• Fisheries and Aquatic Sciences
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• v.12 no.3
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• pp.171-178
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• 2009

The Perciformes include approximately 40% of all bony fishes and are the largest order of vertebrates. This order includes some of the most economically relevant marine fishes, particularly the red seabream, black seabream and rock bream. A 409 bp fragment of the cytochrome b (cyt b) gene and 403 bp and 518 bp fragments of ribosomal RNA (12S and 16S rRNA, respectively) were sequenced from five populations of natural and cultured red seabreams, natural black seabream, and natural and cultured rock breams. The mitochondrial DNA sequences were utilized for the genetic identification and population structural analyses of these three species. Phylogenetic relationships of intra- and inter-species were elucidated using three types of molecular genetic markers from three species of the order Perciformes in Korea. We noted no significant differences in the intra-specific variation of the cyt b and rRNA genes in each population however, inter-specific divergences were greater than intra-specific variation. Inter-specific variation was induced more by transition than transversion type in the cyt b and rRNA genes. The cyt b gene and rRNA genes make it possible to determine the inter-species divergence. The rRNA genes have more conserved sequences than the cyt b gene. Therefore, these genes are expected to prove useful among species belonging to the different genera or families.

• International Journal of Oral Biology
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• v.38 no.1
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• pp.21-27
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• 2013

Anginosus group streptococci (AGS) were classified based on the nucleotide sequences of the 16S rRNA gene (16S rDNA) and comprised Streptococcus anginosus, Streptococcus intermedius, and Streptococcus constellatus. It is known that AGS is a causative factor of oral and systematic diseases. The purpose of this study was to discriminate the 56 clinical strains of AGS isolated from Korean oral cavities using phylogenetic analysis of 16S rDNA and species-specific PCR at the species-level. The 16S rDNA of clinical strains of AGS was sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. PCR was performed to identify the clinical strains using species-specific primers described in previous studies and S. intermedius-specific PCR primers developed in our laboratory. The resulting phylogenetic data showed that the 16S rDNA sequences can delineate the S. anginosus, S. intermedius, and S. constellatus strains even though the 16S rDNA sequence similarity between S. intermedius and S. constellatus is above 98%. The PCR data showed that each species-specific PCR primer pair could discriminate between clinical strains at the species-level through phylogenetic analysis of 16S rDNA nucleotide sequences. These results suggest that phylogenetic analysis of 16S rDNA and PCR are useful tools for discriminating between AGS strains at the species-level.

• Journal of Korean Society of Forest Science
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• v.90 no.4
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• pp.437-444
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• 2001

This paper discusses applications of neural network to forest stand field data processing and determining suitable tree species for site-specific stand characteristics. For site-specific species selection, considered were 5 major coniferous species : P. densiflora for. erecta, L. leptolepis, P. koraiensis, P. densiflora, P. thunbergii. Among 1,320 sample plot data sets, 200 data sets with the highest site index (40 data sets for each species) were chosen as the test sets for investigation. Each data set includes 13 factors describing the site characteristics of the corresponding sample plot. The results of this investigation indicate high performance of neural network in data processing procedures for extracting data sets or measurement parameters without any recognizable pattern. These data sets or measurement parameters are those which have rare effect on site-specific species suitability or disturb pattern classification procedures of neural network because of unrecognizable patterns involved. Also the results have shown high potential of neural network in determining the best-suitable tree species for site characteristics. The % accuracy of the neural network model in determining the best-suitable tree species for site characteristics ranges from 77.6% to 91.8% associated with the combination of Site factors.

• Journal of Life Science
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• v.28 no.9
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• pp.1062-1067
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• 2018

Reliable labeling of fish products can reassure consumers regarding the identity and quality of seafoods. Therefore, techniques that can identify adulteration or mislabeling are valuable. To rapidly identify two Trachurus species, Trachurus japonicus and Trachurus novaezelandiae, a highly efficient, rapid, duplex polymerase chain reaction (PCR) having two species-specific primers simultaneously was identified. This species-specific primer focused on a single nucleotide mismatch in the 3'-terminal base of a primer designed in the mitochondrial cytochrome c oxidase (COI) subunit I DNA. To optimize the duplex PCR condition, gradient PCR reactions were conducted to determine the primer annealing temperature and the primer concentration. The PCR's product was observed on the gel, suggesting that DNA molecules may be useful in differentiating the two species. The length of the amplification fragments were 103 bp for Trachurus japonicus and 214 bp for Trachurus novaezelandiae, which, along with the species-specific primer visualized by agarose gel electrophoresis, enabled accurate distinction of the species of the Trachurus genus. These results indicate that the duplex PCR, which has a species-specific primer based on single nucleotide polymorphism (SNP), can be useful for rapidly differentiating the two species of Trachurus. This duplex PCR analysis is simple, rapid, and reliable, and could be beneficial to protecting consumers' rights.

• Journal of Life Science
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• v.26 no.9
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• pp.1007-1014
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• 2016

A highly efficient, rapid, and reliable multiplex polymerase chain reaction based method for distinguishing ten species of genus Cynoglossus (C. senegalensis, C. abbreviates, C. macrolepidotus, C. arel, C. semilaevis, C. interruptus, C. joyneri, C. lingua, C. robustus, and C. monodi) is described. The species-specific primer sets were designed base on the cytochrome oxidase subunit I gene (1,500 bp). The optimal PCR conditions and primers were selected for ten of Cynoglossus species to determine target base sequences using single PCR. Multiplex PCR using the ten pairs of primers either specifically amplified a DNA fragment of a unique size or failed, depending on each species DNA. The length of amplification fragment of 208 bp for C. senegalensis, 322 bp for C. abbreviates, 493 bp for C. macrolepidotus, 754 bp for C. arel, 874 bp for C. semilaevis, 952 bp for C. interruptus, 1,084 bp for C. joyneri, 1,198 bp for C. lingua, 1,307 bp for C. robustus, and 1,483 bp for C. monodi with the species-specific primers, visualized by agarose gel electrophoresis, allowed perfectly distinction of the Cynoglossus species. The multiplex PCR assay can be easily performed on multiple samples and attain final results in less than 6 hours. This technique should be a useful addition to the molecular typing tools for the tentative identification of Cynoglossus species.

• The Korean Journal of Mycology
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• v.31 no.3
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• pp.121-128
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• 2003

This study was carried out to identify the phylogenetic relationship of Phellinus species and to know its distribution by comparing the DNA sequences of internal transcribed spacer regions(ITS1 and IST2) and 5.8S ribosomal DNA (rDNA) repeat unit. The Phellinus species had their specific sequences in IST1 and 2 regions depending on suedes. The comparison of the ITS sequences of standard strains indicated that the sequences of ITS1 were more variable than those of ITS2. Nine strains of the commercial products of Phellinus species used in this study were identified as P. lintues, P. baumii, P. igniarius, and P. pini. Most of commercial species were P. pini and P. baumii, and P. gilvus was not found. Also, P. linteus was only found in form of mycelial culture rather than fruiting body. Moreover, the species-specific primers were designed based on ITS sequence data. Each species-specific primers were bound in P. lintues(ITSF-PL2R), P. baumii(PB1F-ITS4R), P. igniarius(IF1-IR3), P. pini(PF1-PR3), and P. gilvus(GF2-GR4), respectively. These primer sets would be useful fer the detection of specific-species among unidentified Phellinus species rapidly.

• Molecules and Cells
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• v.39 no.9
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• pp.692-698
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• 2016

Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.

• International Journal of Oral Biology
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• v.36 no.1
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• pp.1-6
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• 2011

The purpose of this study was to develop species-specific real-time quantitative PCR (RT-qPCR) primers for use in the detection of Aggregatibacter actinomycetemcomitans. These primers were designed based on the nucleotide sequences of the RNA polymerase ${\beta}$-subunit gene (rpoB). We assessed the specificity of the primers against nine strains of A. actinomycetemcomitans, eight strains (three species) of the Haemophilus genus, and 40 strains of 40 other oral bacterial species. Primer sensitivity was determined by testing serial dilutions of the purified genomic DNAs of A. actinomycetemcomitans ATCC $33384^T$. Our data reveal that we had obtained species-specific amplicons for all of the tested A. actinomycetemcomitans strains, and that none of these amplicons occurred in any of the other species. Our PCR protocol proved able to detect as little as 2 fg of A. actinomycetemcomitans chromosomal DNA. Our findings suggest that these qRT-PCR primers are suitable for application in epidemiological studies.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.36 no.3
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• pp.317-320
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• 2003

Morphologically similar fish species were subjected to the random amplified polymorphic DNA (RAPD) analysis using universal rice primer (URP). The fish species tested were sea basses (Lateolabrax japonicus and L. maculatus), eels (Anguilla japonica, A. bicolor bicolor, A. rostrata, and A. anguilla), and flounders (Limanda yokohamae and L. herzensteinin). Highly reproducible RAPD patterns were observed with several potential species-specific markers. The results indicate that RAPD technique using URP is useful for distinguishing fish psecies in a rapid manner.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.48 no.2
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• pp.221-232
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• 2015

Broadband echoes measured in live chub mackerel Scomber japonicus, goldeye rockfish Sebastes thompsoni, and fat greenling Hexagrammos otakii with different morphologies and internal characteristics were analyzed in time and frequency domains to understand the species-specific echo feature characteristics for classifying fish species. The mean echo image for each time-frequency representation dataset obtained as a function of orientation angle was extracted to mitigate the effect of fish orientation on acoustic scattering. The joint time-frequency content of the broadband echo signals was obtained using the smoothed pseudo-Wigner-Ville distribution (SPWVD). The SPWVDs were analyzed for each echo signature of the three fish species. The results show that the time-frequency analysis provided species-specific echo structure patterns and metrics of the broadband acoustic signals to facilitate fish species classification.