• Molecules and Cells
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• v.41 no.5
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• pp.465-475
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• 2018

The advent of massively parallel sequencing, also called next-generation sequencing (NGS), has dramatically influenced cancer genomics by accelerating the identification of novel molecular alterations. Using a whole genome sequencing (WGS) approach, we identified somatic coding and noncoding variants that may contribute to leukemogenesis in 11 adult Korean acute myeloid leukemia (AML) patients, with serial tumor samples (primary and relapse) available for 5 of them; somatic variants were identified in 187 AML-related genes, including both novel (SIN3A, C10orf53, PTPRR, and RERGL) and well-known (NPM1, RUNX1, and CEPBA) AML-related genes. Notably, SIN3A expression shows prognostic value in AML. A newly designed method, referred to as "hot-zone" analysis, detected two putative functional noncoding variants that can alter transcription factor binding affinity near PPP1R10 and SRSF1. Moreover, the functional importance of the SRSF1 noncoding variant was further investigated by luciferase assays, which showed that the variant is critical for the regulation of gene expression leading to leukemogenesis. We expect that further functional investigation of these coding and noncoding variants will contribute to a more in-depth understanding of the underlying molecular mechanisms of AML and the development of targeted anti-cancer drugs.

• Journal of Platform Technology
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• v.6 no.4
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• pp.87-95
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• 2018

With the decrease of sequencing price, many national projects that analyzes 0.1 to 1 million people are now in progress. However, large portion of budget of these large projects is dedicated for construction of the cluster system or purchase servers, due to the lack of programs or systems that can handle large amounts of data simultaneously. In this study, we developed NGSOne, a client program that is easy-to-use for even biologists, and performs SNP analysis using hundreds or more of Whole Genome and Whole Exome analysis without construction of their own server or cluster environment. DRAGEN, BWA / GATK, and Isaac / Strelka2, which are representative SNP analysis tools, were selected and DRAGEN showed the best performance in terms of execution time and number of errors. Also, NGSOne can be extended for various analysis tools as well as SNP analysis tools.

• Plant Breeding and Biotechnology
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• v.5 no.2
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• pp.134-142
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• 2017

Resource plants are important and have strong potential for a variety of utilities as crops or pharmaceutical materials. However, most resource plants remain wild and thus their utility for breeding and biotechnology is limited. Molecular markers are useful to initiate genetic study and molecular breeding for these understudied resource plants. We collected various wild collections of Peucedanum japonicum which is indigenous resource plants utilized as oriental medicine and leafy vegetables in Korea. In this study, we produced two independent whole genome sequences (WGSs) from two collections and identified large scale polymorphic simple sequence repeat (pSSR) based on our pipeline to develop SSR markers based on comparison of two WGSs. We identified a total of 452 candidate pSSR contigs. To confirm the accuracy and utility of pSSR, we designed ten SSR primer pairs and successfully applied those to seven collections of P. japonicum. The WGS and pSSR candidates identified in this study will be useful resource for genetic research and breeding purpose for the valuable resource plant, P. japonicum.

• Journal of Microbiology and Biotechnology
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• v.30 no.12
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• pp.1862-1869
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• 2020

The spread of plasmid-mediated colistin resistance has posed a serious threat to public health owing to its effects on the emergence of pandrug-resistant bacteria. In this study, we investigated the prevalence and characteristics of mcr-1-positive Escherichia coli isolated from retail meat samples in Korea. In total, 1,205 E. coli strains were isolated from 3,234 retail meat samples in Korea. All E. coli strains were subjected to antimicrobial susceptibility testing and were examined for the presence of mcr-1 gene. All mcr-1-positive E. coli (n = 10, 0.8%) from retail meat were subjected to pulse-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). The transferability of mcr-1 gene was determined by conjugation assays. The mcr-1-positive strains exhibited diverse clonal types. Our mcr-1 genes were located in plasmids belonged to the IncI2 (n = 1) and IncX4 (n = 8) types, which were reported to be prevalent in Asia and worldwide, respectively. Most mcr-1 genes from mcr-1-positive strains (9/10) were transferable to the recipient strain and the transfer frequencies ranged from 2.4 × 10-3 to 9.8 × 10-6. Our data suggest that the specific types of plasmid may play an important role in spreading plasmid-mediated colistin resistance in Korea. Furthermore, our findings suggest that the retail meat may be an important tool for disseminating plasmid-mediated colistin resistance.

• Journal of Microbiology and Biotechnology
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• v.32 no.11
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• pp.1485-1495
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• 2022

The development of a yeast strain capable of fermenting mixed sugars efficiently is crucial for producing biofuels and value-added materials from cellulosic biomass. Previously, a mutant Pichia stipitis YN14 strain capable of co-fermenting xylose and cellobiose was developed through evolutionary engineering of the wild-type P. stipitis CBS6054 strain, which was incapable of co-fermenting xylose and cellobiose. In this study, through genomic and transcriptomic analyses, we sought to investigate the reasons for the improved sugar metabolic performance of the mutant YN14 strain in comparison with the parental CBS6054 strain. Unfortunately, comparative whole-genome sequencing (WGS) showed no mutation in any of the genes involved in the cellobiose metabolism between the two strains. However, comparative RNA sequencing (RNA-seq) revealed that the YN14 strain had 101.2 times and 5.9 times higher expression levels of HXT2.3 and BGL2 genes involved in cellobiose metabolism, and 6.9 times and 75.9 times lower expression levels of COX17 and SOD2.2 genes involved in respiration, respectively, compared with the CBS6054 strain. This may explain how the YN14 strain enhanced cellobiose metabolic performance and shifted the direction of cellobiose metabolic flux from respiration to fermentation in the presence of cellobiose compared with the CBS6054 strain.

• Korean Journal of Environmental Agriculture
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• v.42 no.4
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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.

• Korean Chemical Engineering Research
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• v.62 no.1
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• pp.36-43
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• 2024

Fishing net waste (FNW) constitutes over half of all marine plastic waste and is a major contributor to the degradation of marine ecosystems. While current treatment options for FNW include incineration, landfilling, and mechanical recycling, these methods often result in low-value products and pollutant emissions. Importantly, FNWs, comprised of plastic polymers, can be converted into valuable resources like syngas and pyrolysis oil through pyrolysis. Thus, this study presents a process for generating high-purity hydrogen (H₂) by catalytically pyrolyzing FNW in a CO₂ environment. The proposed process comprises of three stages: First, the pretreated FNW undergoes Ni/SiO₂ catalytic pyrolysis under CO₂ conditions to produce syngas and pyrolysis oil. Second, the produced pyrolysis oil is incinerated and repurposed as an energy source for the pyrolysis reaction. Lastly, the syngas is transformed into high-purity H₂ via the Water-Gas-Shift (WGS) reaction and Pressure Swing Adsorption (PSA). This study compares the results of the proposed process with those of traditional pyrolysis conducted under N₂ conditions. Simulation results show that pyrolyzing 500 kg/h of FNW produced 2.933 kmol/h of high-purity H₂ under N₂ conditions and 3.605 kmol/h of high-purity H₂ under CO₂ conditions. Furthermore, pyrolysis under CO₂ conditions improved CO production, increasing H₂ output. Additionally, the CO₂ emissions were reduced by 89.8% compared to N₂ conditions due to the capture and utilization of CO₂ released during the process. Therefore, the proposed process under CO₂ conditions can efficiently recycle FNW and generate eco-friendly hydrogen product.

• Clean Technology
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• v.21 no.3
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• pp.200-206
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• 2015

In order to investigate the effect of cerium oxide addition, Cu-ZnO-CeO₂ catalysts were prepared using co-precipitation method for water gas shift (WGS) reaction. A series of Cu-ZnO-CeO₂ catalyst with fixed Cu Content (50 wt%, calculated as CuO) and a given ceria content (e.g., 0, 5, 10, 20, 30, 40 wt%, calculated as CeO₂) were tested for catalytic activity at a GHSV of 95,541 h^-1, and a temperature range of 200 to 400 ℃. Cu-ZnO-CeO₂ catalysts were characterized by using BET, SEM, XRD, H₂-TPR, and XPS analysis. Varying composition of Cu-ZnO-CeO₂ catlysts led the difference characteristics such as Cu dispersion, and binding energy. The optimum 10 wt% doping of cerium facilitated catalyst reduction at lower temperature and improved the catalyst performance greatly in terms of CO conversion. Cerium oxide added catalyst showed enhanced activities at higher temperature when it compared with the catalyst without cerium oxide. Consequently, ceria addition of optimal composition leads to enhanced catalytic activity which is attributed to enhanced Cu dispersion, lower binding energy, and hindered Cu metal agglomeration.

• Transactions of the Korean hydrogen and new energy society
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• v.25 no.6
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• pp.577-585
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• 2014

Nanorod and particle shape $CeO_2$ were synthesized via hydrothermal process and precipitation method, respectively, and used as supports of Pt catalyst for water gas shift (WGS) reaction. Three different durations (12, 48, and 96h) for hydrothermal process were applied for the preparation of nanorod type $CeO_2$. 1.0 wt% of Pt was loaded on the prepared supports with incipient wetness method prior to the catalytic activity tests that were carried out at a GHSV of $95,541h^{-1}$, and a temperature range of 200 to $360^{\circ}C$. Varying duration of hydrothermal process led to the difference in physical characteristics of $CeO_2$ nanorods, such as aspect ratio, BET surface area, pore diameter, and pore volume. Consequently, the catalytic activities of Pt/$CeO_2$ nanorods were affected by the physical characteristics of the supports and appeared to be in the order of Pt/$CeO_2$(12) > Pt/$CeO_2$(48) > Pt/$CeO_2$(96). The comparison of the catalytic activities and results of the analysis (XPS, XRD, SEM, BET and TPR) for the supports revealed that the activity of the catalysts depends on chemical states of the Pt and the support materials in the temperature range that is lower than $280^{\circ}C$. However, the activity is rather dependent on the physical characteristic of the supports because the increased gas velocity limits the mass transfer of reactants in micropores of the supports.