• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1541-1546
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• 2016

Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.490.1-490.1
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• 2014

The ZnO nanowire (NW)-based nanogenerators (NGs) can have rectifying current and potential generated by the coupled piezoelectric and semiconducting properties of ZnO by variety of external stimulation such as pushing, bending and stretching. So, ZnO NGs needed to enhance durability for stable properties of NGs. The durability of the metal electrodes used in the typical ZnO nanogenerators(NGs) is unstable for both electrical and mechanical stability. Indium tin oxide (ITO) is used as transparent flexible electrode but because of high cost and limited supply of indium, the fragility and lack of flexibility of ITO layers, alternatives are being sought. It is expected that carbon nanotube and Ag nanowire conductive coatings could be a prospective replacement. In this work, we demonstrated transparent flexible ZnO NGs by using CNT/Ag nanowire hybrid electrode, in which electrical and mechanical stability of top electrode has been improved. We grew vertical type ZnO NW by hydrothermal method and ZnO NW was coated with hybrid silicone coating solution as capping layer to enhance adhesion and durability of ZNW. We coated the CNT/Ag nanowire hybrid electrode by using bar coating system on a capping layer. Power generation of the ZnO NG is measured by using a picoammeter, a oscilloscope and confirmed surface condition with FE-SEM. As a results, the NGs using the CNT/Ag NW hybrid electrode show 75% transparency at wavelength 550 nm and small change of the resistance of the electrode after bending test. It will be discussed the effect of the improved flexibility of top electrode on power generation enhancement of ZnO NGs.

• Journal of Microbiology and Biotechnology
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• v.33 no.1
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• pp.83-95
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• 2023

These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic Escherichia coli, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium, respectively. Evaluation of the primer sets using singleplex PCR, crosscheck PCR and multiplex PCR revealed high specificity and selectivity without interference of primers or genomic DNAs. Subsequent NGS panel analysis with six artificially contaminated food samples using those primer sets showed that all target genes were multi-detected in one reaction at 10⁸-10⁵ CFU of target strains. However, a few false-positive results were shown at 10⁶-10⁵ CFU. To validate this NGS panel analysis, three sets of qPCR analyses were independently performed with the same contaminated food samples, showing the similar specificity and selectivity for detection and identification. While this NGS panel still has some issues for detection and identification of specific foodborne pathogens, it has much more advantages, especially multiple detection and identification in one reaction, and it could be improved by further optimized NGS panel primer sets and even by application of a new real-time NGS sequencing technology. Therefore, this study suggests the efficiency and usability of NGS panel for rapid determination of origin strain in various foodborne outbreaks in one reaction.

• Journal of Marine Life Science
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• v.3 no.2
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• pp.51-58
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• 2018

Variations in water temperature are known to affect almost every part of fish physiology. The rise in water temperature due to climate change can physically damage fish. This study was conducted to evaluate the health status of the Atlantic salmon (Salmo salar) at high water temperature (20℃) than the optimum water temperature (15℃). Liver tissue exerts important metabolic functions in thermal adaptation. Therefore, liver tissue was used in this study. The evaluation method is to develop the biomarker gene using NGS RNAseq analysis and to examine the expression pattern using RT-qPCR analysis. The NGS RNAseq analysis revealed 1,366 differentially expressed genes, among which 880 genes were increase expressed and 486 genes were decrease expressed. The biomarker genes are such as heat shock protein 90 alpha (Hsp90α), heat shock protein 90 beta (Hsp90β) and cytochrome P450 1A (CYP1A). The selected genes are sensitive to changes in water temperature through NGS RNAseq analysis. Expression patterns of these genes through RT-qPCR were similar to those of NGS RNAseq analysis. The results of this study can be applied to other fish species and it is considered to be useful industrially.

• Journal of Animal Environmental Science
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• v.21 no.3
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• pp.93-98
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• 2015

The objective of this study was to review application of next-generation sequencing (NGS) to investigate microbiome in the livestock sector. Since the 16S rRNA gene is used as a phylogenetic marker, unculturable members of microbiome in nature or managed environments have been investigated using the NGS technique based on 16S rRNA genes. However, few NGS studies have been conducted to investigate microbiome in the livestock sector. The 16S rRNA gene sequences obtained from NGS are classified to microbial taxa against the 16S rRNA gene reference database such as RDP, Greengenes and Silva databases. The sequences also are clustered into species-level OTUs at 97% sequence similarity. Microbiome similarity among treatment groups is visualized using principal coordinates analysis, while microbiome shared among treatment groups is visualized using a venn diagram. The use of the NGS technique will contribute to elucidating roles of microbiome in the livestock sector.

• Development and Reproduction
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• v.27 no.1
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• pp.47-56
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• 2023

Despite the commercialization of Next generation sequencing (NGS) gene testing, only a few studies have addressed the various ethical and legal problems associated with NGS testing in Korea Here, we reviewed the normative issues that emerged at each stage of the wet analysis and bioinformatics analysis of NGS gene testing. In particular, it was in mind to apply various international guidelines and the principles of bioethics to actual clinical practice. Considering the characteristics of NGS testing, wet analysis of additional testing can be justified if presumptive consent is recognized. Furthermore, the medical relationship between diseases needs to be established and it should be clear that the patient would have given consent if the patient had been aware of the correlation between genes. At the stage of bioinformatics analysis, the question of unsolicited findings arises. In case of unsolicited and relevant findings, according to American College of Medical Genetics and Genomics (ACMG), a recognized relationship between genes and diseases needs to be established. In case of unsolicited and not-relevant findings, it is almost impossible to determine whether knowing or not knowing the findings is more beneficial to the patient. However, it seems to be certain that the psychological harm an individual may suffer from such information is likely to be greater if the disease is severe and if there is no cure. The list of genes for which the ACMG guidelines impose reporting obligations is a good reference for judgment.

• ALGAE
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• v.31 no.2
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• pp.137-154
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• 2016

Next generation sequencing (NGS) technologies have revolutionized many areas of biological research due to the sharp reduction in costs that has led to the generation of massive amounts of sequence information. Analysis of large genome data sets is however still a challenging task because it often requires significant computer resources and knowledge of bioinformatics. Here, we provide a guide for an uninitiated who wish to analyze high-throughput NGS data. We focus specifically on the analysis of organelle genome and metagenome data and describe the current bioinformatic pipelines suited for this purpose.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.24 no.1
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• pp.1-6
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• 2021

Next-generation sequencing (NGS) technologies have changed the process of genetic diagnosis from a gene-by-gene approach to syndrome-based diagnostic gene panel sequencing (DPS), diagnostic exome sequencing (DES), and diagnostic genome sequencing (DGS). A priori information on the causative genes that might underlie a genetic condition is a prerequisite for genetic diagnosis before conducting clinical NGS tests. Theoretically, DPS, DES, and DGS do not require any information on specific candidate genes. Therefore, clinical NGS tests sometimes detect disease-related pathogenic variants in genes underlying different conditions from the initial diagnosis. These clinical NGS tests are expensive, but they can be a cost-effective approach for the rapid diagnosis of rare disorders with genetic heterogeneity, such as the glycogen storage disease, familial intrahepatic cholestasis, lysosomal storage disease, and primary immunodeficiency. In addition, DES or DGS may find novel genes that that were previously not linked to human diseases.

• Korean Journal of Veterinary Service
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• v.39 no.1
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• pp.41-49
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• 2016

In the present study, fast and robust methods for the next generation sequencing (NGS) were developed for analysis of PRRSV full genome sequences, which is a positive sensed RNA virus with a high degree of genetic variability among isolates. Two strains of PRRSVs (VR2332 and VR2332-R) which have been maintained in our laboratory were used to validate our methods and to compare with the sequence registered in GenBank (GenBank accession no. EF536003). The results suggested that both of strains had 100% coverage with the reference; the VR2332 had the coverage depth from minimum 3 to maximum 23,012, for the VR2332-R from minimum 3 to maximum 41,348, and 22,712 as an average depth. Genomic data produced from the massive sequencing capacities of the NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequence methods which require the knowledge of conserved regions, the NGS allows de novo assembly of the full viral genomes. Therefore, our results suggested that these methods using the NGS massively facilitate the generation of more full genome PRRSV sequences locally as well as nationally in regard of saving time and cost.

• Journal of Advanced Navigation Technology
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• v.13 no.6
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• pp.957-963
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• 2009

It is necessary for the resource management system to manage for the resource in distributed networking environment. Because of increasing the complexity of vast computer system and business environment, needs of RMS is increasing. Based on the common information model to use of objected oriented technology, through analysis of the reference model for the resource management system of the SNIA, we intend to implement the application program to manage the NGS system that consist of SSD and DRAM. To visualize, it is use the GUI Interface. It is possible for application program(Client) to detect and manage the system that consist of the NGS system. Also, status information that is divided into three cataloges(Minor/Major/Critical) can be displayed and it provide support of configuration functionality to manage devices.