• Journal of Plant Biotechnology
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• v.36 no.4
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• pp.384-391
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• 2009

Previously, two events (H15 and B20) of transgenic pepper (Capsicum annuum L.) that enhanced resistance to Cucumber mosaic virus (CMV) by the introduction of CMV coat protein (CP) gene were constructed. Presently, a single copy number of the CP gene was revealed in H15 and B20 by Southern blot. To predict possible unintended effects due to transgene insertion in an endogenous gene, we carried out sequencing of the 5'-flanking region of the CP gene and a Blastbased search. The results revealed that insertion of the transgene into genes encoding putative proteins may occur in the H15 and B20 transgenic event. Mutiplex polymerase chain reaction (PCR) for simultaneous detection and identification of transgenic pepper was conducted with a set of nine primers. Both transgenic event were differentiated from non-transgenic event by the presence of 267 bp and 430 bp PCR products indicative of CP gene specific primer pairs and primer pairs targeting the CP gene and 35S promoter. H15 and B20 uniquely possessed a 390 bp and 596 bp PCR product, respectively. The presence of a 1115 bp product corresponding to intrinsic pepper actin gene confirmed the use of pepper DNA as the PCR template. The primer set and PCR conditions used presently may allow the accurate and simple identification of CMV resistant transgenic pepper.

• Journal of the Institute of Electronics Engineers of Korea SP
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• v.49 no.2
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• pp.113-121
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• 2012

In this paper, we proposed fast and efficient algorithm for detecting near-duplication based on content based retrieval in large scale video database. For handling large amounts of video easily, we split the video into small segment using scene change detection. In case of video services and copyright related business models, it is need to technology that detect near-duplicates, that longer matched video than to search video containing short part or a frame of original. To detect near-duplicate video, we proposed motion distribution and frame descriptor in a video segment. The motion distribution descriptor is constructed by obtaining motion vector from macro blocks during the video decoding process. When matching between descriptors, we use the motion distribution descriptor as filtering to improving matching speed. However, motion distribution has low discriminability. To improve discrimination, we decide to identification using frame descriptor extracted from selected representative frames within a scene segmentation. The proposed algorithm shows high success rate and low false alarm rate. In addition, the matching speed of this descriptor is very fast, we confirm this algorithm can be useful to practical application.

• Tuberculosis and Respiratory Diseases
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• v.72 no.3
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• pp.293-301
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• 2012

Background: Ventilator-associated pneumonia (VAP) requires prompt and appropriate treatment. Since methicillin-resistant Staphylococcus aureus (MRSA) is a frequent pathogen in VAP, rapid identification of it, is pivotal. Our aim was to evaluate the utility of quantitative polymerase chain reaction (qPCR) as a useful method for etiologic diagnoses of MRSA pneumonia. Methods: We performed qPCR for mecA, S. aureus-specific femA-SA, and S. epidermidis-specific femA-SE genes from bronchoalveolar lavage or bronchial washing samples obtained from clinically-suspected VAP. Molecular identification of MRSA was based on the presence of the mecA and femA-SA gene, with the absence of the femA-SE gene. To compensate for the experimental and clinical conditions, we spiked an internal control in the course of DNA extraction. We estimated number of colony-forming units per mL (CFU/mL) of MRSA samples through a standard curve of a serially-diluted reference MRSA strain. We compared the threshold cycle (Ct) value with the microbiologic results of MRSA. Results: We obtained the mecA gene standard curve, which showed the detection limit of the mecA gene to be 100 fg, which corresponds to a copy number of 30. We chose cut-off Ct values of 27.94 (equivalent to $1{\times}10^4$ CFU/mL) and 21.78 (equivalent to $1{\times}10^5$ CFU/mL). The sensitivity and specificity of our assay were 88.9% and 88.9% respectively, when compared with quantitative cultures. Conclusion: Our results were valuable for diagnosing and identifying pathogens involved in VAP. We believe our modified qPCR is an appropriate tool for the rapid diagnosis of clinical pathogens regarding patients in the intensive care unit.

• BMB Reports
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• v.51 no.11
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• pp.584-589
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• 2018

Secondary prevention via earlier detection would afford the greatest chance for a cure in premalignant lesions. We investigated the exomic profiles of non-malignant and malignant changes in head and neck squamous cell carcinoma (HNSCC) and the genomic blueprint of human papillomavirus (HPV)-driven carcinogenesis in oropharyngeal squamous cell carcinoma (OPSCC). Whole-exome (WES) and whole-genome (WGS) sequencing were performed on peripheral blood and adjacent non-tumor and tumor specimens obtained from eight Korean HNSCC patients from 2013 to 2015. Next-generation sequencing yielded an average coverage of $94.3{\times}$ for WES and $35.3{\times}$ for WGS. In comparative genomic analysis of non-tumor and tumor tissue pairs, we were unable to identify common cancer-associated early mutations and copy number alterations (CNA) except in one pair. Interestingly, in this case, we observed that non-tumor tonsillar crypts adjacent to HPV-positive OPSCC appeared normal under a microscope; however, this tissue also showed weak p16 expression. WGS revealed the infection and integration of high-risk type HPV16 in this tissue as well as in the matched tumor. Furthermore, WES identified shared and tumor-specific genomic alterations for this pair. Clonal analysis enabled us to infer the process by which this transitional crypt epithelium (TrCE) evolved into a tumor; this evolution was accompanied by the subsequent accumulation of genomic alterations, including an ERBB3 mutation and large-scale CNAs, such as 3q27-qter amplification and 9p deletion. We suggest that HPV16-driven OPSCC carcinogenesis is a stepwise evolutionary process that is consistent with a multistep carcinogenesis model. Our results highlight the carcinogenic changes driven by HPV16 infection and provide a basis for the secondary prevention of OPSCC.

• Journal of Animal Science and Technology
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• v.46 no.3
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• pp.307-314
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• 2004

Xenotransplantation of porcine organs has the potential to overcome the severe. shortage of human tissues and organs available for human transplantation. The swine represents an ideal source of such organs because of their plentiful supply and their numerous anatomical and physiological similarities to the human. However, this procedure also carries with a number of safety issues relating to the zoonotic infections. Porcine endogenous retrovinJses(PERVs), \Wich are germ line transmitted and persist without symptoms in the pigs, are most concerning zoonotic viroses. In order to analyze the prevalence of PERV in domestic pigs, four kinds of pigs'(Landrace, Berkshire, Yorkshire, and Duroc) genomic DNA were isolated from their hair follicles. PCR analysis was carried out for detection of PERVs using subgroup A/B/C and E pol sequence primers. All pigs (20 heads) tested had high copy number of PERVs within genomes. Subgroup A/B/C and E pol gene sequences from 20 isolates were determined by direct sequencing. Sequence analysis showed pol sequences are highly conserved among intra- and inter-subspecies(99.l and 98.8%, respectively). As a first report of PERV prevalence in Korea pigs, our data would be the basic concepts of PERV transmission study in xenotransplantation.

• Journal of Plant Biotechnology
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• v.34 no.4
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• pp.347-354
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• 2007

Commercialization of genetically modified (GM) plants will be required the assessment of risks associated with the release of GM plants that should include a detailed risk assessment of their impacts in human health and the environment. Prior to GM plant release, applicants should provide the information on GM crops for approval. We carried out this study to provide the molecular data for risk assessment of the GM Chinese cabbage plants with insect-resistance gene, modified CryIAc, which we obtained by Agrobacterium-transformation. From the molecular analysis with GM Chinese cabbage, we confirmed the transgene copy number and stability, the expression of the transgene, and integration region sequences between the transgene and the Chinese cabbage genome. Based on the unique integration DNA sequences, we designed specific primer set to detect GM Chinese cabbage and set up the GM cabbage detection method by qualitative PCR analysis. Qualitative analysis with GM Chinese cabbage progenies analysis was revealed the same as the result of herbicide treatment. Our results provided the molecular data for risk assessment analysis of GM Chinese cabbage and demonstrated that the primer set proposed could be useful to detect GM Chinese cabbage.

• Journal of KIISE:Computing Practices and Letters
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• v.10 no.6
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• pp.484-498
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• 2004

In this paper. we propose a novel performance monitoring scheme for heterogeneous SOAP nodes. The scheme is basically based on two-level (kernel-level and user-level) packet filtering of TCP flows. By TCP flow, we mean a sequence of raw packet streams on a TCP transaction. In this scheme, we detect and extract SOAP operations embedded in SOAP messages from TCP flows. Therefore, it becomes possible to monitor heterogeneous SOAP nodes deployed on diverse SOAP-based middlewares such as .Net and Apache AXIS. We present two implementation mechanisms for the proposed scheme. The first mechanism tries to identify SOAP operations by analyzing all fragmented SOAP messages on TCP flows. However, a naive policy would incur untolerable overhead since it needs to copy all packets from kernel to user space. The second mechanism overcomes this problem by selectively copying packets from kernel to user space. For selective copying, we use a kernel-level packet filtering method that makes use of some representative TCP flags.(e.g. SIN, FIN and PSH). In this mechanism, we can detect SOAP operations only from the last fragment of SOAP messages in most cases. Finally, we implement a SOAP monitoring system using a component ca]led SOAP Sniffer that realizes our proposed scheme, and show experimental results. We strongly believe that our system will play a vital role as a tool for various services such as transaction monitoring and load balancing among heterogeneous SOAP nodes.

• Annals of Laboratory Medicine
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• v.38 no.6
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• pp.555-562
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• 2018

Background: The emerging mobile colistin resistance gene, mcr-1, is an ongoing worldwide concern and an evaluation of clinical isolates harboring this gene is required in Korea. We investigated mcr-1-possessing Enterobacteriaceae among Enterobacteriaceae strains isolated in Korea, and compared the genetic details of the plasmids with those in Escherichia coli isolates from livestock. Methods: Among 9,396 Enterobacteriaceae clinical isolates collected between 2010 and 2015, 1,347 (14.3%) strains were resistant to colistin and those were screened for mcr-1 by PCR. Colistin minimum inhibitory concentrations (MICs) were determined by microdilution, and conjugal transfer of the mcr-1-harboring plasmids was assessed by direct mating. Whole genomes of three mcr-1-positive Enterobacteriaceae clinical isolates and 11 livestock-origin mcr-1-positive E. coli isolates were sequenced. Results: Two E. coli and one Enterobacter aerogenes clinical isolates carried carried IncI2 plasmids harboring mcr-1, which conferred colistin resistance (E. coli MIC, 4 mg/L; E. aerogenes MIC, 32 mg/L). The strains possessed the complete conjugal machinery except for E. aerogenes harboring a truncated prepilin peptidase. The E. coli plasmid transferred more efficiently to E. coli than to Klebsiella pneumoniae or Enterobacter cloacae recipients. Among the three bacterial hosts, the colistin MIC was the highest for E. coli owing to the higher mcr-1-plasmid copy number and mcr-1 expression levels. Ten mcr-1-positive chicken-origin E. coli strains also possessed mcr-1-harboring IncI2 plasmids closely related to that in the clinical E. aerogenes isolate, and the remaining one porcine-origin E. coli possessed an mcr-1-harboring IncX4 plasmid. Conclusions: mcr-1-harboring IncI2 plasmids were identified in clinical Enterobacteriaceae isolates. These plasmids were closely associated with those in chicken-origin E. coli strains in Korea, supporting the concept of mcr-1 dissemination between humans and livestock.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.3
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• pp.320-333
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• 2019

Objective: The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases due to the hot weather and long-term humidity in Shanghai, which is the main distribution centre for providing Holstein semen to various farms throughout China. Our objective was to determine the genetic mechanisms influencing economically important traits, especially diseases that have huge impact on the yield and quality of milk as well as reproduction. Methods: In our study, we detected the structural variations of 1,092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify copy-number variants (CNVs). Furthermore, we annotated these structural variations using different bioinformatics tools, such as gene ontology, cattle quantitative trait locus (QTL) database and ingenuity pathway analysis (IPA). Results: The average number of high-quality reads was 3,046,279. After filtering, a total of 16,831 deletions, 12,735 insertions and 490 CNVs were identified. The annotation results showed that these mapped genes were significantly enriched for specific biological functions, such as disease and reproduction. In addition, the enrichment results based on the cattle QTL database showed that the number of variants related to milk and reproduction was higher than the number of variants related to other traits. IPA core analysis found that the structural variations were related to reproduction, lipid metabolism, and inflammation. According to the functional analysis, structural variations were important factors affecting the variation of different traits in Shanghai Holstein cattle. Our results provide meaningful information about structural variations, which may be useful in future assessments of the associations between variations and important phenotypes in Shanghai Holstein cattle. Conclusion: Structural variations identified in this study were extremely different from those of previous studies. Many structural variations were found to be associated with mastitis and reproductive system diseases; these results are in accordance with the characteristics of the environment that Shanghai Holstein cattle experience.

• Journal of the Korea Society of Computer and Information
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• v.26 no.6
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• pp.73-80
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• 2021

In this paper, we propose a packet processing method capable of handling large-capacity traffic over 20Gbps using multi-core and huge page memory approaches. As ICT technology advances, the global average monthly traffic is expected to reach 396 exabytes by 2022. With the increase in network traffic, cyber threats are also increasing, increasing the importance of traffic analysis. Traffic analyzed as an existing high-cost foreign product simply stores statistical data and visually shows it. Network administrators introduce and analyze many traffic analysis systems to analyze traffic in various sections, but they cannot check the aggregated traffic of the entire network. In addition, since most of the existing equipment is of the 10Gbps class, it cannot handle the increasing traffic every year at a fast speed. In this paper, as a method of processing large-capacity traffic over 20Gbps, the process of processing raw packets without copying from single-core and basic SMA memory approaches to high-performance packet reception, packet detection, and statistics using multi-core and NUMA memory approaches suggest When using the proposed method, it was confirmed that more than 50% of the traffic was processed compared to the existing equipment.