• Fisheries and Aquatic Sciences
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• v.15 no.2
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• pp.157-162
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• 2012

To analyze nucleotide sequence encoding internal transcribed spacer (ITS) regions specific to the Laminariaceae family, genomic DNA was isolated from six brown algae species distributed along the east coast of Korea. These included three species from the Laminariaceae family (Agarum clathratum Dumortier, Costaria costata [C. Agardh] Saunders, and Saccharina japonica Areschoug) and two species from the Alariaceae family (Undaria pinnatifida [Harvey] Suringer and Ecklonia cava Kjellman), both in the order Laminariales, and one species from the family Sargassaceae in the order Fucales (Sargassum serratifolium). Based on a sequence analysis of ITS-1 and ITS-2 for A. clathratum, C. costata, and E. cava, oligonucleotides were designed from the regions that showed sequence conservation in Laminariaceae. Following polymerase chain reaction using three sets of primers, amplification of ITS-1 and ITS-2 was detected in reactions using genomic DNA isolated from the species belonging to Laminariaceae, but not from the species belonging to the other families. The results indicate that this method can be used for the detection and identification of Laminariaceae species.

• Microbiology and Biotechnology Letters
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• v.39 no.1
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• pp.70-76
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• 2011

PCR-based Weissella species-specific detection method was developed to apply for the discrimination of Korean and Chinese kimchi by detecting a Weissella species only found in Korean or Chinese kimchi. PCR primers were designed from the species-specific sequence in the recN gene of each species. The primers allowed the species-specific detection and identification of nine species in the genera Weissella, and were successfully applied to the detection of W. cibaria, W. confusa, W. koreensis, and W. soli in kimchi with 20 ng template DNA. W. cibaria, W. confusa, and W. koreensis were detected from the Korean kimchi samples tested but W. soli was not detected. However, the four species were detected from Chinese kimchi samples. PCR-based W. soli-specific detection could not be perfectly applied as the Chinese kimchi discriminating method but has significance as an approach to evaluate the potential of scientific verification method based on the difference of microbial community.

• International Journal of Oral Biology
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• v.35 no.1
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• pp.21-25
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• 2010

This study was undertaken to develop species-specific forward and universal reverse PCR primers for the detection of Streptococcus sobrinus. These primers target the variable regions of the 16S ribosomal RNA coding gene (rDNA) and their specificity was tested against 10 strains of S. sobrinus strains and 20 different species of oral bacteria using serial dilutions of the purified genomic DNA of S. sobrinus ATCC $33478^T$. Our data show that species-specific amplicons were obtained from all the S. sobrinus strains tested but not from other species. Both direct and nested PCR could detect as little as 400 pg and 4 fg of genomic DNA from S. sobrinus ATCC $33478^T$, respectively. This result suggests that these PCR primers are highly specific and sensitive and applicable to the detection of S. sobrinus.

• Food Science of Animal Resources
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• v.38 no.2
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• pp.376-390
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• 2018

Cronobacter species have been associated with disease outbreaks and sporadic infections, particularly in premature and immunocompromised infants. Cronobacter species can cause foodborne infections such as neonatal meningitis, septicaemia and necrotising enterocolitis. Accordingly, there is an urgent need to control and monitor the Cronobacter species in food, especially in powdered infant formula (PIF) and other baby foods. Therefore, in this review, the isolation and prevalence of Cronobacter species in infant food including PIF and the recent advance of detection methods are discussed for the better understanding on the current research status of Cronobacter species.

• Korean Journal of Environment and Ecology
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• v.37 no.5
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• pp.327-336
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• 2023

This study aimed to propose an effective method for surveying wild birds by comparing the results of bioacoustic detection with those obtained through a field survey. The study sites were located at Dongbaek-dongsan and a 1100-altitude wetland in Jeju-do, South Korea. The bioacoustic detection was conducted over the course of 12 months in 2020. For the bioacoustic detection, a Song-meter SM4 device was installed at each study site, recording bird songs in 1-min per hour, .wav, and 44,100 Hz format. The findings of the field survey were taken from the 「Long-term trends of Bird Community at Dongbaekdongsan and 1100-Highland Wetland of Jeju Island, South Korea.」 by Banjade et al. (2019). The results of this study are as follows. First, the avifauna identified using bioacoustic detection comprised 29 families and 46 species in Dongbaek-dongsan, and 16 families and 25 species in the 1100-altitude wetland. Second, based on the song frequency, the dominant species in Dongbaek-dongsan were Hypsipetes amaurotis (Brown-eared Bulbul, 33.62%), Horornis diphone (Japanese Bush Warbler, 12.13%), and Zosterops japonicus (Warbling White-eye, 9.77%). In the 1100-altitude wetland the dominant species were Corvus macrorhynchos (Large-billed Crow, 27.34%), H. diphone (19.43%), and H. amaurotis (16.56%). Third, in the field survey conducted at Dongbaek-dongsan, the number of detected bird species was 39 in 2009, 51 in 2012, 35 in 2015, and 45 in 2018, while the bioacoustic detection identified 46 species. In the field survey conducted in the 1100-altitude wetland, the number of detected bird species was 37 in 2009, 42 in 2012, 34 in 2015, and 38 in 2018, while the bioacoustics detection identified 25 species. Overall, 43.6% of the 78 species detected in the field survey in Dongbaek-dongsan (34 species) were identified using bioacoustic detection, and 38.3% of the 47 species detected in the field survey in the 1100-altitude wetland (18 species) were identified using bioacoustic detection. Fourth, the bioacoustic detection identified 9 families and 12 species of birds in Dongbaek-dongsan, and 3 families and 7 species of birds in the 1100-altitude wetland. No results from field survey were available for these species. The identified birds were predominantly nocturnal, including Otus sunia (Oriental Scops Owl) and Ninox japonica (Northern Boobook), passage migrants, including Larvivora cyane (Siberian Blue Robin), L. sibilans (Rufous-tailed Robin), and winter visitors with a relatively small number of visiting individuals, such as Bombycilla garrulus (Bohemian Waxwing) and Loxia curvirostra (Red Crossbill). Fifth, the birds detected in the field survey but not through bioacoustic detection included 18 families and 48 species in Dongbaek-dongsan and 14 families and 27 species in the 1100-altitude wetland; the most representative families were Ardeidae, Accipitridae, and Muscicapidae. This study is significant as it provides essential data supporting the possibility of an effective survey combining bioacoustic detection with field studies, given the increasing use of bioacoustic devices in ornithological studies in South Korea.

• Journal of Korea Multimedia Society
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• v.25 no.11
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• pp.1653-1671
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• 2022

Crop diseases affect crop production, more than 30 billion USD globally. We proposed a classification study of crop species and diseases using deep learning algorithms for corn, cucumber, pepper, and strawberry. Our study has three steps of species classification, disease detection, and disease classification, which is noteworthy for using captured images without additional processes. We designed deep learning approach of deep learning convolutional neural networks based on Mask R-CNN model to classify crop species. Inception and Resnet models were presented for disease detection and classification sequentially. For classification, we trained Mask R-CNN network and achieved loss value of 0.72 for crop species classification and segmentation. For disease detection, InceptionV3 and ResNet101-V2 models were trained for nodes of crop species on 1,500 images of normal and diseased labels, resulting in the accuracies of 0.984, 0.969, 0.956, and 0.962 for corn, cucumber, pepper, and strawberry by InceptionV3 model with higher accuracy and AUC. For disease classification, InceptionV3 and ResNet 101-V2 models were trained for nodes of crop species on 1,500 images of diseased label, resulting in the accuracies of 0.995 and 0.992 for corn and cucumber by ResNet101 with higher accuracy and AUC whereas 0.940 and 0.988 for pepper and strawberry by Inception.

• Fisheries and Aquatic Sciences
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• v.16 no.4
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• pp.273-277
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• 2013

Vibriosis caused by Vibrio anguillarum and edwardsiellosis caused by Edwardsiella tarda are septicemic diseases of many commercially important freshwater and marine fishes, and threaten the aquaculture industry in Korea. Early diagnosis and accurate identification of these two bacterial species could help to prevent these diseases and minimize the damage to cultured marine species. This study designed a duplex polymerase chain reaction (PCR) method for the simultaneous detection of two major fish pathogens: V. anguillarum and E. tarda. Each pair of oligonucleotide primers exclusively amplified the target groEL gene of the specific microorganism. Twenty-two Vibrio and ten non-Vibrio enteric species were used to check the specificity of the primers, which were found to be highly specific for the target species, even among closely related species. The detection limit was 400 pg for V. anguillarum and 4 ng for E. tarda when mixed purified DNA was used as the template. This assay showed high specificity and sensitivity in the simultaneous detection of V. anguillarum and E. tarda from artificially inoculated seawater and fish.

• Genomics & Informatics
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• v.19 no.3
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• pp.30.1-30.8
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• 2021

Salmonella species are among the major pathogens that cause foodborne illness outbreaks. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP) assay for the rapid and sensitive detection of Salmonella species. We designed LAMP primers targeting the hilA gene as a universal marker of Salmonella species. A total of seven Salmonella species strains and 11 non-Salmonella pathogen strains from eight different genera were used in this study. All Salmonella strains showed positive amplification signals with the Salmonella LAMP assay; however, there was no non-specific amplification signal for the non-Salmonella strains. The detection limit was 100 femtograms (20 copies per reaction), which was ~1,000 times more sensitive than the detection limits of the conventional polymerase chain reaction (PCR) assay (100 pg). The reaction time for a positive amplification signal was less than 20 minutes, which was less than one-third the time taken while using conventional PCR. In conclusion, our Salmonella LAMP assay accurately detected Salmonella species with a higher degree of sensitivity and greater rapidity than the conventional PCR assay, and it may be suitable for point-of-care testing in the field.

• Mycobiology
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• v.33 no.2
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• pp.104-108
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• 2005

Genus Phellinus taxonomically belongs to Aphyllophorales and some species of this genus have been used as a medicinal ingredients and Indian folk medicines. Especially, P. linteus and morphological-related species are well-known medicinal fungi that have various biological activities such as humoral and cell-mediated, anti-mutagenic, and anti-cancer activities. However, little is known about the rapid detection for complex Phellinus species. Therefore, this study was carried out to develop specific primers for the rapid detection of P. linteus and other related species. Designing the species-specific primers was done based on internal transcribed spacer sequence data. Each primer set detected specifically P. linteus (PL2/PL5R) and P. baumii (PB1/PB4R). These primer sets could be useful for the rapid detection of specific-species among unidentified Phellinus species. Moreover, restriction fragment length polymorphism analysis of the ITS region with HaeIII was also useful for clarifying the relationship between each 5 Phellinus species.

• Mycobiology
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• v.50 no.5
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• pp.382-388
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• 2022

White mold (or Sclerotinia stem rot), caused by Sclerotinia species, is a major air, soil, or seed-transmitted disease affecting numerous crops and wild plants. Microscopic or culture-based methods currently available for their detection and identification are time-consuming, laborious, and often erroneous. Therefore, we developed a multiplex quantitative PCR (qPCR) assay for the discrimination, detection, and quantification of DNA collected from each of the three economically relevant Sclerotinia species, namely, S. sclerotiorum, S. minor, and S. nivalis. TaqMan primer/probe combinations specific for each Sclerotinia species were designed based on the gene sequences encoding aspartyl protease. High specificity and sensitivity of each probe were confirmed for sclerotium and soil samples, as well as pure cultures, using simplex and multiplex qPCRs. This multiplex assay could be helpful in detecting and quantifying specific species of Sclerotinia, and therefore, may be valuable for disease diagnosis, forecasting, and management.