• 미생물학회지
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• 제55권3호
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• pp.274-277
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• 2019

본 연구에서는 건강한 한국인 분변으로부터 Ruminococcus sp. KGMB03662 균주를 분리하고 유전체서열을 PacBio Sequel 플랫폼을 사용하여 분석하였다. 염색체의 크기는 2,707,502 bp로 G + C 구성 비율은 43.09%, 총 유전자수는 2,484개, 단백질 코딩 유전자는 2,367개, rRNA는 14개 및 tRNA는 53개로 구성되었다. 본 유전체로부터 가수분해효소, 지방산생합성 및 대사와 항생제생합성 및 내성 관련 유전자를 확인하였다. 이러한 유전체의 분석은 KGMB03662 균주가 사람의 건강 및 질병에 관여할 것으로 여겨진다.

• 한국균학회지
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• 제45권2호
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• pp.114-120
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• 2017

표고버섯은 주로 아시아 국가에서 재배되는 식용 버섯이다. 표고버섯은 최근 국내에서 신품종의 개발이 활발히 이루어지고 있으며, 국내외적으로 품종의 보호가 중요해짐에 따라 표고의 품종을 구분할 수 있는 효율적인 마커 개발이 요구되고 있다. 본 연구에서는 산마루1호와 천장3호를 구분할 수 있는 CAPS (cleaved amplified polymorphic sequence) 마커를 개발하였다. 이 연구에서 개발된 CAPS 마커는 단핵균주인 B17의 표준유전체 정보와 연구에 사용된 10개 균주의 resequencing 정보를 바탕으로 개발되었다. 산마루1호는 scaffold9번, 1630048의 염기서열 G가 T로 변한 SNP를 포함하여 PCR 후 제한효소 TspR I을, 천장3호는 scaffold13번, 920681의 염기서열 G가 A로 변한 single nucleotide polymorphism (SNP)를 포함하여 PCR 후, 제한효소 Xho I을 처리하였을 때 다른 균주들과 구분되었다. 따라서 이를 마커로 개발하였다.

• Journal of Genetic Medicine
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• 제2권1호
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• pp.35-39
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• 1998

Duchenne/Becker muscular dystrophy are the major neuromuscular disorders with X-linked recessive inheritance. Preimplantation diagnosis of sex determination has been generally used to avoid male pregnancies with these diseases. However, in order to determine if the embryo is normal, carrier or affected regardless of the sex, there is a need for a combined analysis of specific exon on dystrophin gene as well as sex determination of embryo using the same biopsied blastomere. If the exon deletion is not determinable, further diagnosis of carrier or patient can be performed by haplotype analysis. In this study, we applied the primer extension preamplification (PEP) method, which amplifies the whole genome, in 40 cases of single amniocyte and 40 cases of chorionic villus cell. We analysed haplotypes using two (CA)n dinucleotide polymorphic markers located at the end of 5' and 3' region of the dystrophin gene. Exon 46 of dystrophin gene and DYZ3 on chromosome Y were chosen as a target sequence for coamplification PCR. Upon optimizing the conditions, the amplification rates were 91.25% (73/80) for haplotypes (92.5% in amniocyte, 90% in chorionic villus cell) and 88.75% (71/80) for coamplification (85% in amniocyte, 92.5% in chorionic villus cell). The result of the study indicates that haplotypes analysis and coamplification of dystrophin and Y-specific gene using PEP can be applied to prenatal and preimplantation diagnosis in Duchenne/Becker muscular dystrophy making it possible to determine if the fetus is a carrier or an affected one.

• 환경생물
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• 제30권2호
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• pp.77-89
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• 2012

With the advent of the genomics era powered by DNA sequencing technologies, life science is being transformed significantly and biological research and development have been accelerated. Environmental biology concerns the relationships among living organisms and their natural environment, which constitute the global biogeochemical cycle. As sustainability of the ecosystems depends on biodiversity, examining the structure and dynamics of the biotic constituents and fully grasping their genetic and metabolic capabilities are pivotal. The high-speed high-throughput next-generation sequencing can be applied to barcoding organisms either thriving or endangered and to decoding the whole genome information. Furthermore, diversity and the full gene complement of a microbial community can be elucidated and monitored through metagenomic approaches. With regard to human welfare, microbiomes of various human habitats such as gut, skin, mouth, stomach, and vagina, have been and are being scrutinized. To keep pace with the rapid increase of the sequencing capacity, various bioinformatic algorithms and software tools that even utilize supercomputers and cloud computing are being developed for processing and storage of massive data sets. Environmental genomics will be the major force in understanding the structure and function of ecosystems in nature as well as preserving, remediating, and bioprospecting them.

• 농업과학연구
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• 제45권4호
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• pp.655-663
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• 2018

The insect gut microbiome is known to have important roles in host growth, development, digestion, and resistance against pathogens. In addition, the genetic diversity of the insect gut microbiota has recently been recognized as potential genetic resources for industrial bioprocessing. However, there is limited information regarding the insect gut microbiota to better help us understand their potential benefits for enhanced pig production. With the development of next-generation sequencing methods, whole genome sequence analysis has become possible beyond traditional culture-independent methods. This improvement makes it possible to identify and characterize bacteria that are not cultured and located in various environments including the gastrointestinal tract. Insect intestinal microorganisms are known to have an important role in host growth, digestion, and immunity. These gut microbiota have recently been recognized as potential genetic resources for livestock farming which is using the functions of living organisms to integrate them into animal science. The purpose of this literature review is to emphasize the necessity of research on insect gut microbiota and their applicability to pig production or bioindustry. In conclusion, bacterial metabolism of feed in the gut is often significant for the nutrition intake of animals, and the insect gut microbiome has potential to be used as feed additives for enhanced pig performance. The exploration of the structure and function of the insect gut microbiota needs further investigation for their potential use in the swine industry particularly for the improvement of growth performance and overall health status of pigs.

• The Plant Pathology Journal
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• 제39권5호
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• pp.494-503
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• 2023

Xanthomonas campestris pv. campestris (Xcc) is a plant pathogen of Brassica crops that causes black rot disease throughout the world. At present, 11 physiological races of Xcc (races 1-11) have been reported. The conventional method of using differential cultivars for Xcc race detection is not accurate and it is laborious and time-consuming. Therefore, the development of specific molecular markers has been used as a substitute tool because it offers an accurate and reliable result, particularly a quick diagnosis of Xcc races. Previously, our laboratory has successfully developed race-specific molecular markers for Xcc races 1-6. In this study, specific molecular markers to identify Xcc race 7 have been developed. In the course of study, whole genome sequences of several Xcc races, X. campestris pv. incanae, X. campestris pv. raphani, and X. campestris pv. vesicatoria were aligned to identify variable regions like sequence-characterized amplified regions and insertions and deletions specific to race 7. Primer pairs were designed targeting these regions and validated against 22 samples. The polymerase chain reaction analysis revealed that three primer pairs specifically amplified the DNA fragment corresponding to race 7. The obtained finding clearly demonstrates the efficiency of the newly developed markers in accurately detecting Xcc race 7 among the other races. These results indicated that the newly developed marker can successfully and rapidly detect Xcc race 7 from other races. This study represents the first report on the successful development of specific molecular markers for Xcc race 7.

• 한국환경농학회지
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• 제42권4호
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• pp.269-278
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• 2023

Antibiotics either kill or inhibit the growth of bacteria. However, antibiotic-resistant bacteria are difficult to treat with antibiotics. Infections caused by such bacteria often lead to severe diseases. Antibiotic resistance genes (ARG) can be horizontally transmitted across different bacterial species, necessitating a comprehensive understanding of how ARGs spread across various environments. In this study, we analyzed the plasmid sequences of 33 extended-spectrum beta-lactamases (ESBL) producing Escherichia coli isolated from pigs, farms, and their owners. We conducted an antibiotic susceptibility test (AST) with aztreonam and seven other antibiotics, as well as whole genome sequencing (WGS) of the strains using MinION. Our results demonstrated that the plasmids that did not harbor ARGs were mostly non-conjugative, whereas the plasmids that harbored ARGs were conjugative. The arrangement of these ARGs exhibited a pattern of organization featuring a series of ARG cassettes, some of which were identical across the isolates collected from different sources. Therefore, this study suggests that the sets of ARG cassettes on plasmids were mostly shared between pigs and their owners. Hence, enhanced surveillance of ARG should be implemented in farm environments to proactively mitigate the risk of antibiotic-resistant bacterial infections.

• 한국미생물·생명공학회지
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• 제51권4호
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• pp.403-415
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• 2023

This study aimed to isolate and identify L-(+)-lactic acid-producing bacteria from tree barks collected in Thailand and evaluate the potential strain as probiotics. Twelve strains were isolated and characterized phenotypically and genotypically. The strains exhibited a rod-shaped morphology, high-temperature tolerance, and the ability to ferment different sugars into lactic acid. Based on 16S rRNA gene analysis, all strains were identified as belonging to Weizmannia coagulans. Among the isolated strains, BKMTCR2-2 demonstrated exceptional lactic acid production, with 96.41% optical purity, 2.33 g/l of lactic acid production, 1.44 g/g of lactic acid yield (per gram of glucose consumption), and 0.0049 g/l/h of lactic acid productivity. This strain also displayed a wide range of pH tolerance, suggesting suitability for the human gastrointestinal tract and potential probiotic applications. The whole-genome sequence of BKMTCR2-2 was assembled using a hybridization approach that combined long and short reads. The genomic analysis confirmed its identification as W. coagulans and safety assessments revealed its non-pathogenic attribute compared to type strains and commercial probiotic strains. Furthermore, this strain exhibited resilience to acidic and bile conditions, along with the presence of potential probiotic-related genes and metabolic capabilities. These findings suggest that BKMTCR2-2 holds promise as a safe and effective probiotic strain with significant lactic acid production capabilities.

• 대한바이러스학회지
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• 제26권1호
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• pp.77-90
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• 1996

Nucleocapsid protein (NP)which exists in the particle of hantavirus and surrounds the viral RNA genome is one of the major structural proteins and plays role of antigen to elicit the antibody detected predorminantly right after infection of the virus in the patients of hemorragic fever with renal syndrome (HFRS)or experimental animals. NP is important target antigen in serological diagnostic system of HFRS utilizing whole antigens from the native virus particle, such as IFA, ELISA and Western blotting. Therefore, the preparation of this protein in the level of higher quantity and purity is desirasble for developed dianosis of the disease. The purpose of this study is the cloning of NP gene which exists in the S genome segment of Maaji (MAA) virus and expression of the gene to obtain qualified, genetically engineered NP to be utilized as an immunodiagnostic antigen. First of all, for the purpose of amplifing the MAA-NP gene by PCR, the specific primers were built from the known nucleotide sequence of Hantaan viral NP gene. The viral cDNA of the NP gene was synthesized by using the primers and RNase $H^-$ AMV reverse transcriptase. Thereafter, using this cDNA as a template, the NP gene was amplified specifically by Taq DNA polymrerase. The pT7blue (R)T-overhang vector systems were used for cloning of the amplified NP gene. The expression system was consisted of BL21 (DE3)pLysS and pET16b as a host and a plasmid repectively. Into Ndel site of pET16b, NP gene was ligated with cohesive end for the expression. Insertion of NP gene in the plasmid was confirmed by PCR and mini prep methods. For expression, IPTG was used and the expressed protein was characterized by Western blotting. The MAA-NP was expressed as the form of inclusion body (insoluble fraction)and the protein purified by affinity and metal chealating columns reacted specifically with the sera from patients of HFRS as to be tested by ELISA and Western blotting.

• Journal of Ginseng Research
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• 제44권4호
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• pp.637-643
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• 2020

Background: Ginseng (Panax ginseng Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood. Methods: We developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci to elucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars, breeding lines, and wild populations in Korea and neighboring countries. Results: Most of the 92 markers displayed multiple-band patterns, resulting from genome duplication, which causes confusion in interpretation of their target locus. The five high-resolution markers revealed 3 to 8 alleles from each single locus. The proportion of heterozygosity (H_e) ranged from 0.027 to 0.190, with an average of 0.132, which is notably lower than that of previous studies. Polymorphism information content of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was no statistically significant difference in genetic diversity between cultivated and wild ginseng groups, and they showed intermingled positioning in the phylogenetic relationship. Conclusion: Ginseng has a relatively high level of genetic diversity, and cultivated and wild groups have similar levels of genetic diversity. Collectively, our data demonstrate that current breeding populations have abundant genetic diversity for breeding of elite ginseng cultivars.