• Molecules and Cells
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• v.22 no.1
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• pp.78-88
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• 2006

The phylogeny of the subfamily Tephritinae (Diptera: Tephritidae) was reconstructed from mitochondrial 16S ribosomal RNA gene sequences using 53 species representing 11 currently recognized tribes of the Tephritinae and 10 outgroup species. The minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) monophyly of the Tephritinae was strongly supported; (2) a sister group relationship between the Tephritinae and Plioreocepta was supported by the Bayesian tree; (3) the tribes Tephrellini, Myopitini, and Terelliini (excluding Neaspilota) were supported as monophyletic groups; (4) the non-monophyletic nature of the tribes Dithrycini, Eutretini, Noeetini, Tephritini, Cecidocharini, and Xyphosiini; and (5) recognition of 10 putative tribal groups, most of which were supported strongly by the statistical tests of the interior branches. Our results, therefore, convincingly suggest that an extensive rearrangement of the tribal classification of the Tephritinae is necessary. Since our sampling of taxa heavily relied on the current accepted classification, some lineages identified by the present study were severely under-sampled and other possible major lineages of the Tephritinae were probably not even represented in our dataset. We believe that our results provide baseline information for a more rigorous sampling of additional taxa representing all possible major lineages of the subfamily, which is essential for a comprehensive revision of the tephritine tribal classification.

• Korean Journal of Clinical Laboratory Science
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• v.49 no.2
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• pp.135-140
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• 2017

Polymerase chain reaction (PCR) was used to detect cattle material from processed meat products. Seventy-eight different commercial processed meat products were purchased from several big food marts. Among them, 17 products contained cattle material (10 samples contained only cattle, 5 samples mixed with cattle and porcine, 2 samples mixed with cattle, porcine and chicken). The genomic DNA was extracted directly from the processed meat products, and strain-specific primer targeting the 16S ribosomal RNA mitochondrial gene was used. All PCR products were cloned into the pGEM-T easy vector and sequenced. Consequently, the PCR products were amplified from 10 processed meat products, which contained only cattle material in our conditions. Furthermore, PCR reactions showed the same results at mixed samples. The DNA sequence obtained from pGEM-T easy/PCR products showed more than 95% identity with Bos taurus 16S rRNA gene using homology analysis. In conclusion, we suggest that the method using PCR, as performed in this study, could be useful in detecting cattle material in processed meat products. Moreover, our system could be applicable in inspection procedures to improve the verification of correct labeling for import and export processed meat products.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.739-749
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• 2013

The seasonal and spatial diversity of picocyanobacteria (Pcy) in lakes of the Great Mazurian Lakes (GLM) system was examined by DGGE analysis of molecular markers derived from the 16S-23S internal transcribed spacer (ITS) of the ribosomal operon and the phycocyanin operon (cpcBA-IGS). The study of nine lakes, ranging from mesotrophy to hypereutrophy, demonstrated seasonal variance of Pcy. The richness and Shannon diversity index calculated on the basis of both markers were higher in spring and lower in early and late summer. No statistically significant relationships were found between the markers and trophic status of the studied lakes or Pcy abundance. There were, however, statistically significant relationships between the diversity indices and sampling time. The analysis pointed to a different distribution of the two markers. The ITS marker exhibited more unique sequences in time and space, whereas a greater role for common and ubiquitous sequences was indicated by the cpcBA-IGS data. Examination of the Pcy community structure demonstrated that communities were grouped in highly similar clusters according to sampling season/time rather than to the trophic status of the lake. Our results suggest that time is more important than trophic status in shaping the diversity and structure of Pcy communities. The seasonal changes in picocyanobacteria and differences in diversity and community structures are discussed in the context of well-established ecological hypotheses: the PEG model, intermediate disturbance hypothesis (IDH), and horizontal gene transfer (HGT).

• Korean Journal of Soil Science and Fertilizer
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• v.49 no.2
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1537-1543
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• 2006

A bacterial strain named HY-3 that produces a highly active extracellular protease was isolated from the digestive tract of a spider, Nephila clavata. The bacterium was a Gram-negative, oxidase-negative, catalase-positive, nonhalophilic, nitrate-reducing, facultative anaerobe. Transmission and scanning electron microscopies demonstrated that the isolate was non-spare-forming, straight, rod-shaped, and motile by peritrichous flagella. The G+C content of the DNA was 57.0 mol%. The isoprenoid quinone type was ubiquinone with 8 isoprene units (Q-8). The morphological and biochemical characteristics including the predominant fatty acid and phospholipids profiles placed the isolate HY-3 in the family Enterobacteriaceae. Further biochemical characterization and phylogenetic studies including determination of an almost complete 16S ribosomal DNA sequence suggested that the bacterium was closely related to the genus Serratia. DNA-DNA hybridization analysis revealed that this extracellular protease-producing strain belongs to Serratia proteamaculans, which is also known far its association with insects.

• Journal of Microbiology and Biotechnology
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• v.21 no.6
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• pp.545-555
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• 2011

The diversity elucidation by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of 96 associative diazotrophs, isolated from the feeder roots of tea on enriched nitrogen-free semisolid media, revealed the predominance of Gram-positive over Gram-negative bacteria within the Kangra valley in Himachal Pradesh, India. The Gram-positive bacteria observed belong to two taxonomic groupings; Firmicutes, including the genera Bacillus and Paenibacillus; and Actinobacteria, represented by the genus Microbacterium. The Gram-negative bacteria included ${\alpha}$-Proteobacteria genera Brevundimonas, Rhizobium, and Mesorhizobium; ${\gamma}$-Proteobacteria genera Pseudomonas and Stenotrophomonas; and ${\beta}$-Proteobacteria genera Azospira, Burkholderia, Delftia, Herbaspirillum and Ralstonia. The low level of similarity of two isolates, with the type strains Paenibacillus xinjiangensis and Mesorhizobium albiziae, suggests the possibility of raising species novum. The bacterial strains of different phylogenetic groups exhibited distinct carbon-source utilization patterns and fatty acid methyl ester profiles. The strains differed in their nitrogenase activities with relatively high activity seen in the Gramnegative strains exhibiting the highest similarity to Azospira oryzae, Delftia lacustris and Herbaspirillum huttiense.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.7
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• pp.1057-1065
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• 2002

The antagonistic activities of 30 strains of lactobacilli against Helicobacter pylori were determined and Lactobacillus helveticus CU631 has been selected as the strain which possesses the strongest inhibitory effect in the disc diffusion assay showing inhibition zone diameter of $10{\pm}1.5mm$, whereas those of L. plantarum and L. fermentum have been shown to be $4.0{\pm}0.6mm$. H. pylori G88016 revealed the highest vacuolating toxin producing activity among the 8 strains, the inhibitory activity of L. helveticus CU631 in vacuolating toxin producing activity of H. pylori manifested in the co-culture of two strains and in the 5:5 mixture of supernatant of the two strains. Both L. helveticus CU631 and cell free culture supernatant had a strong inhibitory activities in urease and cytotoxin producing activities of H. pylori NCTC11637 and CJH12. An accelerated proteolytic activity of water soluble peptides by L. helveticus CU631 during the refrigeration storage has been manifested in the cream cheese. DNA seqences of 16S-23S ribosomal RNA spacer region showed typical pattern among the various strains of L. helveticus, which could be used in the identification of L. helveticus CU 631.

• International Journal of Industrial Entomology and Biomaterials
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• v.2 no.1
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• pp.37-53
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• 2001

Two regions of mtDNA genome, cytochrome oxidase subunit I (COI) and 165 ribosomal RNA (165 rRNA) genes, were sequenced for 15 species of the long-horned beetle belonging to four subfamilies and geographic samples of mulberry longicorn beetle, Apriona germari, from two localities in Korea. Ten samples of A. germari collected from Suwon and Busan revealed three COI haplotypes ranging in nucleotide divergence of 0.3% to 0.5%, and the two populations shared one common COI haplotype (80%). The sequence divergence among 15 species of the long-horned beetle was much higher in COI gene (12.3%∼39.4%) than 16S rRNA gene (7.2% to 23.1), and the maximum value in the COI gene is exceptional compared with other relevant studies, including that of Coleoptera. The greatly increased divergence in the COI gene, in facto was stemmed from a peculiar sequence of Prionus insularis belonging to Prioninne, divergence of which ranges from 31.2% to 39.3% from other species. We discussed possible reason of the divergence in this species. Due to the abnormality of COI gene divergence, decrease in phylogenetic signal was severe in COI nucleotide and, subsequently, the converted amino acid sequences, rendering us to put more confidence on the 16S5 rRNA gene data. Although the molecular phylogeny confidently supports the monophyletic origin of Lepturinae, the presence of discrepancy between molecular data and traditional taxonomic views also is a testable hyothesis. One such discrepancy includes taxonomic position of Sophronica obrioides and Theophilea cylindricollis belonging to Lamiinae.

• The Plant Pathology Journal
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• v.28 no.1
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• pp.93-100
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• 2012

The rhizobacterium NJ134, showing strong $in$ $vitro$ antifungal activity against $Fusarium$ $oxysporum$, was isolated from field grown tomato plants and identified as $Pseudomonas$ sp. based on 16S ribosomal DNA sequence and biochemical analyses. The antifungal compound purified by gas chromatography-mass spectrometry, infrared, and nuclear magnetic resonance analyses from NJ134 cultures was polyketide 2,4-diacetylphloroglucinol (DAPG). Analysis of the sequence of part of one of the genes associated with DAPG synthesis, $phlD$, indicated that the DAPG producer NJ134 was a novel genotype or variant of existing genotype termed O that have been categorized based on isolates from Europe and North America. A greenhouse study indicated that about $10^8$ CFU/g of soil NJ134 culture application was required for effective biocontrol of Fusarium wilt in tomato. These results suggest that a new variant genotype of a DAPG-producing strain of $Pseudomonas$ has the potential to control Fusarium wilt under the low disease pressure conditions.

• Mycobiology
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• v.47 no.2
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• pp.173-179
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• 2019

Cladophialophora is characterized by simple hyphomycetes with brown hyphae that give rise to branched chains of pale brown conidia and shows affinities with the Herpotrichiellaceae. A fungal strain belonging to the genus Cladophialophora was isolated from soil in Daegu, Korea. This strain produces numerous greenish to dark black lanose aerial mycelia with hair like structures. It is morphological similar to C. chaetospira, C. inabaensis, and C. multiseptata; however, the conidiophores and conidia sizes of the newly isolated strain (KNU16-032) are clearly different from them. The novelty of the strain was also confirmed based on phylogenetic analysis using the data sets of the internal transcribed spacer region of and the partial sequence of 28S ribosomal DNA region along with the cultural characteristics. Because morphological observations and phylogenetic analysis indicated that the strain is distinct from previously known Cladophialophora species, we propose this species as a new species Cladophialophora lanosa sp. nov., and provide the detailed descriptions in this study.