• Journal of Microbiology and Biotechnology
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• v.16 no.5
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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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• v.15 no.2
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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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• v.13 no.4
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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.

• Journal of Environmental Science International
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• v.23 no.8
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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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• v.14 no.2
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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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• v.11 no.3
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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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• v.5 no.2
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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.

• Journal of Korean Society of Forest Science
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• v.109 no.1
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• pp.23-30
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• 2020

The use of increased computing power, machine learning, and deep learning techniques have dramatically increased in various sectors. In particular, image detection algorithms are broadly used in forestry and remote sensing areas to identify forest types and tree species. However, in South Korea, machine learning has rarely, if ever, been applied in forestry image detection, especially to classify tree species. This study integrates the application of machine learning and forest image detection; specifically, we compared the ability of two machine learning data collection methods, namely image data captured by forest experts (D1) and web-crawling (D2), to automate the classification of five trees species. In addition, two methods of characterization to train/test the system were investigated. The results indicated a significant difference in classification accuracy between D1 and D2: the classification accuracy of D1 was higher than that of D2. In order to increase the classification accuracy of D2, additional data filtering techniques were required to reduce the noise of uncensored image data.

• Applied Biological Chemistry
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• v.46 no.3
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• pp.225-228
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• 2003

This study was carried out to investigate the simple and rapid detection of Salmonella species in different kinds of food using PCR method. The specific primer sets (SIN1 and SIN2) was designed and utilized to amplify a 617 bp DNA fragment from salmonella species. The sensitivity of PCR was 1 pg of purified template DNA or $10^2$ cells from pure culture. The detection limit of Salmonella typhimurium on agarose gel electrophoresis was $10^3{\sim}10^4$ cells/g in the artificially contaminated food samples. These results suggested that this simple method could be applied to industrial fields for detection of Salmonella species in food.

• Korean Journal of Microbiology
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• v.41 no.2
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• pp.117-124
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• 2005

Two bacterial isolates obtained from rotifer and diseased olive flounder larvae, Paralichthys olivaceus, were identified as Vibrio ichthyoenteri based on the results of phenotypic characterization. In an attempt to develop rapid PCR method for the detection of V. ichthyoenteri, we examined the 16S-23S rRNA intergenic spacer region(ISR) of V. ichthyoenteri and developed species-specific primer for V. ichthyoenteri. Analysis of the ISR sequences showed that V. ichthyoenteri contains one type of polymorphic ISRs. The size of ISRs was 348 bp length and did not contain tRNA genes. Mutiple alignment of representative sequences from different V. species revealed several domains of high sequence variability, and allowed to design species-specific primer for detection of V. ichthyoenteri. The specificity of the primer was examined using genomic DNA prepared from 19 different V. species, isolated 18group Vibrio species and most similar sequence of other known Vibrio species. The results showed that the PCR reaction using species-specific primer designed in this study can be used to detect V. ichthyoenteri.