• Journal of Animal Science and Technology
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• v.50 no.6
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• pp.753-762
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• 2008

The primers for RT-PCR and RACE-PCR were designed by aligning the pig genomic sequence and the human complement factor B(CFB) coding sequence(CDS) from the GenBank. Each PCR product was amplified in pig cDNA and sequencing was carried out. The CDS length of pig CFB gene was determined to be 2298 bp. In addition, the pig CDS was more longer than human and mouse orthologs because of insertion and deletion. The identities of porcine nucleotide sequences with those of human and mice were 84% and 80%, and the identities of amino acids were 79% to 77%, respectively. Three complement control protein(CCP) domains, one Von Willebrand factor A(VWFA) domain and a serine protease domain, that are revealed typically in mammals, were found in the pig CFB gene. Based on the CDSs determined, the primers were designed in intron regions for amplification of entire length of exons. In amplification and direct sequencing with genomic DNAs of six pig breeds, three cSNPs(coding single nucleotide polymorphisms) were identified and verified as missense mutations. Using the Multiplex-ARMS method, we genotyped and verified the mutations identified from direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS with two randomly selected DNA samples. The genotype of each sample exhibited the same results using both methods. Therefore, three cSNPs were identified from pig CFB gene and that can be used for haplotype analysis of the swine leukocyte antigen(SLA) class III region. Moreover, the results indicate that the Multiplex-ARMS method should be powerful for genotyping of genes in the SLA region.

• Journal of Animal Science and Technology
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• v.49 no.5
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• pp.549-558
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• 2007

C4B and BAT2, assigned to the SLA class III region, were recently reported on relation with human diseases. The primers for RT-PCR and RACE-PCR for CDS analysis of these genes of pig were designed by aligning the CDSs of humans and mice from GenBank. After we amplified and sequenced with these primers and cDNAs, the full-length CDSs of pig were determined. The CDS lengths of C4B and BAT2 were shown as 5226 bp and 6501 bp. In addition, the identities of nucleotide sequences with human and mouse were 76% to 87%, and the identities of amino acids were 72% to 90%. After we carried out the alignment with determined CDSs in this study and pig genomic sequences from GenBank, the primers for cSNP detection in genome were designed in intron regions that flanked one or more exons. Then, we amplified and directly sequenced with genomic DNAs of six pig breeds. Four cSNPs from C4B and three 3 cSNPs from BAT2 were identified. In addition, amino acid substitution occurred in six cSNP positions except for C4248T of C4B. By the Multiplex-ARMS method, we genotyped seven cSNPs with DNA samples used for direct sequencing. We verified that this result was the same as that analyzed using direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS on two randomly selected DNA samples. The genotype of each sample showed the same result from both methods. Therefore, seven cSNPs were identified from C4B and BAT2 and could be used as the basic data for haplotype analysis of SLA class III region. Moreover, the Multiplex-ARMS method should be powerful for genotyping of genes assigned to the whole SLA region for the xenograft study.

• Pediatric Infection and Vaccine
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• v.23 no.2
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• pp.87-93
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• 2016

Purpose: An outbreak of influenza virus is uncommon in neonatal intensive care unit (NICU). The clinical presentation of influenza virus infection in neonates is diverse. This study was aimed to report an outbreak of influenza A in a NICU and to investigate the clinical characteristics of influenza virus infection in neonates especially preterm infants during the 2011-2012 influenza season in Korea. Methods: We reviewed the medical records of 29 patients who were evaluated by respiratory virus multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) at NICU of Kosin University Gospel Hospital during the 2011-2012 seasonal influenza outbreak in Korea. Results: Eleven patients (37.9%) were influenza A virus RT-PCR positive during the survey periods. They were all preterm infants and three of them had no symptoms. Eight patients had symptoms and it was fever (18%, 2/11), respiratory difficulty (72.7%, 8/11) without symptoms of upper respiratory infection, and gastrointestinal symptoms (27.3%, 3/11). The median duration of symptom was 5 days. There were differences of duration of admission at the test of respiratory RT-PCR, Clinical Risk Index for Babies (CRIB) score, use of mechanical ventilation, and use of dexamethasone before infection between influenza A virus RT-PCR positive and negative group. All 11 patients with influenza A were discharged without any complications. Conclusions: The symptoms of influenza A virus infection in the preterm infants is nonspecific. Influenza A virus should be considered as a possible cause of infection in NICU during the influenza season in the community.

• Journal of Preventive Medicine and Public Health
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• v.48 no.1
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• pp.10-17
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• 2015

Objectives: An outbreak of acute febrile illness occurred in the Republic of Korea Air Force boot camp from May to July 2011. An epidemiological investigation of the causative agent, which was of a highly infective nature, was conducted. Methods: Throat swabs were carried out and a multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) assay was performed to identify possible causative factors. Results: The mean age of patients who had febrile illness during the study period was 20.24 years. The multiplex RT-PCR assay identified respiratory syncytial virus (RSV) as the causative agent. The main symptoms were sore throat (76.0%), sputum (72.8%), cough (72.1%), tonsillar hypertrophy (67.9%), and rhinorrhea (55.9%). The mean temperature was $38.75^{\circ}C$ and the attack rate among the recruits was 15.7% (588 out of 3750 recruits), while the mean duration of fever was 2.3 days. The prognosis was generally favorable with supportive care but recurrent fever occurred in 10.1% of the patients within a month. Conclusions: This is the first epidemiological study of an RSV outbreak that developed in a healthy young adult group. In the event of an outbreak of an acute febrile illness of a highly infective nature in facilities used by a young adult group, RSV should be considered among the possible causative agents.

• Neonatal Medicine
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• v.16 no.2
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• pp.182-189
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• 2009

Purpose: Recently, it is easy to find the causal virus of acute respiratory infections using multiplex RT-PCR. The aim of this study is to show the distribution of respiratory viruses and to define the characteristics of respiratory syncytial virus (RSV) infections compared to other respiratory viral infections. Methods: This was a prospective observational study conducted in the NICU. The infants with acute respiratory infections were performed multiplex RT-PCR using nasal swabs. The demographics, initial symptoms, course of illness, and laboratory and imaging findings were recorded. The infants were divided into RSV and No RSV groups. Results: Twenty-three infants (50%) were in the RSV group. Rhinovirus was the second most common virus. Coinfections with two viruses accounted for 6.5% of respiratory infections. The number of preterm infants, exposure to cigarette smoke and having siblings were not different between the two groups. Infections in the postnatal care center were more common in the RSV group than the No RSV group (60.9% vs. 21.7%, P=.007). Dyspnea (34.8% vs. 8.7%, P=.032) and pneumonia (73.9% vs. 43.5%, P=.036) were more common in the RSV group. The RSV group frequently needed oxygen (52.5% vs. 13.0%, P=.005) and received nothing by mouth (43.5% vs. 13.0%, P=.022). The incidence of right upper consolidation was higher in RSV group (56.5% vs. 8.7%, P=.001). Conclusion: This study showed that other viruses than RSV can induce respiratory infections in neonates and young infants born prematurely. RSV infections have a more severe course of illness than other respiratory viruses. We have to be careful of prevention even for healthy neonates especially in crowed situations, such as the postnatal care center.

• Biomolecules & Therapeutics
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• v.16 no.3
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• pp.184-189
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• 2008

The proto-oncogene protein DEK has been implicated in various human disease including cancer. We have shown that DEK induces caspase-dependent apoptosis in Drosophila by regulating histone acetylation. Reverse transcription-polymerase chain reaction (RT-PCR) method based on annealing control primers was used to screen and identify differentially expressed genes (DEGs) in DEK overexpressed HeLa cells. Among the genes identified, clusterin and fibrillarin have major role in apoptosis pathway regulation. TFIIIC and RPS24 are implicated in HAT mediated transcriptional initiation and cololectal cancer, respectively. To further analyze DEK's role in apoptosis, multiplex PCR was performed. Caspase-3, -7, and -10 and proapoptotic gene bid were newly identified as possible target genes regulated by DEK expression.

• Proceedings of the Korean Society of Veterinary Pathology Conference
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• 2002.11a
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• pp.142-142
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• 2002

돼지의 주요 장염 유발 바이러스인 돼지 전염성 위장염 바이러스 (transmissible gastroenteritis virus; TGEV), 돼지 유행성 설사증 바이러스 (porcine epidemic diarrhea virus; PEDV), 돼지 칼리시 바이러스 (porcine enteric calicivirus; PECV), 돼지 로타바이러스 A 형과 C 형 (porcine rotavirus; PRY, group A and C)을 동시에 감별 진단 할 수 있는 신속하고 정확한 oligonucleotide microarray 진단법을 개발하였다. 이 진단법은 유리슬라이드에 각각의 바이러스에 특이적인 부위에서 제작된 oligonucleotide probe를 찍은 DNA chip을 제작하여 여기에 각각의 바이러스를 역전사하고 cy5-dCTP를 포함한 multiplex PCR을 수행한 다음 hybridization 하였다. 이후 hybridization 결과는 fluorescence scanner를 이용하여 확인하였다. 이 새로운 microarray system은 RT-PCR과 같은 기존의 진단방법보다 소량의 바이러스를 민감하게 검사할 수 있을 뿐 아니라 hybridization을 통해 검사결과의 정확성을 확인할 수 있었다. 따라서 본 연구에서 개발한 microarray system은 돼지의 설사 유발 바이러스를 진단하는데 매우 유용한 진단 방법임을 확인하였다.

• Journal of Digital Convergence
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• v.18 no.12
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• pp.425-434
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• 2020

Background: Viral infection outbreaks are emerging public health concerns. They often exhibit seasonal patterns that could be predicted by the application of big data and bioinformatic analyses. Purpose: The purpose of this study was to identify trends in diarrhea-causing viruses such as rotavirus (Gr.A), norovirus G-I, and norovirus G-II in Cheonan, Korea. The identified related factors of diarrhea-causing viruses may be used to predict their trend and prevent their infections. Method: A retrospective analysis of 4,009 fecal samples from June 2010 to December 2019 was carried out at Dankook University Hospital in Cheonan. Reverse transcription-PCR (RT-PCR) was employed to identify virus strains. Information about seasonal patterns of infection was extracted and compared with local weather data. Results: Out of the 4,009 fecal samples tested using multiplex RT-PCR (mRT-PCR), 985 were positive for infection with Gr.A, G-I, and G-II. Out of these 985 cases, 95.3% (n = 939) were under 10 years of age. Gr.A, G-I, and G-II showed high infection rates in patients under 10 years of age. Student's t-test showed a significant correlation between the detection rate of Gr.A and the relative humidity. The detection rate of G-II significantly correlated with wind-chill temperature. Conclusion: Climate factors differentially modulate rotavirus and norovirus infection patterns. These observations provide novel insights into the seasonal impact on the pathogenesis of Gr.A, G-I, and G-II.

• The Plant Pathology Journal
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• v.40 no.1
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• pp.40-47
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• 2024

Garlic can be infected by a variety of viruses, but mixed infections with leek yellow stripe virus, onion yellow dwarf virus, and allexiviruses are the most damaging, so an easy, inexpensive on-site method to simultaneously detect at least these three viruses with a certain degree of accuracy is needed to produce virus-free plants. The most common laboratory method for diagnosis is multiplex reverse transcription polymerase chain reaction (RT-PCR). However, allexiviruses are highly diverse even within the same species, making it difficult to design universal PCR primers for all garlic-growing regions in the world. To solve this problem, we developed an inexpensive on-site detection system for the three garlic viruses that uses a commercial mobile PCR device and a compact electrophoresis system with a blue light. In this system, virus-specific bands generated by electrophoresis can be identified by eye in real time because the PCR products are labeled with a fluorescent dye, FITC. Because the electrophoresis step might eventually be replaced with a lateral flow assay (LFA), we also demonstrated that a uniplex LFA can be used for virus detection; however, multiplexing and a significant cost reduction are needed before it can be used for on-site detection.

• Korean Journal of Food Science and Technology
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• v.53 no.1
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• pp.1-11
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• 2021

In this review, recent foodborne outbreaks caused by viruses in the Republic of Korea (2010-2019) were analyzed. The human norovirus was found to be the major foodborne virus causing an average of 94.9% of the viral outbreaks. Reverse-transcription polymerase chain reaction (PCR) with electrophoresis has been widely used to detect viruses, but several rapid detection methods, including real-time PCR, multiplex PCR, and quantum dot assay, have also been suggested. For norovirus inactivation studies, surrogates such as murine norovirus and feline calicivirus have been widely used to identify the reduction rate owing to the limitations in laboratory cultivation. Conversely, direct cell infection studies have been conducted for other foodborne viruses such as adenovirus, astrovirus, rotavirus, and hepatitis A or E virus. Moreover, virucidal mechanisms using various physical and chemical treatments have been revealed. These recent studies suggest that rapid in situ detection and effective control are valuable for ensuring food safety against viral infections.