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La Tae-Min,Kim Ji-hoon,Kim Taesoo,Lee Hong-Jae,이윤석,Shin Hyunjin,송용준,Ahn Gyuhee,Hur Won,이중복,Park Seung-Yong,Choi In-Soo,이상원 대한독성 유전단백체 학회 2021 Molecular & cellular toxicology Vol.17 No.4
Background The emergence of antibiotic-resistant bacterial pathogens in the environment has been increasing, posing a threat to public health. Next-generation sequencing technology, which is both low cost and large scale, was used to identify antibiotic-resistance genes or toxin genes in these pathogens. Short-read sequencing cannot fully reconstruct bacterial chromosomes and plasmids carrying toxin genes and antibiotic-resistance genes because of their location on the insertion sequences or repeat regions. Third-generation sequencing generated long reads that could cover the repetitive and/or insertion sequences, allowing for complete chromosome and plasmid reconstruction. However, the optimal protocols for whole-genome sequencing of antibiotic-resistance pathogenic bacteria, from DNA extraction to genome assembly, are still being researched. Objective To develop a pipeline of optimal methods for whole-genome sequencing of bacteria, we compared three commercial DNA extraction kits (column extraction, magnetic bead extraction, and precipitation extraction), two third-generation sequencing platforms (MinION and PacBio), and three assembly methods (flye, unicycler, and unicycler_hybrid). The assembly results were evaluated based on the number of contigs and the detection of anti-microbial-resistance genes. Results Magnetic bead extraction method generated longer N50 read lengths and greater read length distribution than the other two extraction methods. The Flye assembler in combination with magnetic bead extraction and MinION sequencing provided consistent successful plasmid assembly results and detected all antimicrobial-resistance gene in all datasets. Conclusion DNA extraction, sequencing platform, and assembly methods can all have an impact on the results of bacterial whole-genome sequencing. Our findings could be a practical protocol for researchers who use third-generation sequencing to perform bacterial whole-genome sequencing by consistently resolving small plasmids carrying antibiotic-resistance genes. Background The emergence of antibiotic-resistant bacterial pathogens in the environment has been increasing, posing a threat to public health. Next-generation sequencing technology, which is both low cost and large scale, was used to identify antibiotic-resistance genes or toxin genes in these pathogens. Short-read sequencing cannot fully reconstruct bacterial chromosomes and plasmids carrying toxin genes and antibiotic-resistance genes because of their location on the insertion sequences or repeat regions. Third-generation sequencing generated long reads that could cover the repetitive and/or insertion sequences, allowing for complete chromosome and plasmid reconstruction. However, the optimal protocols for whole-genome sequencing of antibiotic-resistance pathogenic bacteria, from DNA extraction to genome assembly, are still being researched. Objective To develop a pipeline of optimal methods for whole-genome sequencing of bacteria, we compared three commercial DNA extraction kits (column extraction, magnetic bead extraction, and precipitation extraction), two third-generation sequencing platforms (MinION and PacBio), and three assembly methods (flye, unicycler, and unicycler_hybrid). The assembly results were evaluated based on the number of contigs and the detection of anti-microbial-resistance genes. Results Magnetic bead extraction method generated longer N50 read lengths and greater read length distribution than the other two extraction methods. The Flye assembler in combination with magnetic bead extraction and MinION sequencing provided consistent successful plasmid assembly results and detected all antimicrobial-resistance gene in all datasets. Conclusion DNA extraction, sequencing platform, and assembly methods can all have an impact on the results of bacterial whole-genome sequencing. Our findings could be a practical protocol for researchers who use third-generation sequencing to perform bacterial whole-genome sequencing by consistently resolving small plasmids carrying antibiotic-resistance genes.
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Genome-Wide Identification of Haploinsufficiency in Fission Yeast
( Seung Tae Baek ),( Sang Jo Han ),( Mi Young Nam ),( Young Dae Kim ),( Li La Kim ),( Hyun Jee Lee ),( Kyung Sun Heo ),( Hye Mi Lee ),( Min Ho Lee ),( Song Kyu Park ),( Pil Jae Maeng ),( Young Woo Par 한국미생물 · 생명공학회 2008 Journal of microbiology and biotechnology Vol.18 No.6
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Kjeldahl 증류법을 활용한 질산성-질소 및 암모니아성-질소 안정동위원소비 분석 및 질소오염원 추적사례 연구
김민섭 ( Min Seob Kim ),박태진 ( Tae Jin Park ),윤숙희 ( Suk Hee Yoon ),임보라 ( Bo La Lim ),신경훈 ( Kyung Hoon Shin ),권오상 ( Oh Sang Kwon ),이원석 ( Won Seok Lee ) 한국하천호수학회(구 한국육수학회) 2015 생태와 환경 Vol.48 No.3
Nitrogen (N) loading from domestic, agricultural and industrial sources can lead to excessive growth of macrophytes or phytoplankton in aquatic environment. Many studies have used nitrogen stable isotope ratios to identify anthropogenic nitrogen in aquatic systems as a useful method for studying nitrogen cycle. In this study to evaluate the precision and accuracy of Kjeldahl processes, two reference materials (IAEA-NO-3, N-1) were analyzed repeatedly. Measured the δ15N-NO3 and δ15N-NH4 values of IAEA-NO-3 and IAEA-N-1 were 4.7±0.2‰ and 0.4±0.3‰, respectively, which are within recommended values of analytical uncertainties. Also, we investigated spatial patterns of δ15N-NO3 and δ15N-NH4 in effluent plumes from a waste water treatment plant in Han River, Korea. δ15N-NO3 and δ15N-NH4 values are enriched at downstream areas of water treatment plant suggesting that dissolved nitrogen in effluent plumes should be one of the main N sources in those areas. The current study clarifies the reliability of Kjeldahl analytical method and the usefulness of stable isotopic techniques to trace the contamination source of dissolved nitrogen such as nitrate and ammonia.
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Cereblon Maintains Synaptic and Cognitive Function by Regulating BK Channel
Choi, Tae-Yong,Lee, Seung-Hyun,Kim, Yoon-Jung,Bae, Jae Ryul,Lee, Kwang Min,Jo, Youhwa,Kim, Soo-Jeong,Lee, A-Ram,Choi, Sekyu,Choi, La-Mee,Bang, Sunhoe,Song, Mi-Ryoung,Chung, Jongkyeong,Lee, Kyung Jin,K The Society 2018 The Journal of neuroscience Vol.38 No.14
<P>Mutations in the cereblon (CRBN) gene cause human intellectual disability, one of the most common cognitive disorders. However, the molecular mechanisms of CRBN-related intellectual disability remain poorly understood. We investigated the role of CRBN in synaptic function and animal behavior using male mouse and Drosophila models. Crbn knock-out (KO) mice showed normal brain and spine morphology as well as intact synaptic plasticity; however, they also exhibited decreases in synaptic transmission and presynaptic release probability exclusively in excitatory synapses. Presynaptic function was impaired not only by loss of CRBN expression, but also by expression of pathogenic CRBN mutants (human R419X mutant and Drosophila G552X mutant). We found that the BK channel blockers paxilline and iberiotoxin reversed this decrease in presynaptic release probability in Crbn KO mice. In addition, paxilline treatment also restored normal cognitive behavior in CrbnKOmice. These results strongly suggest that increased BK channel activity is the pathological mechanism of intellectual disability in CRBN mutations.</P>
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원발성 담즙성 간경변증으로 진단되고 자가면역성 간염의 Feature를 보이는 한국인 환자에 대한 Simplified Scoring Criteria의 의미
김민석 ( Min Suk Kim ),김영석 ( Young Seok Kim ),김상균 ( Sang Gyune Kim ),변진명 ( Jin Myung Byun ),윤라영 ( La Young Yoon ),한동훈 ( Dong Hoon Han ),문종주 ( Jong Joo Moon ),남재형 ( Jae Hyung Nam ),김태진 ( Tae Jin Kim ),이세환 대한내과학회 2013 대한내과학회지 Vol.84 No.2
Background/Aims: The diagnosis of primary billiary cirrhosis (PBC)-autoimmune hepatitis (AIH) overlap syndrome remains challenging. In 2008, a simplified scoring system was proposed by the International Autoimmune Hepatitis Group, which aimed for wider applicability in routine clinical practice. We evaluated the performance of the new simplified AIH scoring criteria as a diagnostic tool for overlap syndrome. Methods: We retrospectively reviewed the clinical histories, chemistry, autoimmune studies, and liver biopsy results of 25 patients diagnosed with PBC who visited Soonchunhyang University Hospital, Bucheon and Seoul, between November 2004 and December 2009. Parameters relevant to the revised and simplified scoring criteria were recorded, and outcomes were compared between those with and without features of overlap syndrome. Results: Of 25 patients with a definite diagnosis of PBC, five (20%) were diagnosed with overlap syndrome using the revised criteria, and 18 patients (72%) were diagnosed with the simplified criteria. Those patients diagnosed according to the simplified scoring criteria revealed an increased frequency of anti-nuclear antibody (p=0.030) and serum IgG levels (p=0.092). Additionally, advanced fibrosis was significantly more frequent in patients with overlap syndrome (p=0.017). Conclusions: The simplified scoring criteria seemed to be useful as a diagnostic tool to recognize overlap syndrome in Korea. However, a relatively small number of patients were included in our study, so further clinical trials based on larger populations should be performed. (Korean J Med 2013;84:211-220)
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