• Fisheries and Aquatic Sciences
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• 제15권2호
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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.

• 한국미생물·생명공학회지
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• 제39권1호
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• pp.70-76
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• 2011

Weissella 속 유산균 검출의 차이를 이용한 한국산 및 중국산 김치 판별의 가능성 검토를 위하여 Weissella 속 9종 균주의 PCR 검출법을 개발하였다. 종(species) 수준에서의 Weissella 속 균주의 특이적 PCR 검출을 위한 primer는 recN 유전자의 염기서열을 이용하여 선정하였으며, 김치로부터 W. cibaria, W. confusa, W. koreensis, W. soli를 모두 검출하기 위해서는 20 ng template DNA가 필요한 것으로 나타났다. 한국산 김치시료로부터는 W. cibaria, W. confusa, W. koreensis가 높은 빈도로 검출되었지만, W. soli는 검출되지 않았다. 한편 중국산 김치시료로부터는 이들 4종의 Weissella 속 균주들이 모두 검출되었다. 본 연구자들이 개발한 W. soli 특이적 PCR 검출은 현시점에서 중국산 김치의 원산지 판별법으로 적용되기에는 한계점을 가지고 있지만, 미생물 군집의 차이를 이용한 새로운 과학적 검증법이 제시되어 그 가능성이 검토되었다는 점에서 의의를 가지고 있다.

• International Journal of Oral Biology
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• 제35권1호
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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.

• 한국축산식품학회지
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• 제38권2호
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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.

• 한국환경생태학회지
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• 제37권5호
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• pp.327-336
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• 2023

본 연구는 야생조류 생물음향 탐지와 현장 조사의 결과 비교를 통해 효과적인 야생조류 조사 방법을 제시하는데 목적이 있다. 연구대상지는 제주 동백동산과 1100고지 습지였다. 생물음향 탐지 기간은 2020년 12개월간이었다. 생물음향 탐지는 시간당 1분씩, .wav, 44,100Hz 포맷으로 생물음향 측정장비(Song meter SM4)를 각 연구대상지에 설치하여 녹음하였다. 현장 조사는 Banjade et al. (2019)의 「제주 동백동산과 1100고지 습지의 조류군집 장기간 동향」 결과를 인용하였다. 연구결과는 다음과 같다. 첫 번째, 생물음향 탐지 기법을 통해 확인된 조류상은 동백동산에서 29과 46종, 1100고지 습지에서 16과 25종이었다. 두 번째, 울음 빈도를 통해 나타난 종 구성은 동백동산에서 직박구리(33.62%), 섬휘파람새(12.13%), 동박새(9.77%) 순으로 나타났고, 1100고지 습지에서 큰부리까마귀(27.34%), 섬휘파람새(19.43%), 직박구리(16.56%) 순으로 나타났다. 세 번째, 동백동산에서 실시한 현장 조사의 경우 2009년 39종, 2012년 51종, 2015년 35종, 2018년 45종이 조사되었고, 생물음향 탐지를 통해 46종이 확인되었다. 1100고지 습지에서 실시한 현장 조사의 경우 2009년 37종, 2012년 42종, 2015년 34종, 2018년 38종이 조사되었고, 생물음향 탐지를 통해 25종이 확인되었다. 종합적으로 현장 조사를 통해 동백동산에서 확인된 78종 중 43.6%인 34종, 1100고지 습지에서 확인된 47종 중 38.3%인 18종이 생물음향 탐지로 확인되었다. 네 번째, 현장 조사에서 확인되지 않았지만, 생물음향 탐지를 통해 확인된 종은 동백동산에서 9과 12종, 1100고지 습지에서 3과 7종으로 대표적으로 소쩍새, 솔부엉이와 같은 야행성 조류, 쇠유리새, 울새와 같은 나그네새, 도래하는 개체수가 상대적으로 적은 황여새, 솔잣새와 같은 겨울철새가 있다. 다섯 번째, 현장 조사에서 확인된 종 중에서 생물음향 탐지를 통해 확인되지 않은 종은 동백동산에서 18과 48종, 1100고지 습지에서 14과 27종으로 대표적으로 백로과, 수리과, 솔딱새과가 있다. 본 연구는 국내에서 생물음향 장비 운용을 통한 조류 연구가 활성화되고 있는 가운데 현장 조사와 생물음향 탐지를 병행했을 때 효과적인 조사를 실시할 수 있다는 기초 자료를 작성했다는 점에서 의미가 있다.

• 한국멀티미디어학회논문지
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• 제25권11호
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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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• 제16권4호
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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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• 제19권3호
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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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• 제33권2호
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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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• 제50권5호
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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.