• Korean Journal of Environment and Ecology
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• v.35 no.5
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• pp.503-524
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• 2021

A largemouth bass (Micropterus salmoides) is an ecosystem disturbance fish species at the highest rank in the aquatic ecosystem, causing a serious imbalance in freshwater ecosystems. Although various attempts have been made to eradicate and control largemouth bass, no effective measures were found. Therefore, it is necessary to find an approach to maximize the effective population reduction based on the unique characteristics of largemouth bass. This study used the transcriptome analysis to derive 182,887 unigene contigs and select 12 types of final target sequences for applying the CRISPR/Cas9 system in the genes of IZUMO1 and Zona pellucida sperm-binding protein, which are proteins involved in sperm-egg recognition. After synthesizing 12 types of sgRNA capable of recognizing each target sequence, 12 types of Cas9-sgRNA ribonucleoprotein (RNP) complexes to be used in subsequent studies were prepared. This study searched the protein-coding gene of sperm-egg through the Next Generation Sequencing (NGS) and edited genes through the CRISPR/Cas9 system to induce infertile individuals that produced reproductive cells but could not form fertilized eggs. Through such a series of processes, it successfully established a composition development process for largemouth bass. It is judged that this study contributed to securing the valuable basic data for follow-up studies to verify its effect for the management of ecological disturbances without affecting the habitat of other endemic species in the same water system with the largemouth bass.

• Korean Journal of Plant Resources
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• v.34 no.5
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• pp.443-450
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• 2021

Peach flesh color is commercially important criteria for classification and has implications for nutritional quality. To breed new yellow-fleshed peach cultivar many cross seedlings and generations should be maintained. Therefore it is necessary to develop early selection molecular markers for screening cross seedlings and germplasm with economically important traits to increase breeding efficiency. For the comparison of transcription profiles in peach varieties with a different flesh color expression, two cDNA libraries were constructed. Differences in gene expression between yellow-fleshed peach cultivar, 'Changhowon Hwangdo' and white-fleshed peach cultivar, 'Mibaekdo' were analyzed by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the two varieties was selected for nucleotide sequence determination and homology searches. Putative single nucleotide polymorphisms (SNPs) were screened from peach EST contigs by high resolution melting (HRM) analysis, SNP ID ppa002847m:cds and ppa002540m:cds displayed specific difference between 17 yellow-fleshed and 21 white-fleshed peach varieties. The SNP markers for distinguishing yellow and white fleshed peach varieties by HRM analysis offers the opportunity to use early selection. This SNP markers could be useful for marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in peach varieties.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.257-264
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• 2021

In this study, we analyzed the food components in the release product that sampled Sinonovacula constricta from the foreshore littoral at Byeongnyang-myeon, Suncheon Bay. We used microscopy and next-generation sequencing (NGS) to evaluate the applicability of morphological and molecular methods to analyze release products. The higher species diversity observed in the NGS method is due to the different levels of species identification, as microscopy displays morphological and anatomical levels of plankton species identification in S. constrita. Moreover, NGS can identify the level of species in the organic matter by using the 18s_V9 primer.

• Journal of Korean Society of Water and Wastewater
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• v.36 no.2
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• pp.97-106
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• 2022

Recently microplastic (MP) biofilm is being attracted as an important environmental issue because it can act as a pollutant carrier in aqueous system. Therefore, this study investigated the MP biofilm communities originated from freshwater. The results showed the bacterial community structure of MP biofilm was distinctively different from the freshwater regardless of biofilm-forming condition and MP type. For MP biofilm communities exposed to raw freshwater, Solimonas variicoloris-like microbe, Frigidibacter albus-like microbe, Nitrospirillum amazonense-like microbe, and Pseudochroococcus couteii-like microbe became abundant, while Acinetobacter johnsonii, Macellibacteroides fermentans, and Sedimentibacter acidaminivorans-like microbe were found as major bacteria for MP biofilm communities exposed to organic rich condition. The results of this study suggest that the unique freshwater biofilm community could be formed on the MP surface.

• Korean Journal of Microbiology
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• v.52 no.1
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• pp.59-64
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• 2016

In this study, a pyrosequencing was performed and analyzed to verify the phylogenetic diversity of actinomycetes in the bamboo (Sasa borealis) soil as a base study to obtain the genetic resources of actinomycetes. It was found that the rhizosphere soil had much various distribution in bacterial communities showing a diversity of 8.15 with 2,868 OTUs, while the litter layer showed a diversity of 7.55 with 2,588 OTUs. The bacterial community in the bamboo soil was composed of 35 phyla and the predominant phyla were Proteobacteria (51-60%), Bacteroidetes (16-20%), Acidobacteria (4-16%) and Actinobacteria (4-14%). In particular, Actinobacteria including Micromonosporaceae and Streptomycetaceae had a diverse distribution of actinomycetes within the six orders, 35 families and 121 genera, and it was characterized that about 83% of actinomycetes within Actinomycetales belonged to the 28 families. Among the dominant actinobacterial populations, Micromonosporaceae, Pseudonocardiaceae and Streptomycetaceae were representative family groups in the bamboo soils.

• The Korea Journal of Herbology
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• v.34 no.6
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• pp.91-97
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• 2019

Objective : To establish a reliable tool between for the distinction of original plants of Sanguisorbae Radix, we analyzed the complete chloroplast genome sequence of Sanguisorbae Radix and identified single nucleotide polymorphisms (SNPs). Materials and methods : The chloroplast genome sequence of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link obtained using next-generation sequencing technology were described and compared with those of other species to develop specific markers. Candidate genetic markers were identified to distinguish species from the chloroplast sequences of each species using Modified Phred Phrap Consed and CLC Genomics Workbench programs. Results : The structure of the chloroplast genome of each sample that had been assembled and verified was circular, and the length was about 155 kbp. Through comparative analysis of the chloroplast sequences, we found 220 nucleotides, 158 SNPs, and 62 Indel (insertion and/or deletion), to distinguish Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link. Finally, 15 specific SNP genetic markers were selected for the verification at positions. Avaliable primers for the dried herb, which is used as medicine, were used to develop the PCR amplification product of Sanguisorbae Radix to assess the applicability of PCR analysis. Conclusion : In this study, we found that Fendel-qPCR analysis based on the chloroplast DNA sequences can be an efficient tool for discrimination of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link.

• Korean Journal of Microbiology
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• v.52 no.3
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• pp.375-379
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• 2016

In this study, the structure and diversity of bacterial community were investigated in the surface and subsurface marine sediments using a NGS method (i.e. illumina sequencing technology). The bacterial community in the surface was distinct from that in the subsurface of marine sediment; with the exception of the phylum Proteobacteria, the relative abundance of Bacteroides phylum were higher in the surface than subsurface, whereas the sequences affiliated to the phyla Chloroflexi and Acidobacteria were relatively more copious in the subsurface than surface sediment. Moreover, interestingly, we observed that the phyla Nitrospinae and Nitrospirae contribute to nitrogen cycle in the marine sediment. This study may present the possibility for the presence of novel microorganisms as unexplored sources and provide basic information on the microbial community structure.

• Pediatric Infection and Vaccine
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• v.29 no.1
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• pp.54-60
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• 2022

Salmonella meningitis is rare yet poses causes significant neurological morbidity in children. Infants, especially those under 3 months of age, and those with immunocompromised states, such as malignancy, malaria, and human immunodeficiency virus infection, are at increased risk for developing Salmonella meningitis. Herein, we describe a case of Salmonella meningitis in a previous healthy 8-year-old girl who presented with high fever, vomiting, and altered mental status. Group D Salmonella species were isolated in cerebrospinal fluid culture, and no abnormal findings were noted in brain magnetic resonance imaging. Immunoglobulin levels and lymphocyte subset counts were within the normal ranges, and no genetic mutation responsible for primary immunodeficiency disease was detected by next-generation sequencing. The patient's condition improved rapidly with third-generation cephalosporin, and no complications or sequalae developed. Nontyphoidal Salmonella can cause meningitis in immunocompetent children and can be successfully treated with early administration of antibiotics.

• KIPS Transactions on Computer and Communication Systems
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• v.8 no.10
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• pp.231-238
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• 2019

Analyzing next-generation genome sequencing data in a conventional way using single server may take several tens of hours depending on the data size. However, in order to cope with emergency situations where the results need to be known within a few hours, it is required to improve the performance of a single genome analysis. In this paper, we propose a parallelized method for pre-processing genome sequence data which can reduce the analysis time by utilizing the big data technology and the highperformance computing cluster which is connected to the high-speed network and shares the parallel file system. For the reliability of analytical data, we have chosen a strategy to parallelize the existing analytical tools and algorithms to the new environment. Parallelized processing, data distribution, and parallel merging techniques have been developed and performance improvements have been confirmed through experiments.

• The Korean Journal of Mycology
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• v.46 no.1
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• pp.69-74
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• 2018

The Rhododendron powdery mildew fungus Erysiphe izuensis has been recorded throughout Asia, including China, Japan, Korea, and Russia. In Korea, E. izuensis has been identified based on morphological characteristics of the anamorph found on introduced Rhododendron spp. We here describe the first identification of E. izuensis collected from Rhododendron yedoense f. poukhanense in Korea. Morphological characteristics of the teleomorph as well as internal transcribed spacer sequences of the species are provided. Moreover, we describe the characteristics of the primary conidia and conidial surface pattern of E. izuensis for the first time.