• Journal of Microbiology and Biotechnology
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• 제18권6호
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• pp.1005-1010
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• 2008

The genus Burkholderia consists of extremely versatile bacteria that occupy diverse niches and are commonly encountered in the rhizosphere of crop plants. In this study, we characterized three plant growth promoting strains assigned as Burkholderia sp. using biochemical and molecular characterization. The Burkholderia spp. strains CBMB40, CBPB-HIM, and CBPB-HOD were characterized using biochemical tests, BIOLOG carbon substrate utilization, fatty acid methyl ester analysis, analysis of recA gene sequences, and DNA-DNA hybridization. The results from these studies indicated that the strains CBMB40, CBPB-HIM, and CBPB-HOD can be assigned under Burkholderia vietnamiensis, Burkholderia ubonensis, and Burkholderia pyrrocinia, respectively.

• Journal of Microbiology and Biotechnology
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• 제17권8호
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• pp.1262-1270
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• 2007

Some hot springs located in the west of Turkey were investigated with respect to the presence of thermophilic microorganisms. Based on phenotyping characteristics and 16S rRNA gene sequence analysis, 16 of the isolates belonged to the genus Geobacillus and grew optimally at about $60^{\circ}C$ on nutrient agar. 16S rRNA gene sequence analysis showed that these isolates resembled Geobacillus species by ${\ge}97%$, but SDS-PAGE profiles of these 16 isolates differ from some of the other species of the genus Geobacillus. However, it is also known that analysis of 16S rRNA gene sequences may be insufficient to distinguish between some species. It is proposed that recN sequence comparisons could accurately measure genome similarities for the Geobacillus genus. Based on recN sequence analysis, isolates 11, IT3, and 12 are strains of G stearothermophilus; isolate 14.3 is a strain of G thermodenitrificans; isolates 9.1, IT4.1, and 4.5 are uncertain and it is required to make further analysis. The presence of xylanase and arabinofuranosidase activities, and their optimum temperature and pH were also investigated. These results showed that 7 of the strains have both xylanase and arabinofuranosidase activities, 4 of them has only xylanase, and the remaning 5 strains have neither of these activities. The isolates 9.1, 7.1, and 3.3 have the highest temperature optima ($80^{\circ}C$), and 7.2, 9.1, AO4, 9.2, and AO17 have the highest pH optima (pH 8) of xylanase. Isolates 7.2, AO4, AC15, and 12 have optimum arabinofuranosidase activities at $75^{\circ}C$, and only isolate AC15 has the lowest pH of 5.5.

• Journal of Microbiology and Biotechnology
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• 제27권1호
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• pp.112-121
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• 2017

Edwardsiella tarda is a gram-negative pathogenic bacterium in aquaculture that can cause hemorrhagic septicemia in fish. Many secreted proteins have already been identified as virulent factors of E. tarda. Moreover, since virulent phenotypes are based on the expression regulation of virulent genes, understanding the expression profile of virulent genes is important. A quantitative RT-PCR is one of the preferred methods for determining different gene expressions. However, this requires the selection of a stable reference gene in E. tarda, which has not yet been systematically studied. Accordingly, this study evaluated nine candidate reference genes (recA, uup, rpoB, rho, topA, gyrA, groEL, rpoD, and 16S rRNA) using the Excel-based programs BestKeeper, GeNorm, and NormFinder under different culture conditions. The results showed that 16S rRNA was more stable than the other genes at different culture growth phases. However, at the same culture time, topA was identified as the reference gene under the conditions of different strains, different culture media, and infection, whereas gyrA was identified under the condition of different temperatures. Thus, in experiments, the expression of gapA and fbaA in E. tarda was analyzed by RT-qPCR using 16S rRNA, recA, and uup as the reference genes. The results showed that 16S rRNA was the most suitable reference gene in this analysis, and that using unsuitable reference genes resulted in inaccurate results.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.140-147
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• 2002

• Journal of Microbiology and Biotechnology
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• 제17권8호
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• pp.1390-1393
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• 2007

In this study, three of the representative EDCs, $17{\beta}$-estradiol, bisphenol A, and styrene, were employed to find their mode of toxic actions in E. coli. To accomplish this, four different stress response genes, recA, katG, fabA, and grpE genes, were used as a representative for DNA, oxidative, membrane, or protein damage, respectively. The expression levels of these four genes were quantified using a real-time RT-PCR after challenge with three different EDCs individually. Bisphenol A and styrene caused high-level expression of recA and katG genes, respectively, whereas $17{\beta}$-estradiol made no significant changes in expression of any of those genes. These results lead to the classification of the mode of toxic actions of EDCs on E. coli.

• 미생물학회지
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• 제28권2호
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• pp.109-113
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• 1990

Mutator 기능을 가지는 플라스미드 pKM101과 이의 돌연변이체 pSL4를 DNA 수복능력이 다른 Esherichia coli B/r(phr, recA, uvrA, uvrB)균주들에 도입하여 돌연변이원인 UV와 MNNG에 대한 보호효과와 mutagenecity를 조사형ㅅ다. pKM101과 pLS4의 mutator 기능과 보호효과는 repair 기능에 따라 다르나 전반적으로 두 플라스미드의 UV와 MNNG에 대한 저향성과 돌연변이율을 증가시켰고 pLS4는 pKM101보다 그효과가 높았다. 이러한 pLS4와 pKM101의 기능적 차이는 이들 플라스미드의 mutator 유전자상에 일어난 변이에 의한 것이라고 생각되었다.

• 생명과학회지
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• 제18권7호
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• pp.912-917
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• 2008

유전자재조합 hG-CSF의 생리활성을 분석하기 위하여 편상의 암세포로부터 분리되어진 cDNA를 이용하여 hG-CSF 유전자를 분리하여 동물세포(CHO cell lines)를 이용하여 재조합 단백질을 생산하였다. 재조합 단백질의 체내 생리활성을 분석하기 위하여0일과 2일에 피하주사 후 5일에 혈액을 채취하여 백혈구 수를 분석하였다. 투여 전과 비교하여 5일째에 백혈구 수는 현저하게 증가하였다. 또한, pEGFP-mUII-hG-CSF벡터를 소 태아로부터 분리되어진 체세포에 형질전환을 시켜서, EGFP signal을 나타내는 세포를 confocal를 이용하여 분리하여 수립하였다. 따라서, 이러한 결과는 유전자재조합 hG-CSF는 체내에서 강력한 생리활성을 나타내며, 또한 당쇄가 첨가되어지고 이중으로 연결되어진 새로운 돌연변이체를 포함하여 고 활성 재조합체의 생산이 가능할 것으로 보이며, pEGFP-mUII-hG-CSF벡터는 복제 형질전환 가축 생산을 위하여 유용하게 사용되어질 것으로 사료된다.

• Animal cells and systems
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• 제3권4호
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• pp.413-415
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• 1999

Our previous report demonstrated that the rhp51$^＋$, a recA and RAD51 homolog of the fission yeast, encodes three transcripts of 1.9, 1.6 and 1.3 kb which have at least six polyadenylation sites. The 3'-end of the gene alone can direct the formation of multiple, discrete 3'ends of the transcripts. To identify the regulatory element required for the 3'-end formation of -rhp51$^＋$ deletion mapping analysis was performed. Northern blot analysis revealed that the 254-bp DNA fragment including 4 distinct poly (A) sites downstream from the Hindlll site, is crucial for normal 3'-end formation. Deletion of the 3'-terminal AU rich region caused appearance of read-through RNA, leading to enhancement of survival rate of the rhp51 deletion mutant in response to DNA damaging agent, methylmethane sulfonate (MMS). The results imply that the rhp51$^＋$ system may be useful for molecular analysis of the 3'-end formation of RNA in the fission yeast.

• BMB Reports
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• 제56권2호
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• pp.108-113
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• 2023

Cohesin is a ring-shaped protein complex that comprises the SMC1, SMC3, and α-kleisin proteins, STAG1/2/3 subunits, and auxiliary factors. Cohesin participates in chromatin remodeling, chromosome segregation, DNA replication, and gene expression regulation during the cell cycle. Mitosis-specific α-kleisin factor RAD21 and meiosis-specific α-kleisin factor REC8 are expressed in embryonic stem cells (ESCs) to maintain pluripotency. Here, we demonstrated that RAD21 and REC8 were involved in maintaining genomic stability and modulating chromatin modification in murine ESCs. When the kleisin subunits were depleted, DNA repair genes were downregulated, thereby reducing cell viability and causing replication protein A (RPA) accumulation. This finding suggested that the repair of exposed single-stranded DNA was inefficient. Furthermore, the depletion of kleisin subunits induced DNA hypermethylation by upregulating DNA methylation proteins. Thus, we proposed that the cohesin complex plays two distinct roles in chromatin remodeling and genomic integrity to ensure the maintenance of pluripotency in ESCs.

• The Plant Pathology Journal
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• 제39권2호
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• pp.191-206
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• 2023

Ground cherry (Physalis pubescens) is the most prominent species in the Solanaceae family due to its nutritional content, and prospective health advantages. It is grown all over the world, but notably in northern China. In 2019 firstly bacterial leaf spot (BLS) disease was identified on P. pubescens in China that caused by both BLS pathogens Xanthomonas euvesicatoria pv. euvesicatoria resulted in substantial monetary losses. Here, we compared whole genome sequences of X. euvesicatoria to other Xanthomonas species that caused BLS diseases for high similarities and dissimilarities in genomic sequences through average nucleotide identity (ANI) and BLAST comparison. Molecular techniques and phylogenetic trees were adopted to detect X. euvesicatoria on P. pubescens using recQ, hrpB1, and hrpB2 genes for efficient and precise identification. For rapid molecular detection of X. euvesicatoria, loop-mediated isothermal amplification, polymerase chain reaction (PCR), and real-time PCR techniques were used. Whole genome comparison results showed that the genome of X. euvesicatoria was more closely relative to X. perforans than X. vesicatoria, and X. gardneri with 98%, 84%, and 86% ANI, respectively. All infected leaves of P. pubescens found positive amplification, and negative controls did not show amplification. The findings of evolutionary history revealed that isolated strains XeC10RQ, XeH9RQ, XeA10RQ, and XeB10RQ that originated from China were closely relative and highly homologous to the X. euvesicatoria. This research provides information to researchers on genomic variation in BLS pathogens, and further molecular evolution and identification of X. euvesicatoria using the unique target recQ gene through advance molecular approaches.