• International Journal of Industrial Entomology and Biomaterials
• /
• v.10 no.1
• /
• pp.25-33
• /
• 2005

Recently a cDNA clone of apoLp-III from Hyphantria cunea was isolated and subjected to computational analysis to compare with other available sequences. Multiple sequence alignments were carried out using the amino acid sequences of apoLp-III from six insects. It was found that the H. cunea apoLp-III has relatively high sequence identities to Spodoptera litura ($69.5\%$), Manduca sexta ($66.8\%$), Galleria mellonella ($65.1\%$), Bombyx mori N4 ($54.3\%$) but less identity to Locusta migratoria ($18.3\%$). The amino acid composition was compared with other insects using EXPASY tools; it shows that alanine (Ala), glutamine (Gln), leucine (Leu) and lysine (Lys) are the major amino acid components of apoLp-III in H. cunea as well as other lepidopterans. Homology modeling performed using PSI-BLAST (PDB template M. sexta) reveals that the apoLp-III molecules consist of five, long amphipathic alpha helical bundles with short loops connecting the helices and shows homology with other insects. Phylogenetic analysis shows that the orthopteran apoLp-III represented by locust was most distantly related to the lepidopteran insects.

• Asian-Australasian Journal of Animal Sciences
• /
• v.18 no.1
• /
• pp.90-95
• /
• 2005

Lactic acid bacteria were isolated from silage, which produce high level of hydrogen peroxide in cell culture supernatant. The 16S rDNA sequences of the isolate matched perfectly with that of Lactobacillus fermentum (99.9%), examined by a 16S rDNA gene sequence analysis and similarity search using the GenBank database, thus named L. fermentum CS12-1. L. fermentum CS12-1 showed resistance to low pH and bile acid. The production of hydrogen peroxide by L. fermentum CS12-1 was confirmed by catalase treatment and high-performance liquid chromatography. L. fermentum CS12-1 accumulated hydrogen peroxide in culture broth as cells grew, and the highest concentration of hydrogen peroxide reached 3.5 mM at the late stationary growth phase. The cell-free supernatant of L. fermentum CS12-1 both before and after neutralization inhibited the growth of enterotoxigenic Escherichia coli K88 that causes diarrhea in piglets.

• The Plant Pathology Journal
• /
• v.35 no.1
• /
• pp.41-50
• /
• 2019

Sugarcane bacilliform viruses (SCBV), which belong to the genus Badnavirus, family Caulimoviridae, are an important DNA virus complex that infects sugarcane. To explore the genetic diversity of the sugarcane-infecting badnavirus complex in China, we tested 392 sugarcane leaf samples collected from Fujian, Yunnan, and Hainan provinces for the occurrence of SCBV by polymerase chain reaction (PCR) assays using published primers SCBV-F and SCBV-R that target the reverse transcriptase/ribonuclease H (RT/RNase H) regions of the viral genome. A total of 111 PCR-amplified fragments (726 bp) from 63 SCBV-positive samples were cloned and sequenced. A neighbor-joining phylogenetic tree was constructed based on the SCBV sequences from this study and 34 published sequences representing 18 different phylogroups or genotypes (SCBV-A to -R). All SCBV-tested isolates could be classified into 20 SCBV phylogenetic groups from SCBV-A to -T. Of nine SCBV phylogroups reported in this study, two novel phylogroups, SCBV-S and SCBV-T, that share 90.0-93.2% sequence identity and show 0.07-0.11 genetic distance with each other in the RT/RNase H region, are proposed. SCBV-S had 57.6-92.2% sequence identity and 0.09-0.66 genetic distance, while SCBV-T had 58.4-90.0% sequence identity and 0.11-0.63 genetic distance compared with the published SCBV phylogroups. Additionally, two other Badnavirus species, Sugarcane bacilliform MO virus (SCBMOV) and Sugarcane bacilliform IM virus (SCBIMV), which originally clustered in phylogenetic groups SCBV-E and SCBV-F, respectively, are first reported in China. Our findings will help to understand the level of genetic heterogeneity present in the complex of Badnavirus species that infect sugarcane.

• Journal of Microbiology and Biotechnology
• /
• v.29 no.12
• /
• pp.1969-1974
• /
• 2019

A Gram-staining-negative, aerobic, light brown pigment bacterium, designated strain CE80^T was isolated from marine sponge Callyspongia elegans in Jeju Island, Republic of Korea. Strain CE80^T grew optimally at 25℃, in the range of pH 5.0-11.0 (optimum 7.0-8.0), and with 1.0-5.0% NaCl (optimum 1-3% (w/v)). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain CE80^T belonged to the genus Labrenzia and was closely related to L. suaedae YC6927^T (98.3%), L. alexandrii DFL-11^T (96.6%), L. aggregata IAM 12614^T (96.6%) L. marina mano18^T (96.5%) and L. alba CECT 5094^T (96.2%). The major fatty acids of strain CE80^T were C_18:1 ω7c, and summed feature. The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamin, one unidentified aminolipid, one phospholipid and four unidentified lipids. The DNA G+C content of strain CE80^T was 55.9 mol%. The major respiratory quinone was Q-10. DNA-DNA relatedness between strain CE80^T and L. suaedae YC6927^T was 56.1±2.8%. On the basis of physiological and biochemical characterization and phylogenetic and chemotaxonomic analysis, strain CE80^T represents a novel species of the Labrenzia, for which the name Labrenzia callyspongiae sp. nov., is proposed. The type strain is CE80^T (=KCTC 42849^T =JCM 31309^T).

• Journal of Microbiology and Biotechnology
• /
• v.19 no.3
• /
• pp.250-256
• /
• 2009

Acinetobacter strain $KNF2022^T$ was isolated from tobacco plant roots during the screening of antiviral substances having inhibitory effects on Tobacco mosaic virus (TMV) and examined by phenotypic, chemotaxonomic, and genetic characterization. It was a nonmotile, Gram-negative bacterium. This strain contained Q-9 as the main respiratory quinone. The major cellular fatty acids of the isolate were 16:0, 18:1 w9c, and 16:1 w7c/15 iso 2OH. The DNA base composition was 44 mol%. Phylogenetic analysis based on the 16S rRNA sequence revealed that the isolate formed an evolutionary lineage distinct from other Acinetobacter species. Based on the evaluation of morphologic, physiologic, and chemotaxonomic characteristics, DNA-DNA hybridization values, and 16S rRNA sequence comparison, we propose the new species Acinetobacter antiviralis sp. nov., the type strain of which is $KNF2022^T$ (=KCTC $0699BP^T$).

• Parasites, Hosts and Diseases
• /
• v.60 no.5
• /
• pp.367-370
• /
• 2022

Fascioliasis is a parasitic infection caused by liver flukes. Although several cases have been reported in Korea, phylogenetic analysis of isolates is lacking. In this study, a 66-year-old woman with right upper quadrant (RUQ) abdominal pain was diagnosed as fascioliasis involving abdominal muscle by imaging study. She received praziquantel treatment, but symptoms were not improved. Lateral movement of the abscess lesion was followed. Trematode parasite was surgically removed from the patient's rectus abdominis muscle. The fluke was identified as Fasciola hepatica based on sequence analysis of 18S rDNA. To determine the phylogenetic position of this Fasciola strain (named Korean Fasciola 1; KF1), the cox1 gene (273 bp) was analyzed and compared with the genes of 17 F. hepatica strains isolated from cows, sheep, goats, and humans from various countries. Phylogenetic analysis showed that KF1 was closely related with the isolates from China goat.

• Korean Journal of Microbiology
• /
• v.43 no.1
• /
• pp.66-71
• /
• 2007

Two isolates of genus Acinetobacter were obtained from Jang-Baek waterfall in North Korea. Morphological characteristics of the isolated 2 strains were Gram-negative, aerobic and rod shape bacteria. Physiological and biochemical characterization of the isolated 2 strains were some different aspect from those of type strains. 16S rDNA sequence analysis showed that the two isolates shared 99.9% sequence similarity. Strains JB10 and $JB15^{T}$ were shown to belong to the Gammaproteobacteria and showed the highest levels of sequence similarity to Acinetobacter tandoii $4N13^{T}$ (97.3%), Acinetobacter haemolyticus $ATCC17906^{T}$ (97.2%), Acinetobacter johnsonii $DSM6963^{T}$ (97.2%), Acinetobacter junii $DSM6964^{T}$ (96.7%), Acinetobacter schindleri $LUH5832^{T}$ (97.0%) and Acinetobacter ursingii $LUH3792^{T}$ (96.6%). The major cellular fatty acid in Acinetobacter type strains and isolated strains included $C_{18:1}\;{\omega}9c\;and\;C_{16:1}\;{\omega}7c/C_{15:0}\;iso\;2OH$. Eventhough it was ascertained that the isolated strains were closely related to genus Acinetobacter, physiological and biochemical characteristics and the result of the isolated strains 16S rDNA analysis indicate some different aspects from those of type strains of genus Acinetohacter It is considered that the isolated JB10 (=KEMC 52-093) and $JB15^{T}\;(=KEMC\;52-094^{T})$ strains be new species of genus Acinetobacter. We name it as Acinetobacter koreensis sp. nov.

• Mycobiology
• /
• v.44 no.4
• /
• pp.277-282
• /
• 2016

In this study, we collected rhizosphere soils and root samples from a post-mining area and a natural forest area in Jecheon, Korea. We extracted spores of arbuscular mycorrhizal fungi (AMF) from rhizospheres, and then examined the sequences of 18S rDNA genes of the AMF from the collected roots of plants. We compared the AMF communities in the post-mining area and the natural forest area by sequence analysis of the AMF spores from soils and of the AMF clones from roots. Consequently, we confirmed that the structure of AMF communities varied between the post-mining area and the natural forest area and showed significant relationship with heavy metal contents in soils. These results suggest that heavy metal contamination by mining activity significantly affects the AMF community structure.

• Parasites, Hosts and Diseases
• /
• v.50 no.3
• /
• pp.263-267
• /
• 2012

The present study was performed to describe 2 human cases infected by the horsehair worm, Parachordodes sp., in Japan. Two gordiid worms were collected in the vomit and excreta of an 80-year-old woman in November 2009 in Kyoto city, and in the mouth of 1-year-old boy in December 2009 in Nara city, Japan, respectively. Both worms were males having bifurcated posterior ends and male gonads in cross sectional specimens. They were identified as Parachordodes sp. (Nematomorpha: Chordodidae) based on the characteristic morphologies of cross sections and areoles in the cuticle. DNA analysis on 18S rRNA partial sequence arrangements was also carried out and both worms were assumed to be close to the genus Paragordionus based on tree analysis, and far from Gordius sp. which has already been reported in humans in Japan. DNA sequencing of the Parachordodes worm does not appear on the database; therefore, more information on the gene sequences of the genus Parachordodes from humans, animals, or intermediates is required.

• Journal of fish pathology
• /
• v.17 no.3
• /
• pp.159-169
• /
• 2004

Bacterial wihte enteritis ocurred by infection of V. ichthyoenteri is a devastating disease in olive flounder (Paralichthys olivaceus) hatcheries in Korea. Since white enteritis has been a problem in aquqtic industries, necessity of a rapid detection method is increased. In an attempt to develop rapid PCR method the detection of V. ichthyoenteri, we examined the 16S-23S rRNA intergenic spacer region(ISR) of V. ichthyoenteri and developed species-specific primer for V. ichthyoenteri. The intergenic spacers were amplified by primers complementary to conserved region of 16S and 23S rRNA genes. The intergenic spacer region between the 16S and 23S rRNA genes of V. ichthoenteri were investigated by PCR fragment length typing and DNA sequencing. Analysis of the ISR sequences showed that V. ichthyoenteri contains one types of polymorphic ISRs. The size of ISRs ranged 348bp length and not contains tRNA genes. Mutiple alignment of representative sequences from different Vibrio species revealed several domains of high sequence variability, and allowed to design species-specific primer for detection of Vibrio ichthyoenteri. PCR. The specific of the primer was examined using genomic DNA prepared from 19 different Vibrio species, isolated 18group Vibrio species. The results showed that the PCR reaction using species-specific primer designed in this study can be used to detect V. ichthyoenteri.