• International Journal of Industrial Entomology and Biomaterials
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• v.1 no.2
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• pp.171-175
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• 2000

Determined sequences of 384 randomly selected clones in a PCR-based cDNA library of Antheraea yamamai could identify expressed sequence tags (ESTs) of highly expressed gene. One EST (fibroin) appeared 15 times, one EST (40S ribosomal protein S18) twelve times, one EST (ribosomal protein S24a) eleven times, ten times (ribosomal protein S8), nine times (60S ribosomal protein L10A), seven times (60S ribosomal protein S15A, S17, S17 and seroin), six times (ribosomal protein S8), five times (ribosomal protein S24, mariner transposase and P8 protein), four times (serpin 2), three times (heat shock protein 70 and poly A binding protein), and the remaining 6 ESTs twice (amylase, KIAA1006, elongation factor-1, transposon mag, translation initiation factor 4C, QM protein, transposase). Therefore, the 94 EST make it possible to identify 24 redundant clones that are candidates for highly expressed genes in posterior silk gland of this insect. The 24 redundant EST clones were identified in GenBank, but none of them was related to A. yamamai, suggesting that there are many unidentified genes which are highly expressed in the A. yamamai genome.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.2
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• pp.176-183
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• 2016

A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia.

• Journal of Ginseng Research
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• v.41 no.1
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• pp.31-35
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• 2017

Background: Korean ginseng (Panax ginseng) is a well-known medicinal plant of Oriental medicine that is still in practice today. Until now, a total of 11 Korean ginseng cultivars with unique features to Korean ginseng have been developed based on the pure-line-selection method. Among them, a new cultivar namely G-1 with different agricultural traits related to yield and content of ginsenosides, was developed in 2012. Methods: The aim of this study was to distinguish the new ginseng cultivar G-1 by identifying the unique single-nucleotide polymorphism (SNP) at its 45S ribosomal DNA and Panax quinquefolius region than other Korean ginseng cultivars using multiplex amplification-refractory mutation system-polymerase chain reaction (ARMS-PCR). Results: A SNP at position of 45S ribosomal DNA region between G-1, P. quinquefolius, and the other Korean ginseng cultivars was identified. By designing modified allele-specific primers based on this site, we could specifically identified G-1 and P. quinquefolius via multiplex PCR. The unique primer for the SNP yielded an amplicon of size 449 bp in G-1 cultivar and P. quinquefolius. This study presents an effective method for the genetic identification of the G-1 cultivar and P. quinquefolius. Conclusion: The results from our study shows that this SNP-based approach to identify the G-1 cultivar will be a good way to distinguish accurately the G-1 cultivar and P. quinquefolius from other Korean ginseng cultivars using a SNP at 45S ribosomal DNA region.

• Journal of Embryo Transfer
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• v.28 no.4
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• pp.355-360
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• 2013

Precise, rapid and simple methods for species identification in animals are among the most important techniques in the livestock industry and research fields including meat classification. In this study, polymerase chain reaction (PCR) based molecular identification using inter species polymorphisms were examined by PCR-restriction fragment length polymorphism (RFLP) analysis for mitochondrial DNA (mtDNA) cytochrome b (CYTB) gene sequences among four mammalian livestock animals (cattle, horse, goat and pig). The results from PCR-RFLP analysis using the AluI restriction enzyme were also provided for the species-specific band patterns among CYTB gene sequences in these four species. The AluI-digestion for CYTB genes provided interesting migration patterns differentially displayed according to each species. Cattle and horse had one AluI-recognition site at different nucleotide positions and their AluI-digested fragments showed different band patterns on the gels. Pig had two AluI-recognition sites within the amplified CYTB sequences and produced three bands on the gels. Goat had no AluI-recognition site and was located at the same position as the uncut PCR product. The results showed the species-specific band patterns on a single gel among the four livestock animal species by AluI-RFLP. In addition, the results from blind tests for the meat samples collected from providers without any records showed the identical information on the species recorded by observing their phenotypes before slaughter. The application of this PCR-RFLP method can be useful and provide rapid, simple, and clear information regarding species identification for various tissue samples originating from tested livestock species.

• 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.41 no.3
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• pp.185-191
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• 2013

Several yeast colonies were isolated from wild flowers collected from East, West and South coast areas of Korea by plating of flower suspensions on the YPD plates containing antibiotics, streptomycin and ampicillin. Polymerase chain reactions (PCR) were performed for the amplification of D1/D2 region of 26S rDNA for those colonies. PCR-amplified nucleotide sequences were compared using BLAST for their identification. As results, 27 yeast strains belonged to 15 species were isolated from wild flowers collected at Donghae, where is located in eastern coast of Korea. Also, 34 strains belonged to 17 species were isolated from wild flowers of Daecheon, where is located in western coast of Korea. In addition, 22 strains belonged to 13 species were isolated from wild flowers collected at Wando, where is located in southern coast of Korea. Among those 45 species isolated from 3 different collection sites, only 4 species including Cryptococcus laurentii, Metschnikowia koreensis, Pseudozyma rugulosa, and Rhodotorula mucilaginosa were found from all 3 different collection sites. And 5 species including Cryptococcus aureus, Cryptococcus flavus, Hanseniaspora uvarum, Pichia guilliermondii, and Rhodosporidium fluviale were overlapped from the at least 2 different collection sites. Other 23 species were found only in a specific collection sites implying that each area has distinctive yeast flora.

• Animal cells and systems
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• v.5 no.4
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• pp.333-339
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• 2001

Common carp (Cyprinus carpio) and its aquaculture breed Israeli carp samples were obtained from two separate aquaculture facilities under the similar raising conditions during two years in the Kunsan National University, Korea. Genomic DNA was isolated from the common carp and Israeli carp for identification of genetic characteristics and genomic polymorphisms by polymerase chain reaction amplification of DNA using arbitrary primers. The arbitrary primer No.21 (ACTTCGCCAC) yielded the highest number of fragments with the average of 15.0 among the primers used in Israeli carp. A tota1 of 294 polymorphic products in common carp and 336 in Israeli carp were observed by random primers. The average number of polymorphic products generated by random RAPD primer No. 2 (GTAGAC-CCGT) showed 8.0 in Israeli carp. On average, each random RAPD primer produced 5.4 amplified polymorphic products in common carp and 6.2 in Israeli carp. An average genetic similarity (BS value) was 0.44$\pm$0.05 within the common carp and 0.32$\pm$0.04 within the Israeli carp. The degree of similarity frequency (BS) between two carps was 0.67 as generated by the primer No. 19 (GACGGATCAG). The average level of bandsharing was 0.57$\pm$0.03 between the two carps. Accordingly, the two carp populations were genetically a little distant. The electrophoretic analysis of PCR-RAPD products showed middle levels of variation between the two carp populations. This result implies that the genetic diversity among intra-population may be higher when compared with that between the two carps. The RAPD polymorphism generated by these random primers might be used as a genetic marker for populations or lines identification in important aquacultural carp.

• Korean Journal of Plant Resources
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• v.26 no.3
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• pp.397-402
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• 2013

Morus Folium (Sang-yeop in Korean) is one of the most important Oriental medicinal plants. In Korea, both M. alba and M. cathayana are regarded as the botanical sources for Morus Folium. In order to discriminate M. alba and M. cathayana from their adulterant, M. tricuspidata, mitochondrial NADH dehydrogenase subunit 7 (nad7) intron 2 region was targeted for molecular analysis with universal primers. DNA polymorphisms, including SNP sites, insertions, and deletions, were detected among these three species sequencing data. Based on these DNA polymorphisms, specific primers were designed for the three species respectively. Multiplex PCR was conducted for molecular authentication of M. alba, M. cathayana, and M. tricuspidata with specific primers. The present results indicate that it is possible to identify Morus Folium from its adulterant using mitochondrial nad7 intron 2 region. The established multiplex-PCR system was proved to be effective for identification of Morus Folium. The results indicate that mitochondrial introns can be used for inter-specific polymorphic study, and the described method can be applied for molecular identification of medicinal materials.

• Bulletin of the Korean Chemical Society
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• v.27 no.5
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• pp.657-662
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• 2006

Identification of accessible sites in targeted RNAs is a major limitation to the effectiveness of antisense oligonucleotides. A class of antisense oligodeoxynucleotides, known as the “10-23” DNA enzyme or DNAzyme, which is a small catalytic DNA, has been shown to efficiently cleave target RNA at purine-pyrimidine junctions in vitro. We have designed a strategy to identify accessible cleavage sites in the target RNA, which is hepatitis C virus nonstructural gene 3 (HCV NS3) RNA that encodes viral helicase and protease, from a pool of random DNAzyme library. A pool of DNAzymes of 58 nucleotides-length that possess randomized annealing arms, catalytic core sequence, and fixed 5'/3'-end flanking sequences was designed and screened for their ability to cleave the target RNA. The screening procedure, which includes binding of DNAzyme pool to the target RNA under inactive condition, selection and amplification of active DNAzymes, incubation of the selected DNAzymes with the target RNA, and target site identification on sequencing gels, identified 16 potential cleavage sites in the target RNA. Corresponding DNAzymes were constructed for the selected target sites and were tested for RNA-cleavage in terms of kinetics and accessibility. These selected DNAzymes were effective in cleaving the target RNA in the presence of $Mg^{2+}$. This strategy can be applicable to identify accessible sites in any target RNA for antisense oligonucleotides-based gene inactivation methods.

• Journal of Plant Biotechnology
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• v.43 no.4
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• pp.457-465
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• 2016

Microsatellites are one of the most suitable markers for identification of variety, as they have the capability to discriminate between narrow genetic variations. The polymorphism level between 120 microsatellite primer pairs and 148 soybean varieties was investigated through the fluorescence based automatic detection system. A set of 16 primer pairs showed highly reproducible polymorphism in these varieties. A total of 204 alleles were detected using the 16 microsatellite markers. The number of alleles per locus ranged from 6 to 28, with an average of 12.75 alleles per locus. The average polymorphism information content (PIC) was 0.86, ranging from 0.75 to 0.95. The unweighted pair group method using the arithmetic averages (UPGMA) cluster analysis for 148 varieties were divided into five distinctive groups, reflecting the varietal types and pedigree information. All the varieties were perfectly discriminated by marker genotypes. These markers may be useful to complement a morphological assessment of candidate varieties in the DUS (distinctness, uniformity and stability) test, intervening of seed disputes relating to variety authentication, and testing of genetic purity in soybean varieties.