• Journal of Microbiology and Biotechnology
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• 제31권12호
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• pp.1672-1683
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• 2021

Vibrio parahaemolyticus is recognized as one of the most important foodborne pathogens responsible for gastroenteritis in humans. The bla_CARB-17 gene is an intrinsic β-lactamase gene and a novel species-specific genetic marker of V. parahaemolyticus. In this study, a loop-mediated isothermal amplification (LAMP) assay combined with a lateral flow dipstick (LFD) was developed targeting this bla_CARB-17 gene. The specificity of LAMP-LFD was ascertained by detecting V. parahaemolyticus ATCC 17802 and seven other non-V. parahaemolyticus strains. Finally, the practicability of LAMP-LFD was confirmed by detection with V. parahaemolyticus-contaminated samples and natural food samples. The results showed that the optimized reaction parameters of LAMP are as follows: 2.4 mmol/l Mg²⁺, 0.96 mmol/l dNTPs, 4.8 U Bst DNA polymerase, and an 8:1 ratio of inner primer to outer primer, at 63℃ for 40 min. The optimized reaction time of the LFD assay is 60 min. Cross-reactivity analysis with the seven non-V. parahaemolyticus strains showed that LAMP-LFD was exclusively specific for V. parahaemolyticus. The detection limit of LAMP-LFD for V. parahaemolyticus genomic DNA was 2.1 × 10^-4 ng/μl, corresponding to 630 fg/reaction and displaying a sensitivity that is 100-fold higher than that of conventional PCR. LAMP-LFD in a spiking study revealed a detection limit of approximately 6 CFU/ml, which was similar with conventional PCR. The developed LAMP-LFD specifically identified the 10 V. parahaemolyticus isolates from 30 seafood samples, suggesting that this LAMP-LFD may be a suitable diagnostic method for detecting V. parahaemolyticus in aquatic foods.

• Journal of Gastric Cancer
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• 제12권2호
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• pp.73-80
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• 2012

Purpose: The specific aim of this study is to unravel a DNA copy number alterations, and to search for novel genes that are associated with the development of Korean gastric cancer. Materials and Methods: We investigated a DNA copy number changes in 23 gastric adenocarcinomas by array-comparative genomic hybridization and quantitative real-time polymerase chain reaction analyses. Besides, the expression of UQCRFS1, which shows amplification in array-CGH, was examined in 186 gastric cancer tissues by an immunohistochemistry, and in 9 gastric cancer cell lines, as well as 24 gastric cancer tissues by immunoblotting. Results: We found common gains at 48 different loci, and a common loss at 19 different loci. Amplification of UQCRFS1 gene at 19q12 was found in 5 (21.7%) of the 23 gastric cancers in an array-comparative genomic hybridization and DNA copy number were increased in 5 (20.0%) out of the 25 gastric cancer in quantitative real-time polymerase chain reaction. In immunohistochemistry, the overexpression of the protein was detected in 105 (56.5%) out of the 186 gastric cancer tissues. Statistically, there was no significant relationship between the overexpression of UQCRFS1 and clinicopathologic parameters (P>0.05). In parallel, the overexpression of UQCRFS1 protein was confirmed in 6 (66.7%) of the 9 gastric cancer cell lines, and 12 (50.0%) of the 24 gastric cancer tissues by immunoblotting. Conclusions: These results suggest that the overexpression of UQCRFS1 gene may contribute to the development and/or progression of gastric cancer, and further supported that mitochondrial change may serve as a potential cancer biomarker.

• Journal of Plant Biotechnology
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• 제33권1호
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• pp.19-25
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• 2006

저온저항성 BN115 gene과 표지유전자로서 kanamycin에 저항성 있는 nptII gene을 가지고 있는 식물발현용 binary vector pBin19/BNl15가 도입된 A. tumefacience MP90을 국화잎과 공동배양 하였다. 또한 particle bombardment를 이용하여 목적으로 하는 유전자가 식물체에 안정적으로 도입되어 발현됨을 PCR 및 Real-Time PCR 검정으로 확인하였다. 국화잎과 공동배양에 사용된 Agrobacterium은 $5.0{\times}1.0{\mu}m$로 non-sporing, motile, rod 형이며, Callus는 pin이나 cork-borer에 의해 상처 난 잎 가장자리로부터 형성되어 식물체가 재분화 되었다. 유전자 도입조건은 Agrobacterium을$O.D._{600}{\approx}0.5$에서 20분간 공동배양 할 때, Particle bombardment는 helium 압력을 1,100 psi, target 거리를 9 cm로 유지했을 때, 가장 효율이 높았다. 5mg/L kanamycin이 들어 있는 배지에서 선발된 형질전환체는 PCR 분석으로 형질전환여부를 판별할 수 있었으며, 선발 10개체 중 9개체에서 purified pBN115와 같은 크기의 밴드가 형성되었다. Taq-Man probe를 이용한 Real-Time PCR 결과 $45{\sim}0.00045ng/{\mu}{\ell}$ 범위에서 pBN115 gene을 10배씩 serial dilution한 amplification plot는 일정한 간격으로 standard curve를 보였으며, slope는 -3.313975, R2는 0.998319이었다. Amplification plots의 형질전환체 $C_T$값은 $20.75{\sim}33.81$범위였으며, 유전자 copy수는 정량분석을 기초로 산출하였다. pBN115의 plasmid DNA를 serial dilution했을 때, standard는 $5.6{\times}10^{10}/45ng{\sim} 5.6{\times}10^5/0.00045ng\;copies/{\mu}{\ell}$이 었으며, 형질전환체는 $3.86{\times}10^8{\sim}12565.71 copies/{\mu}{\ell}$이었다. 따라서 PCR, Real-Time PCR 분석 결과 저온저항성 유전자가 국화의 genome에 안정적으로 도입되었음이 확인되었다.

• 대한임상검사과학회지
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• 제40권2호
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• pp.98-105
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• 2008

Colorectal carcinoma from various cancers is fourth ranked occurred to Korean. Due to western dietary life, this cancer has been increased continuously. Therefore, the further study will be needed to find a candidate gene involved in the development and progression of colorectal carcinoma as well as to diagnose and treatment helpfully. The purpose of this study was designed to find a carcinogenesis gene using microsatellite marker on chromosomes 7th and 20th from 30 colon cancer patients. The amplification was investigated in order of D20S97 57% (17/30), D20S101 57% (17/30), D20S119 53% (16/30), D7S483 50% (15/30), D7S495 47% (14/30), D7S498 47% (14/30). The genetic mutation pattern depends on loci of colorectal carcinoma was shown highly amplified with 3.77 from colon cancer than with 2.08 from right colorectal carcinoma (P<0.018). The genetic mutation with lymph nodes was investigated higher with 4.13 at metastasized group than with 1.93 at non-metastasized group (P<0.001). There was no difference at comparison between histological classfication and serological CEA increase as well as on genetic mutated pattern depends on disease stage. It is suggested that the amplification on chromosomes 7q and 20q determines a pivotal role from first stage to metastasis cancer and also functions as an useful marker on diagnosis and treatment of colorectal carcinoma patients as well as follow-up checkup. Recently, the diagnosis and study using genetic analyzer are necessary for efficient application. Fortunately, several university hospitals run this genetic analyzer currently so it is expected that this method makes full use of clinical application.

• Journal of Microbiology and Biotechnology
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• 제29권3호
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• pp.454-464
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• 2019

Salmonellosis is a highly contagious bacterial disease that threatens both human and poultry health. Tests that can detect Salmonella in the field are urgently required to facilitate disease control and for epidemiological investigations. Here, we combined loop-mediated isothermal amplification (LAMP) with a chromatographic lateral flow dipstick (LFD) to rapidly and accurately detect Salmonella. LAMP primers were designed to target the Salmonella invA gene. LAMP conditions were optimized by adjusting the ratio of inner to outer primers, $MgSO_4$ concentration, dNTP mix concentration, amplification temperature, and amplification time. We evaluated the specificity of our novel LAMP-LFD method using six Salmonella species and six related non-Salmonella strains. All six of the Salmonella strains, but none of the non-Salmonella strains, were amplified. LAMP-LFD was sensitive enough to detect concentrations of Salmonella enterica subsp. enterica serovar Pullorum genomic DNA as low as $89fg/{\mu}l$, which is 1,000 times more sensitive than conventional PCR. When artificially contaminated feed samples were analyzed, LAMP-LFD was also more sensitive than PCR. Finally, LAMP-LFD gave no false positives across 350 chicken anal swabs. Therefore, our novel LAMP-LFD assay was highly sensitive, specific, convenient, and fast, making it a valuable tool for the early diagnosis and monitoring of Salmonella infection in chickens.

• 한국식물병리학회지
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• 제14권6호
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• pp.589-593
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• 1998

DNA amplification by polymerase chain reaction (PCR) was used to specifically detect Plasmodiophora brassicae, causing clubroot of crucifers. On the basis of DNA sequence informations, an oligonucleotide primer set specific for the pathogen was designed form small subunit gene (18S-like) and internal transcribed spacer (ITS) region of ribosomal DNA. Primer ITS 5/PB-C produced an amplification product of approximately 520 bp in length with DNA from P. brassicae. However, no amplification product was produced with DNAs from several soil-borne fungi, Didymella bryoniae and Rhizopus stolonifer. Using these primers, the clubroot pathogen was readily detected from infected roots of crucifers, but not from healthy roots. Southern hybridization analysis further confirmed that the amplification product was originated from P. brassicae.

• Asian Pacific Journal of Cancer Prevention
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• 제14권3호
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• pp.1655-1659
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• 2013

Background: HER-2/neu is a proto-oncogene that encodes a transmembrane tyrosine kinase growth factor which is crucial for stimulating growth and cellular motility. Overexpression of HER-2/neu is observed in 10-35% of human breast cancers and is associated with pathogenesis, prognosis as well as response to therapy. Given the imperative role of HER-2/neu overexpression in breast cancer, it is important to determine the magnitude of amplification which may facilitate a better prognosis as well as personalized therapy in affected patients. In this study, we determined HER-2/neu protein expression by immunohistochemistry (IHC) concurrently with HER-2/neu DNA amplification by quantitative real time-polymerase chain reaction (Q-PCR). Materials and Methods: A total of 53 paired tissue samples from breast cancer patients were frozen-sectioned to characterize the tumour and normal tissues. Only tissues with 80% tumour cells were used in this study. For confirmation, Q-PCR was used to determine the HER-2/neu DNA amplification. Results: We found 20/53 (37.7%) of the tumour tissues to be positive for HER-2/neu protein overexpression using IHC. Out of these twenty, only 9/53 (17%) cases were in agreement with the Q-PCR results. The concordance rate between IHC and Q-PCR was 79.3%. Approximately 20.7% of positive IHC cases showed no HER-2/neu gene amplification using Q-PCR. Conclusion: In conclusion, IHC can be used as an initial screening method for detection of the HER-2/neu protein overexpression. Techniques such as Q-PCR should be employed to verify the IHC results for uncertain cases as well as determination of HER-2/neu gene amplification.

• 한국물환경학회지
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• 제22권6호
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• pp.1014-1021
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• 2006

SMMIAR (Submerged Moving Media Intermittent Aeration Reactor) Process is a very efficient system which remove ammonia to nitrogen gas in one reactor. In this study, we determined the diversity of ammonia oxidizing bacteria and denitrifying bacteria using specific PCR amplification and the clone library construction. An ammonia monooxygenase gene(amoA) was analyzed to investigate the diversity of nitrifiers. Most of amoA gene fragments (27/29, 93%) were same types and they are very similar (>99%) to the sequences of Nitrosomonas europaea and other clones isolated from anoxic ammonia oxidizing reactors. ANAMMOX related bacteria have not determined by specific PCR amplification. A nitrite reductase gene(nirK) was analyzed to investigate the diversity of denitrifying bacteria. About half (9/20, 45%) of denitrifiers were clustered with Rhodobacter and most of others were clustered with Mesorhizobium (6/20, 30%) and Rhizobium (3/20, 15%). All of these nirK gene clones were clustered in alpha-Proteobacteria and this result is coincide with other system which also operate nitrification and denitrification in one reactor. The molecular monitoring of the population of nitrifiers and denitrifiers would be helpful for the system stabilization and scale-up.

• Bulletin of the Korean Chemical Society
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• 제33권1호
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• pp.69-75
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• 2012

Five-channel electrochemical chips were fabricated based on the Micro-electromechanical System (MEMS) technology and were used as platforms to develop DNA arrays. Different kinds of thiolated DNA strands, whose sequences were related to white spot syndrome virus (WSSV) gene, were separately immobilized onto different working electrodes to fabricate a combinatorial biosensor system. As a result, different kinds of target DNA could be analyzed on one chip via a simultaneous recognition process using potassium ferricyanide as an indicator. To perform quantitative target DNA detection, a limit of 70 nM (S/N=3) was found in the presence of 600 nM coexisting noncomplementary ssDNA. The real samples of loop-mediated isothermal amplification (LAMP) products were detected by the proposed method with satisfactory result, suggesting that the multichannel chips had the potential for a high effective microdevice to recognize specific gene sequence for pointof-care applications.

• Journal of Microbiology and Biotechnology
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• 제17권10호
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• pp.1616-1621
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• 2007

We have established a SYBR Green-based realtime PCR method using AnyDirect solution, which enhances PCR from whole blood, for direct amplification of the virA gene of Shigella flexneri and the invA gene of Salmonella typhimurium from human feces without prior DNA purification. When we compared the efficiency of conventional or realtime PCR amplification of the virA and invA genes from the supernatant of boiled feces supplemented with S. flexneri and S. typhimurium in the presence or absence of AnyDirect solution, amplification products were detected only in reactions to which AnyDirect solution had been added. The detection limit of real-time PCR was $1{\times}10^4\;CFU/g$ feces for S. flexneri and $2{\times}10^4\;CFU/g$ feces for S. typhimurium; this sensitivity level was comparable to other studies. Our real-time PCR assay with AnyDirect solution is simple, rapid, sensitive, and specific, and allows simultaneous detection of S. flexneri and S. typhimurium directly from fecal samples without prior DNA purification.