• Journal of Life Science
• /
• v.28 no.9
• /
• pp.1118-1126
• /
• 2018

In this study, investigated the general characteristics and diagnostic methods types of streptococcosis among various fish disease pathogens that caused a lot of economic damaged to aquaculture fish based on the previous research paper. Streptococcosis infection of fish is considered a reemerging disease affecting a variety of wild and cultured fish throughout the world. Calssifiacation of Gram positive cocci based on DNA-DNA hybridization coupled with 16S sequencing has shown that at least five different species are considered of significance as fish pathogens: Lactococcus garvieae, L. piscium, Streptococcus iniae, S. agalactiae, S. paruberis, Vagococcus salmoninarum. Symptoms of infection with streptococcosis disease such as body color change, eyeball abnormality, gill discoloration, bleeding, abdominal distension, swelling of the kidney and spleen. In addition, it usually occurs from June to October when the water temperature rise a lot of fish death. Currently, 16S rRNA, 16S-23S rRNA intergenic spacer region (ISR), Random Amplified polymorphic DNA (RAPD), Ribotyion (RT), Loop-mediated isothermal amplification (LAMP) are among the methods for diagnosing streptococcosis. Among them, the LAMP method, which is high applicable to the aquaculture farm has attracted the spotlight, but due to problems such as confirmation of results. This seems to minimize the economic loss of streptococcosis which complements the problem so that it can be easily used from the diagnosis to the results confirmation.

• Research in Plant Disease
• /
• v.26 no.2
• /
• pp.79-87
• /
• 2020

Fusarium wilt caused by Fusarium oxysporum f. sp. fragariae (Fof) is the most important diseases of a strawberry field in Korea. We surveyed phylogenetic analysis, pathogenicity test, and fungicide response about Fof isolates isolated from Korea. Twenty-seven isolates of F. oxysporum isolated from strawberry plants were conducted in this study. Specific amplification by Fof specific primer was confirmed in all 26 isolates except Fo080701 isolate. The nuclear ribosomal intergenic spacer region and the translation elongation factor EF-lα gene sequences of isolates revealed three main lineages. Most of all isolates were contained DNA lineage group 1, but 2 and 3 group was shown only one and three isolates, respectively. All isolates were shown in pathogenicity with cv. Seolhyang. The EC₅₀ mean values of prochloraz ranged 0.02-0.1 ㎍/ml except for Fo080701 and effectively inhibited mycelial growth at low concentrations. The EC₅₀ value of metconazole was also 0.04-0.22 ㎍/ml, showing a similar inhibitory effect to that of prochloraz. The EC₅₀ value of pyraclostrobin was 0.23-168.01 ㎍/ml, which was different according to the strain. In the field trial, boscalid+fludioxonil, fluxapyroxad+pyraclostrobin, and prochloraz manganese were selected as the effective fungicides for controlling Fusarium wilt.

• Journal of Plant Biotechnology
• /
• v.45 no.2
• /
• pp.102-109
• /
• 2018

Thistle is a perennial plant that is widely used for medicinal purposes. Information on the genetic diversity of thistle populations are great important for their conservation and germ plasmic utilization. Although thistle is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish them from other similar species from different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from the nuclear ribosomal DNA internal transcribed spacer (ITS) regions of genomic sequences to identify distinct Korean-specific thistle species via an amplification refractory mutation system (ARMS)-PCR and high resolution melting (HRM) curve analyses. We performed molecular authentication of four different kinds of thistle species from different regions using DNA sequences in the ITS intergenic region. We also developed a quantitative PCR assay using species-specific ITS primers, which allowed us to estimate the ratio of Korean-specific thistle species using varying ratios of mixed genomic DNA templates from the two species. The SNP markers developed in this study are useful for rapidly identifying specific thistle species from different countries.

• Molecules and Cells
• /
• v.27 no.3
• /
• pp.365-381
• /
• 2009

The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast MatK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our molecular trees support Ohwi's original treatment of Megaleranthis saniculifolia to Trollius chosenensis Ohwi.

• Biomedical Science Letters
• /
• v.25 no.1
• /
• pp.40-53
• /
• 2019

Of the Acinetobacter spp., A. baumannii (genospecies 2) is the most clinically significant in terms of hospital-acquired infections worldwide. It is difficult to perform Acinetobacter-related taxonomy using phenotypic characteristics and routine laboratory methods owing to clusters of closely related species. The ability to accurately identify Acinetobacter spp. is clinically important because antimicrobial susceptibility and clinical relevance differs significantly among the different genospecies. Based on the medical importance of pathogenic Acinetobacter spp., the distribution and characterization of Acinetobacter spp. isolates from 123 clinical samples was determined in the current study using four typically applied bacterial identification methods; partial rpoB gene sequencing, amplified rRNA gene restriction analysis (ARDRA) of the intergenic transcribed spacer (ITS) region of the 16~23S rRNA, the $VITEK^{(R)}$ 2 system (an automated microbial identification system) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). A. baumannii isolates (74.8%, 92/123) were the most common species, A. nosocomialis (10.6%, 13/123) and A. pittii isolates (7.5%, 9/123) were second and third most common strains of the A. calcoaceticus-A. baumannii (ACB) complex, respectively. A. soli (5.0%, 6/123) was the most common species of the non-ACB complex. RpoB gene sequencing and ARDRA of the ITS region were demonstrated to lead to more accurate species identification than the other methods of analysis used in this study. These results suggest that the use of rpoB genotyping and ARDRA of the ITS region is useful for the species-level identification of Acinetobacter isolates.

• Mycobiology
• /
• v.46 no.2
• /
• pp.92-100
• /
• 2018

The filamentous Ascomycota Colletotrichum gloeosporioides sensu lato is a fungus that has been reported worldwide as a causal agent of anthracnose disease in avocado and other crops. In Mexico, this species affects fruits from an early stage of development in the orchard until the post-harvest stage. Although fungicides are continuously applied to control Colletotrichum species, pericarp cankers and soft rot mesocarp in fruits are still frequently observed. Considering the lack of a precise description of the causative agent, the aim of the current study was to determine the pathogens involved in this symptomatology. Twenty-four isolates were consistently obtained from the pericarp of avocado fruits cv. "Hass" collected in the central avocado-producing area of Mexico. Morphological features such as colony growth, conidia size, and mycelial appressorium were assessed. Bayesian multilocus phylogenetic analyses were performed using amplified sequences of the internal transcribed spacer region of the nuclear ribosomal DNA; actin, chitin synthase, glyceraldehyde-3-phosphate dehydrogenase partial genes; and APn2-Mat1-2 intergenic spacer and mating type Mat1-2 partial gene from the nine selected isolates. In addition, fruits were inoculated with a conidial suspension and reproducible symptoms confirmed the presence of Colletotrichum fructicola in this area. This pathogenic species can now be added to those previously reported in the country, such as C. acutatum, C. boninense, C. godetiae, C. gloeosporioides, and C. karstii. Disease management programs to reduce the incidence of anthracnose should include C. fructicola to determine its response to fungicides that are routinely applied, considering that the appearance of new species is affecting the commercial quality of the fruits and shifting the original population structure.

• Journal of Plant Biotechnology
• /
• v.48 no.1
• /
• pp.26-33
• /
• 2021

Angelica is a widely used medicinal and perennial plant. Information on the genetic diversity of Angelica populations is essential for their conservation and germ plasmic utilization. Although Angelica is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish it from other similar species from different countries. This developed single nucleotide polymorphism (SNP) markers derived from nuclear ribosomal DNA internal transcribed spacer regions genomic sequences to identify distinct Korean-specific Angelica species via amplification refractory mutation system (ARMS)-PCR curve analyses. We performed molecular authentication of different kinds of Korean-specific Angelica species such as A. gigas Nakai and A. gigas Jiri using DNA sequences in the ITS intergenic region. The SNP markers developed in this study are useful for rapidly identifying specific Angelica species from different countr.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.3
• /
• pp.490-495
• /
• 2007

Lactic acid bacteria (LAB) are beneficial for the gastrointestinal tract and reinforce immunity in human health. Recently, many functional products using the lactic acid bacteria have been developed. Among these LAB, Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium longum, and Bifidobacterium bifidum are frequently used for probiotic products. In order to monitor these LAB in commercial probiotic products, a multiplex PCR method was developed. We designed four species-specific primer pairs for multiplex PCR from the 16S rRNA, 16S-23S rRNA intergenic spacer region, and 23S rRNA genes in Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium longum, and Bifidobacterium bifidum. Using these primer pairs, 4 different LAB were detected with high specificity in functional foods. We suggest that the multiplex PCR method developed in this study would be an efficient tool for simple, rapid, and reliable identification of LAB used as probiotic strains.

• Journal of Microbiology and Biotechnology
• /
• v.25 no.3
• /
• pp.321-327
• /
• 2015

Nocardia salmonicida is one of the main pathogens of fish nocardiosis. The purpose of this study was to build a loop-mediated isothermal amplification (LAMP) method for the rapid and sensitive detection of N. salmonicida. A set of four primers were designed from the 16S-23S rRNA intergenic spacer region of N. salmonicida, and conditions for LAMP were optimized as incubating all the reagents for 60 min at 64℃. LAMP products were judged with agar gel electrophoresis as well as with the naked eye after the addition of SYBR Green I. Results showed the sensitivity of the LAMP assay was 1.68 × 10³ CFU/ml (16.8 CFU per reaction) and 10-fold higher than that of PCR. The LAMP method was also effectively applied to detect N. salmonicida in diseased fish samples, and it may potentially facilitate the surveillance and early diagnosis of fish nocardiosis.

• Parasites, Hosts and Diseases
• /
• v.49 no.4
• /
• pp.381-384
• /
• 2011

The first human case with trichinellosis was reported in 1964 in Tibet, China. However, up to the present, the etiological agent of trichinellosis has been unclear. The aim of this study was to identify a Tibet Trichinella isolate at a species level by PCR-based methods. Multiplex PCR revealed amplicon of the expected size (173 bp) for Trichinella spiralis in assays containing larval DNA from Tibet Trichinella isolate from a naturally infected pig. The Tibet Trichinella isolate was also identified by PCR amplification of the 5S ribosomal DNA intergenic spacer region (5S ISR) and mitochondrial largesubunit ribosomal RNA (mt-lsrDNA) gene sequences. The results showed that 2 DNA fragments (749 bp and 445 bp) of the Tibet Trichinella isolate were identical to that of the reference isolates of T. spiralis. The Tibet Trichinella isolate might be classifiable to T. spiralis. This is the first report on T. spiralis in southwestern China.