• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• 제37권5호
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• pp.396-402
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• 2011

Introduction: Epidermal growth factor is a single-chain polypeptide consisting of 53 amino acids with potent mitogenic activity that stimulates the proliferation of a range of normal and neoplastic cells through an interaction with its specific receptor (epidermal growth factor receptor, EGFR). This interaction plays a key role in tumor progression including the induction of tumor cell proliferation. An increased EGFR copy number have been associated with a favorable response to EGFR tyrosine kinase inhibitors therapy. In contrast, K-ras mutations tend to predict a poor response to such therapy. The aim of this study was to determine the correlation between the clinicopathological factors and the up-regulation of EGFR expression and Kras mutations in oral squamous cell carcinoma. Materials and Methods: This study examined the immunohistochemical staining of EGFR, K-ras mutation detection with peptide nucleic acid (PNA)-based real-time polymerase chain reaction (PCR) clamping in 20 specimens from 20 patients with oral squamous cell carcinoma. Results: 1. In the immunohistochemical study of poorly differentiated and invasive oral squamous cell carcinoma, a high level of EGFR staining was observed. The correlation between immunohistochemical EGFR expression and histological differentiation, as well as the tumor size of the specimens was significant (Pearson correlation analysis, significance [r] >0.5, P<0.05). 2. In PNA-based real-time PCR clamping analysis, a K-ras mutation was not detected in all specimens. Conclusion: These findings suggest that the up-regulation of the EGFR may play a role in the progression and invasion of oral squamous cell carcinoma that is, independent of a K-ras mutation.

• 대한본초학회지
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• 제39권3호
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• pp.37-47
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• 2024

Objectives : Because predicting the potential efficacy and mechanisms of Korean medicines is challenging due to their high complexity, employing an approach based on network pharmacology could be effective. In this study, network pharmacological analysis was utilized to anticipate the effects of YunPye-Hwan (YPH) in treating Chronic obstructive pulmonary disease (COPD). Methods : Compounds and their related target genes of YPH were gathered from the TCMSP and PubChem databases. These target genes of YPH were subsequently compared with gene sets associated with COPD to assess correlation. Next, core genes were identified through a two-step screening process, and finally, functional enrichment analysis of these core genes was conducted using both Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Results : A total of 15 compounds and 437 target genes were gathered, resulting in a network comprising 473 nodes and 14,137 edges. Among them, 276 genes overlapped with gene sets associated with COPD, indicating a significant correlation between YPH and COPD. Functional enrichment analysis of the 18 core genes revealed biological processes and pathways such as "miRNA Transcription," "Nucleic Acid-Templated Transcription," "DNA-binding Transcription Factor Activity," "MAPK signaling pathway," and "TNF signaling pathway" were implicated. Conclusion : YPH exhibited significant relevance to COPD by modulating cell proliferation, differentiation, inflammation, and cell death pathways. This study could serve as a foundational framework for further research investigating the potential use of YPH in the treatment of COPD.

• Journal of Microbiology and Biotechnology
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• 제27권4호
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• pp.838-843
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• 2017

Sepsis is a major health problem worldwide, with an extremely high rate of morbidity and mortality, partly due to delayed diagnosis during early disease. Currently, sepsis diagnosis requires bacterial culturing of blood samples over several days, whereas PCR-based molecular diagnosis methods are faster but lack sensitivity. The use of biosensors containing nucleic acid aptamers that bind targets with high affinity and specificity could accelerate sepsis diagnosis. Previously, we used the systematic evolution of ligands by exponential enrichment technique to develop the aptamers Antibac1 and Antibac2, targeting the ubiquitous bacterial peptidoglycan. Here, we show that these aptamers bind to four gram-positive and seven gram-negative bacterial sepsis agents with high binding efficiency. Thus, these aptamers could be used in combination as biological recognition elements in the development of biosensors that are an alternative to rapid bacteria detection, since they could provide culture and amplification-free tests for rapid clinical sepsis diagnosis.

• Asian Pacific Journal of Cancer Prevention
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• 제16권17호
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• pp.7997-8002
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• 2015

Gene amplification is an important mechanism in the development and progression of cancer. Currently, gene amplification status is generally determined by in situ hybridization (ISH). Multiplex ligation-dependent probe amplification (MLPA) is a PCR-based method that allows copy number detection of up to 50 nucleic acid sequences in one reaction. The aim of the present study was to compare results for HER2, CCND1, MYC and ESR1 gene amplification detected by MLPA with fluorescent in situ hybridization (FISH) and chromogenic in situ hybridization (CISH) as clinically approved methods. Tissue samples of 170 invasive breast cancers were collected. All were ER positive. Tissue samples had previously been tested for HER2 using immunohistochemistry. Amplification of the selected genes were assessed using MLPA, FISH and CISH and results were compared. HER2 MLPA and ISH results were also compared with HER2 immunohistochemistry (IHC) which detects protein overexpression. Amplification of HER2, CCND1, MYC and ESR1 by MLPA were found in 9%, 19%, 20% and 2% of samples, respectively. Amplification of HER2, CCND1, MYC and ESR1 by FISH was noted in 7%, 16%, 16% and 1% of samples, respectively. A high level of concordance was found between MLPA/FISH (HER2: 88%, CCND1: 88%, MYC: 86%, ESR1: 92%) and MLPA/CISH (HER2: 84%). Of all IHC 3+ cases, 91% were amplified by MLPA. In IHC 2+ group, 31% were MLPA amplified. In IHC 1+ group, 2% were MLPA amplified. None of the IHC 0 cases were amplified by MLPA. Our results indicate that there is a good correlation between MLPA, IHC and ISH results. Therefore, MLPA can serve as an alternative to ISH for detection of gene amplification.

• 한국산학기술학회논문지
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• 제18권10호
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• pp.551-558
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• 2017

조직특이적 프로모터 및 벡터를 연구하고 검증하기 위해서는 조직 및 종의 특이성을 유지하는 세포 시스템을 개발하는 것이 바람직하다. 이러한 시스템은 형질전환동물 모델에 대한 효과적인 대안이다. 우리는 베타 카제인 (CSN2)의 세포 형태와 mRNA 수준에 기초하여 일차 배양으로부터 돼지 유선 상피 세포 주 (PMECs)를 확립하였다. 선택된 PMECs는 cytokeratin 항체에 의해 염색되었으며, 유선 상피 세포에 존재한다고 생각되어지는 유즙 단백질 유전자 (CSN2, 락토페린 및 유청 단백질)를 발현하는 것으로 나타났다. 또한, 3D 배양에서 PMECs932-7의 acini 구조를 확인하기 위해 살아있는 세포를 핵산에 결합하는 SYTO-13으로 염색하였다. 우리는 마트리겔 (matrigel)에 있는 PMECs의 acini가 말초 세포의 응집에 의해 형성되고 공간의 lumen을 특징으로 한다는 것이 관찰하였다. 우리는 PMECs의 matrigel 사용법과 세포 밀도를 포함한 세포 배양 조건의 영향을 시험함으로서 시스템을 시연했다. 이러한 결과는 PMCEs의 유선 상피 세포는 유전적 또는 구조적 특징을 갖고 있음을 시사하고 있다.

• Fisheries and Aquatic Sciences
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• 제9권1호
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• pp.7-13
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• 2006

Using biochemical methods, we determined the potential of local female shrimp populations as breeding stock to select the best adult prawns for improving larval production. As condition indexes, we selected total RNA, DNA, their ratio, and trypsin activity. The DNA content in the pleopods of each local population was similar, i.e., between $0.90{\pm}0.06\;and\;1.02{\pm}0.04(SE){\mu}g/mg$. In comparison, the RNA contents differed markedly between $2.00{\pm}0.09$ and $0.96{\pm}0.08\;{\mu}g/mg$. Therefore, the RNA/DNA (R/D) ratio in the pleopod could be used as a condition index because it represents a biochemical characteristic of the population. The mean pleopodal R/D ratio of the Goheung population was the highest at $2.52{\pm}0.19$, which indicated the best condition. Trypsin activity was influenced little by shrimp condition and more by the amount of food ingested. The gonadosomatic index (GSI) and R/D ratio in the gonads provided offsetting information about the instantaneous gonad maturity. The Goheung population had the highest instantaneous GSI, despite some spawning. Based on the condition indexes and time of gonad maturation, the Goheung shrimp population is suitable for use as breeding stock.

• 한국군사과학기술학회지
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• 제27권4호
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• pp.507-515
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• 2024

Microbial forensics is a scientific discipline for analyzing evidence related to biological crimes by identifying the origin of microorganisms. Multiple locus variable number tandem repeat analysis(MLVA) is one of the microbiological analysis methods used to specify subtypes within a species based on the number of tandem repeat in the genome, and advances in next generation sequencing(NGS) technology have enabled in silico anlysis of full-length whole genome sequences. In this paper, we analyzed unknown samples provided by Robert Koch Institute(RKI) through The United Nations Secretary-General's Mechanism(UNSGM)'s external quality assessment exercise(EQAE) project, which we officially participated in 2023. We confirmed that the 3 unknown samples were B. anthracis through nucleic acid isolation and genetic sequence analysis studies. MLVA results on 32 loci of B. anthracis were analysed by using genome sequences obtained from NGS(NextSeq and MinION) and Sanger sequencing. The MLVA typing using short-reads based NGS platform(NextSeq) showed a high probability of causing assembly error when a size of the tandem repeats was grater than 200 bp, while long-reads based NGS platform(MinION) showed higher accuracy than NextSeq, although insertion and deletion was observed. We also showed hybrid assembly can correct most indel error caused by MinION. Based on the MLVA results, genetic identification was performed compared to the 2,975 published MLVA databases of B. anthracis, and MLVA results of 10 strains were identical with 3 unkonwn samples. As a result of whole genome alignment of the 10 strains and 3 unknown samples, all samples were identified as B. anthracis strain A4564 which is associated with injectional anthrax isolates in heroin users.

• Tuberculosis and Respiratory Diseases
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• 제47권6호
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• pp.747-756
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• 1999

연구배경: 폐결핵을 확진하는 방법은 결핵균의 증명이며 결핵균 동정을 하는 고전적인 방법인 항산균 도말 검사와 결핵균 배양 검사에 대해 상호 보완적으로 폐결핵의 보다 신속한 진단을 하는데 있어서 MTD의 유용성을 알아보고자 하였다. 방 법: 1997년 11월부터 1998년 5월까지 부산대학교 병원에 내원하여 폐결핵이 의심된 187명의 환자로부터 얻은 호흡기검체 267건(객담 187건, 기관지 세척액 94건)에 대해 각각 항산균 도말, 결핵균 배양 검사, MTD를 시행한 결과를 임상 소견과 연관지어 비교 분석하였다. 결 과: 1) 객담 검체에서 항산균 도말 검사, 결핵균 배양 결과와 비교하였을 때 항산균 도말 양성인 경우 결핵균 배양 검사와 비교한 MTD의 민감도는 75.6%, 도말 음성인 경우 결핵균 배양 검사와 비교한 MTD의 민감도는 61.9%, 특이도는 85.6%였다. 2) 기관지 세척액에서 항산균 도말 검사, 결핵균 배양 결과와 비교하였을 때 항산균 도말 양성인 경우 결핵균 배양 검사와 비교한 MTD의 민감도는 89.5%, 특이도는 28.6%, 도말 음성인 경우 결핵균 배양 검사와 비교한 MTD의 민감도는 89.5%, 특이도는 67.3%였다. 3) 객담과 기관지 세척액을 합한 경우 항산균 도말검사, 결핵균 배양 결과와 비교하였을 때 항산균 도말 양성인 경우에서 결핵균 배양 검사와 비교한 MTD의 민감도는 79.7%, 특이도는 20.0%를 보였으며, 항산균 도말 음성인 경우 결핵균 배양 검 사와 비교한 MTD의 민감도는 75.0%, 특이도는 80.3%를 보였다. 4) 결핵균 배양 결과와 비하여 MTD의 결과가 일치하지 않는 경우 MTD의 민감도는 67.5%, 특이도는 84.3%였으나 불일치 해결후에 MTD의 민감도는 79.2%, 특이 도는 84.4%를 보여 향상된 결과를 보였다. 5) 항산균 도말 음성, 결핵균 배양 음성이며 MTD만 양성인 31예에서 임상 경과 추적 및 항결핵제 치료 반응 웅의 분석에서 14예에서만 최종 폐결핵으로 진단되었으며 이 경우 MTD의 민감도는 45.2%였으며 진성 양성을 확인할 수 있었다. 6) 항산균 도말 음성, MTD 음성에서 mycobacterium species로 자란 13 건의 검체에서 Mycobacterium tuberculosis와 nontuberculous mycobacteria를 분리하기 위해 accuprobe M.tuberculosis complex culture kit를 이용하여 11건에서 M.tuberculosis로 배양되었으며 2건(17.3%)에서 비결핵 항산균이 배양되었다. 결 론: 이상의 결과로 볼 때 MTD는 빠르고 정확한 결핵균 진단에 유용한 것으로 생각되며, 폐결핵 진단에 있어서 MTD는 항산균 도말 검사 및 배양 검사와 병행함으로써 유용성이 높으며, 고전적인 진단 방법을 대체하기 보다는 상호 보완적인 방법으로 판단된다.

• 대한수혈학회지
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• 제29권3호
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• pp.310-319
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• 2018

배경: 최근 차세대염기서열분석법(Next Generation Sequencing: NGS)을 이용한 HLA 형별 분석에 대한 연구가 활발히 진행되고 있다. 이에 HLA 고해상도 분석법의 내재적 한계인 위상 모호성의 문제를 해결하고, 대량 검체 처리가 가능한 NGS 기반 고해상도 HLA 형별 검사법을, 자체 기술로 개발하고자 본 연구를 실시하였다. 방법: HLA NGS를 위한 핵산 추출 조건, 라이브러리 제작 및 PCR 체계 확립, 그리고 생물정보학을 이용한 HLA 형별 분석법을 개발하였다. 본 기관에서 개발한 NGS 기반 HLA 형별 검사의 정확성을 알아보기 위해 SSOP법으로 HLA 형별을 알고 있는 192개 검체와 SBT법으로 HLA 형별을 알고 있는 28개 검체에 대해 NGS 기반으로 검사한 HLA-A, -B 그리고 -DR 형별 결과를 비교해 보았다. 결과: 두 단계의 PCR을 통한 DNA 라이브러리 제작과 MiSeq (Illumina Inc., San Diego, USA) 기기를 이용한 NGS 시퀸싱 그리고 데이터 분석 시스템을 구축하였다. 기존에 HLA 형별을 알고 있는 220개 혈액 검체에 대해 NGS 기반 HLA 형별검사 결과가 모두 일치함을 확인하였다. 결론: NSG 기반 HLA 형별 검사법은 많은 검체를 효율적인 시간 내에 처리가 가능하여 조혈모세포기증 희망자 HLA 검사 등에 유용할 것으로 기대된다.

• 한국식품영양학회지
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• 제17권3호
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• pp.254-259
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• 2004

Primer 20가지로 Listeria spp.에 대해 screening을 하여 병원균인 L. monocytogenes를 구별하게 하는 RAPD-PCR의 band pattern을 나타내는 10-mer random primer가 OPG-13이 라는 것을 알았다. OPG-13은 GC%가 70%이므로 계산상으로는 annealing 온도가 34$^{\circ}C$이다. 32～36$^{\circ}C$까지 다섯 가지의 온도로 annealing한 결과 L. monocytogenes만이 갖는 특정한 크기의 band가 역시 34$^{\circ}C$에서 형성됨을 알아냈고, 34$^{\circ}C$를 annealing 온도로 정하였다. Line 1부터 4까지 1. monocytogenes ATCC15313, 19111, 19112, 19113은 2개의 700 bp와 1500 bp band를 형성하였고 그 밖의 Listeria spp.들 Line 6부터 11까지 L. ivanovii ATCC 19119, L. grayi ATCC19120, L. murrayi ATCC25401, L. innocua ATCC33090, L. welshimeri ATCC35897, L. seeligeri ATCC35967은 약 2,000 ～ 2,300 bp크기 한 개의 band를 보여 병원성 균과 비병원성 균이 매우 확실하게 구분되는 band pattern이 나타나는 이러한 결과로 10-mer random primer인 OPG-13을 이용한 RAPD-PCR 방법이 병윈균인 L. monocytogenes를 검색하는데 이용될 수 있음을 확인할 수 있었다.