• Tuberculosis and Respiratory Diseases
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• 제77권5호
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• pp.227-229
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• 2014

Segniliparus species is a novel genus that is reported to be the new emerging respiratory pathogens. Here, we report a very rare case of S. rugosus pulmonary infection in an immunocompetent patient with non-cystic fibrosis. The organism was identified by 16S rRNA gene sequencing. The patient was successfully treated with antibiotics.

• Genomics & Informatics
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• 제19권1호
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• pp.3.1-3.12
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• 2021

Functional interpretation of noncoding genetic variants associated with complex human diseases and traits remains a challenge. In an effort to enhance our understanding of common germline variants associated with lung cancer, we categorize regulatory elements based on eight major cell types of human lung tissue. Our results show that 21.68% of lung cancer-associated risk variants are linked to noncoding regulatory elements, nearly half of which are cell type-specific. Integrative analysis of high-resolution long-range chromatin interactome maps and single-cell RNA-sequencing data of lung tumors uncovers number of putative target genes of these variants and functionally relevant cell types, which display a potential biological link to cancer susceptibility. The present study greatly expands the scope of functional annotation of lung cancer-associated genetic risk factors and dictates probable cell types involved in lung carcinogenesis.

• International Journal of Oral Biology
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• 제46권2호
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• pp.81-84
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• 2021

Salivary glands are exocrine glands that secrete saliva into the oral cavity, and secreted saliva plays essential roles in oral health. Therefore, maintaining the salivary glands in an intact state is required for proper production and secretion of saliva. To investigate a specific signaling pathway that might affect the maintenance of mouse submandibular gland (SMGs), RNA sequencing was performed. In SMGs, downregulated expression patterns of Rho-associated protein kinase (ROCK) signaling pathway-related genes, including Rhoa, Rhob, Rhoc, Rock1, and Rock2, were observed. Gene expression profiling analyses of these genes indicate that the ROCK signaling pathway is a potential signal for SMG maintenance.

• The Plant Pathology Journal
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• 제38권3호
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• pp.220-228
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• 2022

Pollen is a vector for viral transmission. Pollenmediated viruses cause serious economic losses in the fruit industry. Despite the commercial importance of pollen-associated viruses, the diversity of such viruses is yet to be fully explored. In this study, we performed metatranscriptomic analyses using RNA sequencing to investigate the viral diversity in imported apple and kiwifruit pollen. We identified 665 virus-associated contigs, which corresponded to four different virus species. We identified one virus, the apple stem grooving virus, from pear pollen and three viruses, including citrus leaf blotch virus, cucumber mosaic virus, and lychnis mottle virus in kiwifruit pollen. The assembled viral genome sequences were analyzed to determine phylogenetic relationships. These findings will expand our knowledge of the virosphere in fruit pollen and lead to appropriate management of international pollen trade. However, the pathogenic mechanisms of pollen-associated viruses in fruit trees should be further investigated.

• Pediatric Infection and Vaccine
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• 제6권1호
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• pp.123-130
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• 1999

목 적 : 무균성뇌막염은 소아에서 주로 발생하는 질환으로, 흔히 장 바이러스에 의해 초래 된다. 저자들은 그동안 우리나라에서 분리된 무균성뇌막염 원인바이러스의 5'-NCR에 대한 sequencing을 통하여 prototype과의 homology를 비교하고 이 연구를 진단에 이용하기 위한 기초자료로 이용하기 위하여 본 연구를 시도하였다. 방 법 : 과거 4년간 우리나라에서 분리한 장바이러스 Coxsackie B1, Echovirus 3, 7, 9, 30 을 이용하여 RNA를 분리하고 RT-PCR을 이용하여 DNA를 합성한 후, direct sequencing을 이용하여 WHO에서 얻은 prototype과 homology를 비교하였다. 결 과 : 1) PCR product는 155bp와 440bp부위에 특징적인 띠를 관찰할 수 있었다. 2) 155bp에 관한 sequencing homology를 보면 prototype의 Coxsackie virus와 echovirus 는 92.1%의 homology를 보였다. 3) 환자에서 분리한 Coxsackie B1은 prototype과 94.1%의 homology를 보였다. 4) 환자에서 분리한 Echovirus 3은 92.8%, Echovirus 7은 92.8%, Echovirus 9는 94.1%, Echovirus 30은 82.9%의 homology를 보였다. 결 론 : 장바이러스의 5'-NCR은 homology가 높아서 진단에 이용하기에 좋으며 이 부위를 통한 typing을 위해서는 더 긴 부위를 sequencing할 필요가 있다.

• 한국동물위생학회지
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• 제42권4호
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• pp.297-300
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• 2019

In countries with FMD vaccination, as in Korea, typical clinical signs do not appear, and even in FMD positive cases, it is difficult to isolate the FMDV or obtain whole genome sequence. To overcome this problem, more rapid and simple NGS system is required to control FMD in Korea. FMDV (O/Boeun/ SKR/2017) RNA was extracted and sequenced using Ion Torrent's bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. The whole genome sequencing of raw data generated data of 1,839,864 (mean read length 283 bp) reads comprising a total of 521,641,058 (≥Q20 475,327,721). Compared with FMDV (GenBank accession No. MG983730), the FMDV sequences in this study showed 99.83% nucleotide identity. Further study is needed to identify these differences. In this study, fast and robust methods for benchtop next generation sequencing (NGS) system was developed for analysis of Foot-and-mouth disease virus (FMDV) whole genome sequences.

• 한국동물학회:학술대회논문집
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• 한국동물학회 1999년도 한국생물과학협회 학술발표대회
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• pp.225.1-225
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• 1999

No Abstract, See Full Text

• 한국작물학회:학술대회논문집
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• 한국작물학회 2020년도 춘계학술대회
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• pp.21-21
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• 2020

• Journal of Microbiology and Biotechnology
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• 제18권10호
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• pp.1678-1682
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• 2008

To investigate lactic acid bacterial population in Korean traditional rice wines, biotyping was performed using cell morphology and whole-cell protein pattern analysis by SDS-PAGE, and then the isolates were identified by 16S rRNA sequencing analysis. Based on the morphological characteristics, 103 LAB isolates were detected in wine samples, characterized by whole-cell protein pattern analysis, and they were then divided into 18 patterns. By 16S rRNA gene sequencing, the isolates were identified as Lactobacillus paracasei, Lb. arizonensis, Lb. plantarum, Lb. harbinensis, Lb. parabuchneri, Lb. brevis, and Lb. hilgardii when listed by their frequency of occurrence. It was found that the difference in bacterial diversity between rice and grape wines depends on the raw materials, especially the com position of starch and glucose.

• 한국동물위생학회지
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• 제39권1호
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• pp.1-6
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• 2016

In this study, Bacillus licheniformis which has been used as probiotics was isolated from Korean traditional fermented soybean. A total of 69 strains were presumptively identified as B. licheniformis by phenotypic methods. Based on PCR amplification and 16S rRNA gene sequencing, the multilocus sequence typing of gyrA and rpoB, followed by phylogenetic analysis was performed. The isolates were distinctly differentiated and found to be closely related to B. amyloliquefaciens, B. subtilis, and B. aerius. The partial 16S rRNA gene sequences of those strains matched those of B. sonorensis (97%) and B. aerius (98%) in the phylogenetic tree. In contrast, multilocus phylogenetic analysis (MLPA) showed that only 61 (86.9%) out of 69 strains were B. licheniformis. The rest of those strains were found to be B. subtilis (5.8%), B. amyloliquefaciens (2.9%), and B. sonorensis (2.9%), respectively. Therefore, our results suggested that since the 16S rRNA gene sequencing alone was not sufficient to compare and discriminate closely related lineages of Bacillus spp., it was required to analyze the MLPA simultaneously to avoid any misleading phenotype-based grouping of these closely related species.