• Journal of Microbiology and Biotechnology
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• 제16권5호
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• pp.740-747
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• 2006

Amplification by universal consensus sequences in pathogenic bacterial DNA would allow rapid identification of pathogenic bacteria, and amplification of genus-specific and species-specific sequences of pathogenic bacterial DNA might be used for genotyping at the genus and species levels. For design of probes for molecular diagnostics, several tools are available as stand-alone programs or as Web application. However, since most programs can design only a few probe sets at one time, they are not suitable for large-scale and automatic probes design. Therefore, for high-throughput design of specific probes in diagnostic array development, an automated design tool is necessary. Thus, we developed a Web-based automatic system for design of genus-specific and species-specific probes for pathogen detection. The system is available at http://www.miprobe.com.

• Journal of Microbiology and Biotechnology
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• 제15권2호
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• pp.310-320
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• 2005

A membrane-based oligonucleotide array was used to detect predominant bacterial species in human fecal samples. Digoxygenin-labeled 16S rDNA probes were generated by PCR from DNA that had been extracted from fecal samples or slurries. These probes were hybridized to an array of 120 oligonucleotides with sequences specific for 40 different bacterial species commonly found in human feces, followed by color development using an alkaline phosphatase-conjugated antibody and NBT /BCIP. Twenty of the species were detected by this method, but E. coli, which was present at $\~$1 $\times 10$^5$ CFU per gram feces, was not detected. To improve the sensitivity of this assay, reverse transcriptase-PCR was used to generate probes from RNA extracted from fecal cultures. Coupled with a chemiluminescence detection method, this approach lowered the detection limit for E. coli from $\~1$ $\times 10$^6$ to ${\leq}$ 1 $\times 10$^5$ These results indicate that the membrane-array method with reverse transcriptase-PCR and chemiluminescence detection can simultaneously identify bacterial species present in fecal samples at cell concentrations as low as${\leq}$ 1 $\times 10$^5$ CFU per gram.

• JSTS:Journal of Semiconductor Technology and Science
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• 제13권4호
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• pp.395-401
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• 2013

In-situ optical emission spectroscopy (OES) is employed for leak detection in plasma etching system. A misprocessing is reported for significantly reduced silicon etch rate with chlorine gas, and OES is used as a supplementary sensor to analyze the gas phase species that reside in the process chamber. Potential cause of misprocessing reaches to chamber O-ring wear out, MFC leaks, and/or leak at gas delivery line, and experiments are performed to funnel down the potential of the cause. While monitoring the plasma chemistry of the process chamber using OES, the emission trace for nitrogen species is observed at the chlorine gas supply. No trace of nitrogen species is found in other than chlorine gas supply, and we found that the amount of chlorine gas is slightly fluctuating. We successfully found the root cause of the reported misprocessing which may jeopardize the quality of thin film processing. Based on a quantitative analysis of the amount of nitrogen observed in the chamber, we conclude that the source of the leak is the fitting of the chlorine mass flow controller with the amount of around 2-5 sccm.

• 한국환경과학회지
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• 제23권8호
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• pp.1495-1505
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• 2014

The objective of this study was to evaluate survival rate and fish movement (migration) using a tagging approach of passive integrated transponder (PIT) in Juksan Weir, which was constructed as a four major river restoration projects. For this study, survival rates of each fish species and the mobility of fish individuals were analyzed during 2 weeks by the insertion of PIT tags to various fish species in the laboratory. According to tagging tests in the laboratory, the survival rate 37.5% (30 survivals of 80 individuals) after the insertion of PIT tags. The survival rate of Carassius auratus and Hemibarbus labeo was 100% and 80% after the insertion of the tags, respectively, whereas it was only 13.3% for Zacco platypus. In the field experiments of Juksan Weir, 6 species and 157 individuals from 8 species (563 individuals) were detected in the fixed automatic data-logging system, indicating a detection rate of 27.9% in the fishway of Juksan Weir. In the meantime, some species with no or low detection rates in the fixed automatic data-logging system were turn out to be stagnant-type species, which prefer stagnant or standing water to live.

• Journal of Microbiology and Biotechnology
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• 제14권2호
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• pp.284-289
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• 2004

A PCR assay for the rapid detection of Vibrio vulnificus strains was developed using a virulence gene for elastase found in various Vibrio species. The DNA sequences in the elastase gene facilitated the identification of a species-specific probe for pathogenic V. vulnificus strains from both clinical and environmental sources. Using an elastase gene-based PCR reaction, a species-specific 507-bp PCR product was visualized by agarose gel electrophoresis. Three different DNA extraction methods were then compared to improve the simplicity and rapidity of detection. A PCR assay using the conventional DNA extraction or boiling method was able to detect as few as 25 V. vulnificus cells, making the detection limits at least 1-log-scale lower than that for the EDT A-treated DNA extraction method. In particular, the boiling method, which does not require purification of the chromosomal DNA, was very effective in terms of simple and rapid detection. Meanwhile, the detection limit in a mixed bacterial culture that included other bacteria, such as Escherichia coli or Bacillus subtilis, was two V. vulnificus cells, which was 1-log-scale lower than that for the control. Accordingly, when coupled with a new DNA extraction method, the elastase gene-based PCR can provide a rapid, specific, and sensitive method for identifying V. vulnificus in clinical and environmental samples.

• International Journal of Advanced Culture Technology
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• 제11권3호
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• pp.260-267
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• 2023

We aimed to investigate the proportions of MTB- and NTM-positive tests and the distribution patterns of species isolated by contracted testing agencies in South Korea. Respiratory specimens submitted to contracted testing agencies in South Korea for AFB culture from January 2014 to December 2021 were included (533,713 specimens in total). Trends based on MTB and NTM detection, patient sex and age, culture medium type, and testing year were analyzed. MTB and NTM positive detection increased in the patients. The average ages of MTB- and NTM-positive patients increased in those aged ≥61 years. For solid culture, the MTB detection rate decreased from 5.9% in 2014 to 3.3% in 2018 and increased to 4.7% in 2021; the NTM detection rate increased from 2.1% in 2014 to 3.4% in 2018 and 3.7% in 2021. For liquid culture, the MTB detection rate decreased from 8.3% in 2014 to 5.5% in 2018 and increased to 6.0% in 2021; the NTM detection rate increased from 3.5% in 2014 to 5.5% in 2018 and decreased to 5.3% in 2021. An isolation ratio reversal between MTB and NTM was observed in 2018. In this study, we provide information on mycobacterial isolation rates and species distributions using AFB culture test results from Korea's referral laboratories. Increased MTB- and NTM-isolation rates were observed in individuals aged ≥60 years, indicating the need for regular testing and focused management for them. Expanding liquid culture applications, which show higher positivity rates than solid culture methods, is necessary.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• 제5권2호
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• pp.60-67
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• 2024

Hitchhiker insect species from international vessels entering Korea in 2022 were monitored. A total of 947 samples of hitchhiker insects were collected using a simple collection method by hand. Among them, 856 individuals were classified as 374 species of 86 families in 10 orders through integrative analysis with DNA barcoding and morphological examination. The rest 91 individuals were identified only to the family level. As a result of examining the distribution of the 374 species (856 individuals), 38 species (71 individuals) were confirmed as not-distributed species in Korea, including six species (11 individuals) as 'regulated species' listed by the Korean Animal and Plant Quarantine Agency. Of 38 not-distributed species, 10 species were detected multiple times (at least twice). Accordingly, it is necessary to strengthen monitoring of the area around the port of entry along with continuous surveillance to prevent invasion of species detected multiple times. For monitoring alien hitchhiker insect species, this study provided detection information and biological data for alien species.

• 한국산림과학회지
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• 제109권1호
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• pp.23-30
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• 2020

최근 급변하는 컴퓨터 기술의 발전을 통해 컴퓨터 비전과 머신러닝을 이용한 사물인식 기법이 다양한 학문 분야에서 사용되고 있다. 국내의 연구 사례를 보면 주로 대면적 산림을 분석하기 위한 이미지 학습 및 객체인식 기법이 사용되는 반면 개체목 단위의 수종 분류 및 특징을 학습하는 연구는 아직 미미한 실정이다. 이에 본 연구는 한국의 침엽수 5종을 대상으로 이미지 학습을 통한 자동분류 연구의 가능성을 분석해 보았다. 데이터 형태에 따른 분류 결과의 차이를 분석하기 위하여 산림전문가가 직접 촬영한 영상(D1)과 웹크롤링을 이용한 영상(D2)을 사용하여 수종 분류를 실시하였다. 그 결과 D1과 D2의 분류 정확도에 유의미한 차이가 있는 것으로 나타났으며, D1은 D2보다 높은 분류 정확도를 나타냈다. 또한, D2의 분류 정확도를 높이기 위해서는 검열되지 않은 영상 데이터의 노이즈를 줄이기 위한 추가 데이터 필터링 기법이 필요한 것으로 사료된다.

• Applied Biological Chemistry
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• 제46권3호
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• pp.225-228
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• 2003

여러 종류의 식품에서 Salmonella 균주를 손쉽고 빠르게 검출하기 위하여, Salmonella 장독소 유전자(stn)를 기초로 제작한 primer (STN1, STN2)를 이용하여 PCR을 수행한 결과 617 hp의 특이적인 DNA단편을 얻을 수 있었다. PCR 민감도는 순수 배양한 균체에서 추출한 template DNA는 1 pg까지 검출이 가능하였고, 직접 균체를 template로 이용한 경우에는 $10^2\;cells$까지 검출이 가능하였다. Salmonella typhimurium을 인위적으로 접종시킨 식품에서는 식품 1 g당 $10^3{\sim}10^4$ cells까지 검출할 수 있었다. 이러한 결과는 PCR을 이용하여 Salmonella에 오염된 식품에서 이들 균주를 간편하고 신속하게 검출할 수 있을 것이다.

• 미생물학회지
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• 제41권2호
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• pp.117-124
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• 2005

Rotifer와 병든 넙치 자어로부터 분리된 2개의 균주는 표현형적인 특성 확인 결과 Vibrio ichthyoenteri로 확인이 되었다. V. ichthyoenteri를 검출하기 위래 고감도 PCR 방법 개발을 하기 위래 V. ichthyoenteri 16S-23S rRNA intergenic spacer region(ISR)을 분석하였고, V. ichthyoenteri중 특이적 primer를 개발하였다. V. ichthyoenteri 의 ISR를 분석한 결과 1개의 다형성 ISR type서열을 포함하고 있었다. ISR서열은 길이는 348bp이며 tRNA gene을 가지고 있지 않았다. 이 서열을 가지고 이미 알려진 다른 Vibrio 종의 ISR 서열과 mutiple alignment를 수행한 결과 여러 영역에서 높은 가변성을 나타내어 가변 부위를 표적으로 하여 V. ichthyoenteri를 검출하기 위한 종 특이적 primer를 제작하였다. 제작된 primer의 특이성을 확인하기 위해 Vibrio 표준균주 19종의 genomic DNA와 분리균주 18 group에 genomic DNA 그리고 V. ichthyoenteri와 가장 유사한 서열을 가지고 있다고 알려진 Vibrio 종의 genomic DNA를 가지고 시험하였다. 그 결과 본 연구에서 제작된 종 특이적 primer를가지고 PCR 반응을 하면 V. ichthyoenteri를 검출 할 수가 있다.