• International Journal of Industrial Entomology and Biomaterials
• /
• v.33 no.2
• /
• pp.121-131
• /
• 2016

Ten microsporidian isolates from Samia cynthia ricini, and Antheraea assamensis in India along with a Nosema reference strain (NIK-1s_mys) from B. mori India were characterised morphologically and molecular based tools. The test isolates observed elongated oval in shape while reference strain was oval and ranging from 3.80 to 4.90 m in length and 2.60 to 3.05 m in width. The ribosomal DNA region 'IGS' of test isolates assessed by PCR amplification, followed by cloning and sequencing. IGS sequence and phylogenetic analysis of test microsporidian isolates showed very close relationship with three Nosema references species: N. philosamia, N. antheraea isolated from Philosamia cynthia ricini and Antheraea perny in China respectively and N. disstriae from Malacosma disstriae in Canada. The clustering pattern of dendogram reveals all test isolates appear distinct from Nosema std. (NIK-1s_mys) India used as reference strain in the study. The result suggests IGS indeed a suitable and highly applicable molecular tool for identifying and characterise the microsporidian isolates in similar population.

• Journal of Sericultural and Entomological Science
• /
• v.51 no.2
• /
• pp.137-141
• /
• 2013

In this study, nucleotide sequence structures of intergenic transcribed spacer (ITS) 1, complete 5.8S ribosomal RNA gene and ITS 2 region were analyzed to identify three Peruvian entomopathogenic fungal isolates. The isolates had highly conserved sequence region in 5.8S rRNA gene and unique sequences in ITS 1 and 2 region among them. 5.8S rRNA gene regions were highly conserved and showed high homoloies among tested isolates. In contrast, ITS region showed species-specific sequence region, resulting in inter-genus differencies. Scanning electron microscopic images of these isolates supported the result of ITS-based identification. From these result, Peruvian entomopathogenic fungal isolate J270, J278, were identified as Beauveria bassiana and J271 was identified as Lecanicillium attenuatum.

• Korean Chemical Engineering Research
• /
• v.48 no.2
• /
• pp.147-156
• /
• 2010

There are four key factors for gas-phase biofilters; biocatalysts(microorganisms), packing materials, design/operating techniques, and diagnosis/management techniques. Biofilter performance is significantly affected by microbial community structures as well as loading conditions. The microbial studies on biofilters are mostly performed on basis of culture-dependent methods. Recently, advanced methods have been proposed to characterize the microbial community structure in environmental samples. In this study, the physiological, biochemical and molecular methods for profiling microbial communities are reviewed, and their applicability to biofilters is discussed. Community-level physiological profile is based on the utilization capability of carbon substrate by heterotrophic community in environmental samples. Phospholipid fatty acid analysis method is based on the variability of fatty acids present in cell membranes of different microorganisms. Molecular methods using DNA directly extracted from environmental samples can be divided into "partial community DNA analysis" and "whole community DNA analysis" approaches. The former approaches consist in the analysis of PCR-amplified sequence, the genes of ribosomal operon are the most commonly used sequences. These methods include PCR fragment cloning and genetic fingerprinting such as denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism, ribosomal intergenic spacer analysis, and random amplified polymorphic DNA. The whole community DNA analysis methods are total genomic cross-DNA hybridization, thermal denaturation and reassociation of whole extracted DNA and extracted whole DNA fractionation using density gradient.

• Journal of Plant Biotechnology
• /
• v.44 no.3
• /
• pp.235-242
• /
• 2017

Cudrania tricuspidata Bureau is a widely-used, medicinal, perennial and woody plant. Obtaining information about the genetic diversity of plant populations is highly important with regard toconservation and germplasm utilization. Although C. tricuspidata is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish Korean-specific ecotypes from other ecotypes from different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from the chloroplast and nuclear genomic sequences, which serve to to identify distinct Korean-specific ecotypes of C. tricuspidata via amplification refractory mutation system (ARMS)-PCR and high resolution melting (HRM) curve analyses. We performed molecular authentication of twelve C. tricuspidata ecotypes from different regions using DNA sequences in the maturaseK (MatK) chloroplast intergenic region and nuclear ribosomal DNA internal transcribed spacer (ITS) regions. The SNP markers developed in this study are useful for rapidly identifying specific C. tricuspidata ecotypes from different regions.

• Weed & Turfgrass Science
• /
• v.3 no.3
• /
• pp.183-189
• /
• 2014

The genus Echinochloa (L.) P. Beauv. comprised of approximately 30-40 species in the tropical and warm temperate regions of the world, including numerous interspecific and intraspecific types which make the genus difficult to identify. As an attempt to identify the species within the genus easier, the taxonomy of the genus Echinochloa, Poaceae in Korea was reviewed on the basis of sequencing data derived from nuclear ribosomal DNA internal transcribed spacer (ITS) and external transcribe spacer and chloroplast DNA trnL intron, trnL-F intergenic spacer and matK regions using a total of 46 accessions representing all the species in Korea. The results of maximum parsimony found separate lineage comprised of E. colona and E. frumentaceae which are not Korean species, but no resolution within Korean Echinochloa species, supporting the suggestion of Yamaguchi group that E. crus-galli, E. oryzoides, and E. esculenta should be considered to belong to the same species. However, the relationship between these three species and the other species, i.e. E. oryzicola should be better understood with more detail studies.

• Journal of Microbiology and Biotechnology
• /
• v.11 no.6
• /
• pp.1046-1054
• /
• 2001

Bioleaching is the process in which insoluble metal sulfide is oxidized by specialized iron- and/or sulfur-oxidizing lithotrophic bacteria in acidic, metal-rich environments. Most of these processes are carried out by the genus Thiobacillus. Three novel Thiobacillus strains (Thiobacillus thiooxidans AZ11, Thiobacillus thiooxidans MET, and thiobacillus thiooxidans TAS) associated with bioleaching have been isolated from soil and sludge (Korean patent No. 1999-0073060 for T. thiooxidans AZ11, Korean patent No. 1999-0005798 for T. thiooxidans MET, and Korean patent No. 1999-0073059 for T. thiooxidans TAS). A partial sequence of 16S ribosomal RNA gene (16S rDNA) and the entire sequence of 16S/23S intergenic spacer region (ISR) were determined in the three above novel strains and in Thiobacillus ferrooxidans ATCC19859 as a reference strain. When phylogenetic analysis was performed based on G+C contents and sequence alignments, T. ferroxidans ATCC19859 was found to be closely related to previously registered T. ferrooxidans strains in a monophyletic manner, while the three novel T. thiooxidans strains were classified in a paraphyletic manner. Close examination on the base composition of 16S/23S ISR revealed that the 5\` part (nucleotide residues 21-200) was specific for the genus Thiobacillus. On the other end, the 3\` part (nucleotide residues 201-520) showed specificity in T. ferrooxidans strains, but not in T. thiooxidans strains. These results suggest that the proximal and distal halves of 16S/23S could be used as a genetic marker for the identification of the genus Thiobacillus and the species T. ferrooxidans, respectively.

• 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.

• Korean Journal Plant Pathology
• /
• v.14 no.4
• /
• pp.350-357
• /
• 1998

A total of 12 strains of fluorescent Pseudomonas isolated from the cultivated mushrooms such as Agaricus bisporus and Pleurotus ostreatus were collected. They consisted of pathogenic Pseudomonas spp. and epiphytic Pseudomonas spp. of the cultivated mushroom. To analyze the phylogenetic relationship of these strains, ITS I region, the 16S-23S intergenic spacer region in the ribosomal RNA (rRNA) operon, was cloned and sequenced. The spacer regions of these strains were 495∼527 nucleotides in length and contained the genes encoding isoleucine-tRNA (tRNAIle) and alanine-tRNA (tRNAAla). The reciprocal homologies of each ITS I sequence among these strains were in the range of 84.2%∼98.8%. According to the analysis of ITS I sequences, the fluorescent Pseudomonas spp. were phylogenetically classified into three clusters. Cluster I consisted of Pseudomonas fluorescens, P. tolaasii, P. gingeri’, and P.‘reactans’(WLRO). Cluster II comprised Pseudomonas fluorescens biovar C and F. Cluster III composed P. agarici. Cluster I and II could be classified into P. fluorescens complex. P. agarici formed an independent taxon clearly separable from P. florescens complex.

• 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.

• 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.