, IUM-1495 and AY-581431 strains were genetically very similar. Therefore, all IUM and NCBI gene bank strains of P. nebrodensis were genetically same with some variations.

• Animal cells and systems
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• 제1권1호
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• pp.129-134
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• 1997

HLA-A2 is one of the most diversified HLA-class I antigen with 17 subtypes so far identified at the molecular level. HLA-A*02 subtyping has significant implications on the tissue typing for organ and bone marrow transplantations. Recently, DNA-based typing methods have been successfully applied to the elucidation of HLA gene polymorphisms. In the present study, HLA-A*O2 genotyping was established by using nested polymerase chain reaction-sequence specific primers (PCR-SSP) and distribution of A*O2 alleles were determined in Korean individuals. Genomic DNA prepared from four B-lymphoblastoid cell lines and lymphocytes from serologically defined 48 HLA-A2 Korean individuals by phenol/chloroform extractions was typed. The results of the four B-lymphoblastoid cells were consistent with the previous data typed by PCR analysis. Five A*O2 alleles-A*0201, A*0203, A*0206, A*0207 and A*0210-were commonly observed in a total of 17 A*02 alleles. Of these, A*0207 (f=49.0%) was the most frequent allele in Korean population. A*0206 (f=28.3%) and A*0201 (f=17.0%) were also found frequently while A*0203 and A*0210 types were observed in less than 5%. In conclusion, the high level of discrimination for HLA-A*O2 alleles will prove useful and informative in the study of transplant survival, and may identify the importance of allelic differences not readily detectable by serology on host and donor compatibility.

• 한국식물학회:학술대회논문집
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• 한국식물학회 1999년도 제13회 식물생명공학심포지움 New Approaches to Understand Gene Function in Plants and Application to Plant Biotechnology
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• pp.11-15
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• 1999

In order to evlauate feasibility of the gene tagging by the maize transposable element Ac in heterologous plant systems, we have investigated physical distances and directions of transposition of the element in Arabidopsis thaliana and tobacco cultured cell line BY-2. We prepared a T-DNA construct that carried a non-autonomous derivative of Ac with a site for cleavage by endonuclease I-Scel (designated dAc-I-RS element). Another cleavage site was also introduced into the T-DNA region outside dAc-I-RS. A number of transgenic Arabidopsis plants were generated, each of which had a single copy of the T-DNA at a different chromosomal location. To examine the pattern of transposition, three out of these transgenic plants were crossed with the Arabidopsis plant that carried the gene for Ac transposase and progeny in which dAc-I-RS had been transposed were isolated. After digestion of the genomic DNA of these progeny with I-SceI, sizes of segment of DNA were determined byd pulse-field gel electrophoresis. We also performed linkage analysis for the transposed elements and sites of mutations near the elements. Our results with three transgenic lines showed that 50% of all transposition events had occurred within 1,700 kilo-base pairs (kb) on the same chromosome, with 35% within 200 kb, and that the elements transposed in both directions on the chromosome with roughly equal probability. The data thus indicate that the Ac-Ds system is most useful for tagging of genes that are present within 200 kb of the chromosomal site of Ac in Arabidopsis. In addition, determination of the precise localization of the transposed dAc-I-RS element should definitely assist in map-based cloning of genes around insertion sites. In the present paper, we report typical examples of such gene isolation studies.

• 한국식물학회:학술대회논문집
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• 한국식물학회 1985년도 워크샵 및 심포지엄 북한산국립공원의 식생
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• pp.51-57
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• 1985

In order to evlauate feasibility of the gene tagging by the maize transposable element Ac in heterologous plant systems, we have investigated physical distances and directions of transposition of the element in Arabidopsis thaliana and tobacco cultured cell line BY-2. We prepared a T-DNA construct that carried a non-autonomous derivative of Ac with a site for cleavage by endonuclease I-Scel (designated dAc-I-RS element). Another cleavage site was also introduced into the T-DNA region outside dAc-I-RS. A number of transgenic Arabidopsis plants were generated, each of which had a single copy of the T-DNA at a different chromosomal location. To examine the pattern of transposition, three out of these transgenic plants were crossed with the Arabidopsis plant that carried the gene for Ac transposase and progeny in which dAc-I-RS had been transposed were isolated. After digestion of the genomic DNA of these progeny with I-SceI, sizes of segment of DNA were determined byd pulse-field gel electrophoresis. We also performed linkage analysis for the transposed elements and sites of mutations near the elements. Our results with three transgenic lines showed that 50% of all transposition events had occurred within 1, 700 kilo-base pairs (kb) on the same chromosome, with 35% within 200 kb, and that the elements transposed in both directions on the chromosome with roughly equal probability. The data thus indicate that the Ac-Ds system is most useful for tagging of genes that are present within 200 kb of the chromosomal site of Ac in Arabidopsis. In addition, determination of the precise localization of the transposed dAc-I-RS element should definitely assist in map-based cloning of genes around insertion sites. In the present paper, we report typical examples of such gene isolation studies.

• 한국균학회지
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• 제39권3호
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• pp.180-184
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• 2011

본 연구는 URP-PCR 핵산지문법을 이용한 Paecilomyces spp.와 Cordyceps spp.의 종간, 종내 유전적 다양성분석을 실시 하였다. 12종류의 20mer의 URP primer가적용된 바 URP2F, URP2R, URP9F, URP4R, URP17R는 종간에 특이적인 PCR다형성밴드를 형성하였으며 Cordypces militaris 균주간에는 4가지 type의 PCR 다형성이 관찰되었다. 그러나 Paecilomyces japonica의 균주내에는 동일한 PCR 다형성을 나타내었다. URP-PCR profile을 이용하여 경동시장에서 수집한 미 동정 동충하초를 동정 할 수 있었다.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2014년도 추계학술대회 및 정기총회
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• pp.49-49
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• 2014

In order to find indigenous beneficial fungal species from crop field soils of Nigeria, 23 soil samples were collected from various places of Nigeria in June, 2013 and fungi were isolated through serial dilution technique. Isolated fungi were purified and differentiated according to their morphological and microscopic characteristics. In total, 38 different representative isolates were recovered and the genomic DNA of each isolates was extracted using QIAGEN$^{(R)}$ Plasmid Mini Kit (QIAGEN Sciences, USA) and the identification of fungi was carried out by sequence analysis of internal transcribed spacer (ITS) region of the 18S ribosomal DNA (18S rDNA). Recovered isolates belonged to 9 fungal genera comprising Fusarium, Aspergillus, Chaetomium, Coniothyrium, Dipodascaceae, Myrothecium, Neosartorya, Penicillium and Trichoderma. Aspergillus spp., Penicillium spp. and Trichoderma spp. were the most dominant taxa in this study. The antagonistic potentiality of species belonged to Trichoderma against 10 phytopathogenic fungi (F. oxysporum, C. gloesporoides, P. cytrophthora, A. alternata, A. solani, S. rolfsii, F. solani, R. solani, S. sclerotiorum and P. nicotiana) was assessed in vitro using dual culture assay. The dual culture assay results showed varied degree of antagonism against the tested phytopathogens. The potential Trichoderma spp. will be further evaluated for their antagonistic and plant growth promotion potentiality under in vivo conditions.

• 한국동물위생학회지
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• 제30권3호
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• pp.353-362
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• 2007

A total of 1,354 samples was collected from bovine and porcine carcass from January 2005 to December 2006 in a slaughter house. Twenty five strains(1.8%) of Listeria monocytogenes were isolated from 1,354 samples using selective media. Ten(1.4%) L monocytogenes were isolated from the 677 of bovine carcasses, and 15(2.2%) were isolated from the 677 of porcine carcasses. Among 15 L mono-cytogenes from porcine, 11 siolates were serovars 1/2c, followed by 1/2b (3 strains, 20.0%) and 1/2a(1 strain) Out of 10 bovine samples, positive cases in 1/2a were 9 strains (90.0%), 1/2b were 1 strains(10.0%). PCR primers were selected to amplify a 520-base pair(bp) DNA fragment from the listeolysin O gene (hlyA) of L mono-cytogenes. A 520-bp product was detected in PCR with DNA from L monocytogenes, but not from the other Listeria species tested. A total of 25 L monocytogenes strains were analysed by PFGE after digestion with Apa I. PFGE analysis of genomic DNA showed the $14{\sim}18$ fragments ranging in size from 30 to 550 kb, resulting in 14 patterns.

• Journal of Microbiology and Biotechnology
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• 제27권7호
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• pp.1266-1271
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• 2017

Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces sample, possesses the ability to enhance the longevity and immune response of a Caenorhabditis elegans host. To explore the characteristics of strain JDFM216 at the genetic level, we performed whole-genome sequencing using the PacBio system. The circular draft genome has a total length of 2,076,427 bp and a total of 2,682 encoding sequences were identified. Five phylogenetically featured genes possibly related to the longevity and immune response of the host were identified in L. fermentum strain JDFM216. These genes encode UDP-N-acetylglucosamine 1-carboxyvinyltransferase (E.C. 2.5.1.7), ErfK/YbiS/YcfS/YnhG family protein, site-specific recombinase XerD, homocysteine S-methyltransferase (E.C. 2.1.1.10), and aspartate-ammonia ligase (E.C. 6.3.1.1), which are involved in peptidoglycan synthesis and amino acid metabolism in the gut environment. Our findings on the genetic background of L. fermentum strain JDFM216 and its potential candidate genes for host longevity and immune response provide new insight for the application of this strain in the food industry as newly isolated functional probiotic.

• Biotechnology and Bioprocess Engineering:BBE
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• 제6권2호
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• pp.117-127
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• 2001

The high-level expression of a human single chain urokinase-type plasminogen activator (scu-PA) was achieved by employing a methotrexate (MTX)-dependent gene amplification system in Chinese hamster ovary (CHO) cells. By cotransfecting and coamplifying a scu-PA expression plasmid and dihydrofolate reductase (DHFR) minigene, several scu-PA expressing CHO cell lines were selected and gene-amplified. These recombinant cell lines, NGpUKs, secreted a completely processed scu-PA of 54 kD and up to 60mg/L was accumulated in the culture medium when they were adapted to an optimal MTX concentration. Over 95% of the scu-PA expressed was secreted in the culture medium and identified having the proper function of a plasminogen activator when activated by plasmin. Based on a genomic Southern analysis, a representative subclone, MGpUK-5, exhibited MTX-dependent scu-PA gene amplification, plus the initial single-copy gene of scu-PA eventually turned into about 150 copies of the amplified gene of scu-PA after gradual adaptation to 2.0$\mu$M of MTX. Meanwhile, the transcripts kof the scu-PA gene increased, although -early saturation of transcription was identified at 0.1$\mu$M of MTX. The scu-PA production by the MGpUK-5 subclone also increased relative to the gene amplification and increased transcripts, however, the relationship was not linearly proportional. Accordingly, since the MGpUK cell lines expressed elevated levels of enzymatically active scu-PA, these cell lines could be applied to the largescale production of scu-PA.

• Genomics & Informatics
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• 제6권3호
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• pp.153-156
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• 2008

Complex diseases such as stroke and cancer have two or more genetic loci and are affected by environmental factors that contribute to the diseases. Due to the complex characteristics of these diseases, identifying candidate genes requires a system-level analysis of the following: gene ontology, pathway, and interactions. A database and user interface, termed StrokeBase, was developed; StrokeBase provides queries that search for pathways, candidate genes, candidate SNPs, and gene networks. The database was developed by using in silico data mining of HGNC, ENSEMBL, STRING, RefSeq, UCSC, GO, HPRD, KEGG, GAD, and OMIM. Forty candidate genes that are associated with cerebrovascular disease were selected by human experts and public databases. The networked cerebrovascular disease gene maps also were developed; these maps describe genegene interactions and biological pathways. We identified 1127 genes, related indirectly to cerebrovascular disease but directly to the etiology of cerebrovascular disease. We found that a protein-protein interaction (PPI) network that was associated with cerebrovascular disease follows the power-law degree distribution that is evident in other biological networks. Not only was in silico data mining utilized, but also 250K Affymetrix SNP chips were utilized in the 320 control/disease association study to generate associated markers that were pertinent to the cerebrovascular disease as a genome-wide search. The associated genes and the genes that were retrieved from the in silico data mining system were compared and analyzed. We developed a well-curated cerebrovascular disease-associated gene network and provided bioinformatic resources to cerebrovascular disease researchers. This cerebrovascular disease network can be used as a frame of systematic genomic research, applicable to other complex diseases. Therefore, the ongoing database efficiently supports medical and genetic research in order to overcome cerebrovascular disease.