• Biomedical Science Letters
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• v.10 no.4
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• pp.333-339
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• 2004

A multiplex PCR assay targeting the yst and 16S rRNA genes of Yersinia enterocolitica was developed to specifically identify pathogenic Y. enterocolitica from pure culture. Simultaneous amplification of 145 and 416 bp fragments of the yst and 16S rRNA genes of Y. enterocolitica was obtained using the primer pairs in a single reaction. Validation of the assay was performed with the reference Yersinia strains and other members of the family Enterobacteriaceae. The defined primer pairs amplified the targeted sequence from only pathogenic Y. enterocolitica strains, whereas none of the other bacterial species yielded any amplified fragments. Within an assay time of 4 h, this assay offers a very specific, reliable, and inexpensive alternative to the conventional phenotypic assays used in clinical laboratories to identify pathogenic Y. enterocolitica.

• The Korea Journal of Herbology
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• v.29 no.6
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• pp.45-53
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• 2014

Objectives : Due to the morphological similarity of in the roots of herbal medicine, the official herbal medicine is very difficult to authenticate between the original plants of Patriniae Radix and two adulterant Patrinia species. Therefore, we introduced DNA barcode analysis to establish a powerful tool for the authentication of Patriniae Radix from its adulterants. Methods : To analyze DNA barcode regions, genomic DNA was extracted from twenty-nine specimens of Patrinia scabiosaefolia, Patrinia villosa, Patrinia saniculifolia, and Patrinia rupestris, and internal transcribed spacer 2(ITS2), matK and rbcL genes were amplified. For identification of species specific sequences, a comparative analysis was performed by the ClastalW based on entire sequences of ITS2, matK and rbcL genes, respectively. Results : In comparison of three DNA barcode sequences, we identified 22, 22, and 12 species-specific nucleotides enough to distinguish each four species from ITS2, matK and rbcL gene, respectively. The sequence differences at the corresponding positions were available genetic marker nucleotides to discriminate the correct species among analyzed four species. These results indicated that comparative analysis of ITS2, matK and rbcL genes were useful genetic markers to authenticate Patriniae Radix. Conclusions : The marker nucleotides enough to distinguish P. scabiosaefolia, P. villosa, P. saniculifolia, and P. rupestris, were obtained at 22 SNP marker nucleotides from ITS2 and matK DNA barcode sequences, but they were confirmed at 12 SNP marker nucleotides from rbcL. These differences could be used to authenticate Patriniae Radix from its adulterants as well as discriminating each four species.

• Molecules and Cells
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• v.43 no.8
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• pp.728-738
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• 2020

Time and cost-effective production of next-generation sequencing data has enabled the performance of population-scale comparative and evolutionary studies for various species, which are essential for obtaining the comprehensive insight into molecular mechanisms underlying species- or breed-specific traits. In this study, the evolutionary and functional analysis of Korean native pig (KNP) was performed using single nucleotide polymorphism (SNP) data by comparative and population genomic approaches with six different mammalian species and five pig breeds. We examined the evolutionary history of KNP SNPs, and the specific genes of KNP based on the uniqueness of non-synonymous SNPs among the used species and pig breeds. We discovered the evolutionary trajectory of KNP SNPs within the used mammalian species as well as pig breeds. We also found olfaction-associated functions that have been characterized and diversified during evolution, and quantitative trait loci associated with the unique traits of KNP. Our study provides new insight into the evolution of KNP and serves as a good example for a better understanding of domestic animals in terms of evolution and domestication using the combined approaches of comparative and population genomics.

• Journal of Microbiology
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• v.42 no.4
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• pp.365-368
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• 2004

The occurrence of strA-strB streptomycin-resistance genes within transposon Tn5393 was examined in Pseudomonas syringae pv. actinidiae, P. syringae pv. syringae, and P. marginalis, isolated from kiwifruit plants in Korea and Japan. PCR amplification with primers specific to strA-strB revealed that three of the tested Pseudomonas species harbored these genes for a streptomycin-resistance determinant. Tn5393, containing strA-strB, was also identified with PCR primers designed to amplify parts of tnpA, res, and tnpR. No IS elements were detected within tnpR, nor were they found in the intergenic region between tnpR and strA. Nucleotide sequence analysis indicated that the strA sequence of P. syringae pv. actinidiae contained a single nucleotide alteration at position 593 (CAA $\rightarrow$CGA), as compared to Tn5393a in P. syringae pv. syringae. This resulted in an amino acid change, from Gin to Arg.

• Journal of Pharmacopuncture
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• v.12 no.1
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• pp.13-20
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• 2009

Objective : This study developed species-specific PCR and PCR-RFLP to detect the adulteration of Fel ursi products with cattle and pig bile juices. Methods : All the primers for PCR and PCR-RFLP in this study were designed based on nucleotide sequences of cytochrome b genes in the mitochondria. Results : The species-specific PCR amplified a DNA fragment of 214, 214, 295, and 167 bp from Fel ursi product, bear fur, cattle bile juice, and pig bile juice, respectively. The survey using the speciesspecific PCR indicated that some of commercial Fel ursi products were adulterated with cattle and pig bile juices. PCR-RFLP using the restriction endonucleases, HaeIII and HinfI enabled differentiation among Fel ursi product, cattle bile juice, and pig bile juice. Bear furs from two animals showed variations in PCR-RFLP patterns with HaeIII. Discussion : The detection methods of the species-specific PCR and PCR-RFLP could be useful in eliminating adulterated Fel ursi products from the market.

• Journal of Ginseng Research
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• v.44 no.1
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• pp.135-144
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• 2020

Background: Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P. quinquefolius and P. trifolius) from North America and five (P. ginseng, P. notoginseng, P. japonicus, P. vietnamensis, and P. stipuleanatus) from Asia. Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. Results: We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. Conclusion: The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.

• BMB Reports
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• v.37 no.1
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• pp.107-113
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• 2004

Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.

• Korean Journal of Medicinal Crop Science
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• v.23 no.6
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• pp.439-445
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• 2015

Background : Correct identification of Panax species is important to ensure food quality, safety, authenticity and health for consumers. This paper describes a high resolution melting (HRM) analysis based method using internal transcribed spacer (ITS) and 5.8S ribosomal DNA barcoding regions as target (Bar-HRM) to obtain barcoding information for the major Panax species and to identify the origin of ginseng plant. Methods and Results : A PCR-based approach, Bar-HRM was developed to discriminate among Panax species. In this study, the ITS1, ITS2, and 5.8S rDNA genes were targeted for testing, since these have been identified as suitable genes for use in the identification of Panax species. The HRM analysis generated cluster patterns that were specific and sensitive enough to detect small sequence differences among the tested Panax species. Conclusion : The results of this study show that the HRM curve analysis of the ITS regions and 5.8S rDNA sequences is a simple, quick, and reproducible method. It can simultaneously identify three Panax species and screen for variants. Thus, ITS1HRM and 5.8SHRM primer sets can be used to distinguish among Panax species.

• The Plant Pathology Journal
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• v.22 no.2
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• pp.168-173
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• 2006

To develop the diagnostic method for the viral infection in apple, the partial genes corresponding to the N-terminal region of RNA polymerase of Apple stem grooving virus (ASGV) and coat protein of Apple chlorotic leaf spot virus (ACLSV) were characterized from the infected apple cultivars in Korea. Based on the nucleotide sequences of the characterized partial genes, the virus gene-specific primers were designed for the detection of ASGV and ACLSV infected in species of Malus. The RT-PCR using the primers for the genes of ASGV and ACLSV successfully gave rise to 404 and 566 bp DNA fragments, respectively. Using those viral gene-specific primers, the multiplex RT-PCR assays were also established to diagnose the mixed infection by ASGV and ACLSV simultaneously. Furthermore, the control primers, which have to be included for the RT-PCR as an internal control, were designed using the nucleotide sequence of the gene encoding elongation factor $1{\alpha}(EF1{\alpha})$. This multiplex RT-PCR including the control primers provides more reliable, rapid and sensitive assay for the detection of ASGV and ACLSV infected in Korean apple cultivars.

• Development and Reproduction
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• v.14 no.4
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• pp.261-268
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• 2010

As in the O. mykiss electrophoretic profiles of RNA, the signals of each RNA sample from 9 individual tissues such as liver, muscle, brain, heart, pituitary gland, kidney, intestine, spleen and gill similar to positive control were obtained. The tissue distributions of the complimentary DNA (cDNA) of O. mykiss four genes were analyzed using quantitative real-time PCR with primer sets for tissue expression analysis. In this rainbow trout species, author obtained bands of various sizes, ranged from 700 bp to 1,400 bp. A dissociation curve was made at the end of each run to make sure that there was no non-specific amplification. Supplementarily, the Ct of each DNA was compared. The Ct values of vinculin with rainbow trout tissues were determined in a manner similar to those for agouti-related protein (AgRP) and melanocortin receptors (MC4R I and MC4R II). Further, obtained Cts for standard curve of each DNA were affected by specific product (vinculin, AgRP and MC4R II genes). After several experiments with four individual genes of rainbow trout, author estimated a variation ratio of the mean Ct value of the DNA extracted using the comparative CTt method was 37.27, and the standard deviation was 5.33. The correlation coefficient between the Ct values and the concentration of cDNA was -0.98, -0.99, -0.91 and -0.86, respectively (vinculin, AgRP, MC4R I and MC4R II genes). Since this correlation showed high linearity, the straight line obtained was used as a standard for the O. mykiss tissues reared in aquarium. A PCR efficiency of 100% is ideally achieved when the slopes are close to the theoretical value of -3.31. According to quantification method, the results of quantification are strongly affected by the DNA fragmentation. The size of most DNA fragments obtained from various tissues of rainbow trout used in the experiment was approximately 100 bp. According to the four slopes, an efficiency of nearly 100% was estimated for four genes detection methods. Additionally, further analysis with more individuals and primers will be required to fully establish optimization in rainbow trout.