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Volume 50(2); April 2012
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Research Support, Non-U.S. Gov'ts
TBC: A Clustering Algorithm Based on Prokaryotic Taxonomy
Jae-Hak Lee , Hana Yi , Yoon-Seong Jeon , Sungho Won , Jongsik Chun
J. Microbiol. 2012;50(2):181-185.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1214-6
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AbstractAbstract PDF
High-throughput DNA sequencing technologies have revolutionized the study of microbial ecology. Massive sequencing of PCR amplicons of the 16S rRNA gene has been widely used to understand the microbial community structure of a variety of environmental samples. The resulting sequencing reads are clustered into operational taxonomic units that are then used to calculate various statistical indices that represent the degree of species diversity in a given sample. Several algorithms have been developed to perform this task, but they tend to produce different outcomes. Herein, we propose a novel sequence clustering algorithm, namely Taxonomy-Based Clustering (TBC). This algorithm incorporates the basic concept of prokaryotic taxonomy in which only comparisons to the type strain are made and used to form species while omitting full-scale multiple sequence alignment. The clustering quality of the proposed method was compared with those of MOTHUR, BLASTClust, ESPRITTree, CD-HIT, and UCLUST. A comprehensive comparison using three different experimental datasets produced by pyrosequencing demonstrated that the clustering obtained using TBC is comparable to those obtained using MOTHUR and ESPRIT-Tree and is computationally efficient. The program was written in JAVA and is available from http://sw. ezbiocloud.net/tbc.

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  • Application of Machine Learning to Solid Particle Erosion of APS-TBC and EB-PVD TBC at Elevated Temperatures
    Yuan Liu, Ravi Ravichandran, Kuiying Chen, Prakash Patnaik
    Coatings.2021; 11(7): 845.     CrossRef
  • Effects of Disease Resistant Genetically Modified Rice on Soil Microbial Community Structure According to Growth Stage
    Soo-In Sohn, Young-Ju Oh, Jae-Hyung Ahn, Hyeon-jung Kang, Woo-Suk Cho, Yoonsung Cho, Bum Kyu Lee
    Korean Journal of Environmental Agriculture.2019; 38(3): 185.     CrossRef
  • Effects of the Brown Seaweed Laminaria japonica Supplementation on Serum Concentrations of IgG, Triglycerides, and Cholesterol, and Intestinal Microbiota Composition in Rats
    Jae-Young Kim, Young Min Kwon, In-Sung Kim, Jeong-A. Kim, Da-Yoon Yu, Bishnu Adhikari, Sang-Suk Lee, In-Soon Choi, Kwang-Keun Cho
    Frontiers in Nutrition.2018;[Epub]     CrossRef
  • hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Units Based on Homopolymer Compaction
    Seunghyun Park, Hyun-soo Choi, Byunghan Lee, Jongsik Chun, Joong-Ho Won, Sungroh Yoon
    IEEE/ACM Transactions on Computational Biology and Bioinformatics.2018; 15(2): 441.     CrossRef
  • Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing
    Jakub Kreisinger, Dagmar Čížková, Lucie Kropáčková, Tomáš Albrecht, Roberto Ambrosini
    PLOS ONE.2015; 10(9): e0137401.     CrossRef
  • Metagenomic Insights into the Bioaerosols in the Indoor and Outdoor Environments of Childcare Facilities
    Su-Kyoung Shin, Jinman Kim, Sung-min Ha, Hyun-Seok Oh, Jongsik Chun, Jongryeul Sohn, Hana Yi, Vishnu Chaturvedi
    PLOS ONE.2015; 10(5): e0126960.     CrossRef
  • Effect of genetically modified rice producing resveratrol on the soil microbial communities
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    Journal of the Korean Society for Applied Biological Chemistry.2015; 58(6): 795.     CrossRef
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    Journal of Eukaryotic Microbiology.2015; 62(2): 196.     CrossRef
  • Unveiling abundance and distribution of planktonic Bacteria and Archaea in a polynya in Amundsen Sea, Antarctica
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    Polar Biology.2014; 37(4): 587.     CrossRef
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    Environmental Science and Pollution Research.2014; 21(5): 3722.     CrossRef
  • Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations
    Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt
    Bioinformatics.2014; 30(11): 1530.     CrossRef
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  • A Unique Prokaryotic Assemblage of Wall Biofilm of a Volcanic Cave (Daesubee) in Jeju
    Jong-Geun Moon, Man-Young Jung, Jong-Geol Kim, Soo-Je Park, Dae-Shin Kim, Jong-Shik Kim, Sung-Keun Rhee
    The Korean Journal of Microbiology.2013; 49(2): 184.     CrossRef
  • Resolving Ambiguity of Species Limits and Concatenation in Multilocus Sequence Data for the Construction of Phylogenetic Supermatrices
    Douglas Chesters, Alfried P. Vogler
    Systematic Biology.2013; 62(3): 456.     CrossRef
  • CLUSTOM: A Novel Method for Clustering 16S rRNA Next Generation Sequences by Overlap Minimization
    Kyuin Hwang, Jeongsu Oh, Tae-Kyung Kim, Byung Kwon Kim, Dong Su Yu, Bo Kyeng Hou, Gustavo Caetano-Anollés, Soon Gyu Hong, Kyung Mo Kim, George E. Fox
    PLoS ONE.2013; 8(5): e62623.     CrossRef
  • Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era
    Mincheol Kim, Ki-Hyun Lee, Seok-Whan Yoon, Bong-Soo Kim, Jongsik Chun, Hana Yi
    Genomics & Informatics.2013; 11(3): 102.     CrossRef
  • Bacterial Diversity in the Guts of Sea Cucumbers (Apostichopus japonicus) and Shrimps (Litopenaeus vannamei) Investigated with Tag-Encoded 454 Pyrosequencing of 16S rRNA Genes
    Eun Soo Noh, Young-Sam Kim, Dong-Hyun Kim, Kyoung-Ho Kim
    The Korean Journal of Microbiology.2013; 49(3): 237.     CrossRef
  • Bacterial diversity in ornithogenic soils compared to mineral soils on King George Island, Antarctica
    Ok-Sun Kim, Namyi Chae, Hyun Soo Lim, Ahnna Cho, Jeong Hoon Kim, Soon Gyu Hong, Jeongsu Oh
    Journal of Microbiology.2012; 50(6): 1081.     CrossRef
Identification and Enumeration of Microcystis Using a Sandwich Hybridization Assay
Jing Ping Zhu , Xian Li , Shi Du
J. Microbiol. 2012;50(2):186-190.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1418-9
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AbstractAbstract PDF
Based on sequence analyses of phycocyanin intergenic spacers (PC-IGS) from Microcystis, Anabaena, Aphanizomenon, and Planktothrix (Oscillatoria) strains, a genus-specific probe pair TF/TR was designed, and a sandwich hybridization assay was established to quantitatively detect Microcystis. Through BLAST and cyanobacterial culture tests, TF/TR was demonstrated to be specific for Microcystis. A calibration curve for the sandwich hybridization assay was established, and the lowest detected concentration was 100 cell/ml. Laboratory and field samples were analyzed with both sandwich hybridization assay and microscopy. The biotic and abiotic components of the samples were of little disturbance to the sandwich hybridization assay. The results showed no distinct difference between the two methods. In this study, a sandwich hybridization assay was established to detect Microcystis, providing an alternative to traditional microscopic, morphology- based methods.

Citations

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  • The Need to Increase Strain-Specific DNA Information from the Invasive Cyanobacteria Sphaerospermopsis aphanizomenoides and Cuspidothrix issatschenkoi
    Daniela R. de Figueiredo
    Water.2025; 17(4): 579.     CrossRef
  • Molecular techniques for understanding harmful algal blooms: A review
    Jackson Sanders, Senjie Lin
    Harmful Algae.2025; 148: 102909.     CrossRef
  • Sandwich Hybridization Assay for In Situ Real-Time Cyanobacterial Detection and Monitoring: A Review
    Ping Gong, Anna K. Antrim, Sarah R. Bickman, Emily G. Cooley, Seung Ho Chung
    Biosensors.2022; 12(8): 640.     CrossRef
Isolation and Characterization of Plant Growth-Promoting Rhizobacteria from Wheat Roots by Wheat Germ Agglutinin Labeled with Fluorescein Isothiocyanate
Jian Zhang , Jingyang Liu , Liyuan Meng , Zhongyou Ma , Xinyun Tang , Yuanyuan Cao , Leni Sun
J. Microbiol. 2012;50(2):191-198.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1472-3
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  • 35 Crossref
AbstractAbstract PDF
Thirty-two isolates were obtained from wheat rhizosphere by wheat germ agglutinin (WGA) labeled with fluorescein isothiocyanate (FITC). Most isolates were able to produce indole acetic acid (65.6%) and siderophores (59.3%), as well as exhibited phosphate solubilization (96.8%). Fourteen isolates displayed three plant growth-promoting traits. Among these strains, two phosphate-dissolving ones, WS29 and WS31, were evaluated for their beneficial effects on the early growth of wheat (Triticum aestivum Wan33). Strain WS29 and WS31 significantly promoted the development of lateral roots by 34.9% and 27.6%, as well as increased the root dry weight by 25.0% and 25.6%, respectively, compared to those of the control. Based on 16S rRNA gene sequence comparisons and phylogenetic positions, both isolates were determined to belong to the genus Bacillus. The proportion of isolates showing the properties of plant growth-promoting rhizobacteria (PGPR) was higher than in previous reports. The efficiency of the isolation of PGPR strains was also greatly increased by WGA labeled with FITC. The present study indicated that WGA could be used as an effective tool for isolating PGPR strains with high affinity to host plants from wheat roots. The proposed approach could facilitate research on biofertilizers or biocontrol agents.

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Journal Article
Detecting Nonculturable Bacteria in the Active Mycorrhizal Zone of the Pine Mushroom Tricholoma matsutake
Ryota Kataoka , Zaki Anwar Siddiqui , Junichi Kikuchi , Masaki Ando , Rina Sriwati , Ai Nozaki , Kazuyoshi Futai
J. Microbiol. 2012;50(2):199-206.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1371-7
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AbstractAbstract PDF
The fungus Tricholoma matsutake forms an ectomycorrhizal relationship with pine trees. Its sporocarps often develop in a circle, which is commonly known as a fairy ring. The fungus produces a solid, compact, white aggregate of mycelia and mycorrhizae beneath the fairy ring, which in Japanese is called a ‘shiro’. In the present study, we used soil dilution plating and molecular techniques to analyze the bacterial communities within, beneath, and outside the T. matsutake fairy ring. Soil dilution plating confirmed previous reports that bacteria and actinomycetes are seldom present in the soil of the active mycorrhizal zone of the T. matsutake shiro. In addition, the results showed that the absence of bacteria was strongly correlated with the presence of T. matsutake mycorrhizae. The results demonstrate that bacteria, especially aerobic and heterotrophic forms, and actinomycetes, are strongly inhibited by T. matsutake. Indeed, neither bacteria nor actinomycetes were detected in 11.3% of 213 soil samples from the entire shiro area by culture-dependent
methods
. However, molecular techniques demonstrated that some bacteria, such as individual genera of Sphingomonas and Acidobacterium, were present in the active mycorrhizal zone, even though they were not detected in soil assays using the dilution plating technique.

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Research Support, Non-U.S. Gov'ts
Molecular Analysis of Spatial Variation of Iron-Reducing Bacteria in Riverine Alluvial Aquifers of the Mankyeong River
So-Jeong Kim , Dong-Chan Koh , Soo-Je Park , In-Tae Cha , Joong-Wook Park , Jong-Hwa Na , Yul Roh , Kyung-Seok Ko , Kangjoo Kim , Sung-Keun Rhee
J. Microbiol. 2012;50(2):207-217.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1342-z
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AbstractAbstract PDF
Alluvial aquifers are one of the mainwater resources in many countries. Iron reduction in alluvial aquifers is often a major anaerobic process involved in bioremediation or causing problems, including the release of As trapped in Fe(III) oxide. We investigated the distribution of potential iron-reducing bacteria (IRB) in riverine alluvial aquifers (B1, B3, and B6 sites) at the Mankyeong River, Republic of Korea. Inactive iron reduction zones, the diversity and abundance of IRB can be examined using a clone library and quantitative PCR analysis of 16S rRNA genes. Geobacter spp. are potential IRB in the iron-reducing zone at the B6 (9 m) site, where high Fe(II) and arsenic (As) concentrations were observed. At the B3 (16 m) site, where low iron reduction activity was predicted, a dominant clone (10.6%) was 99% identical in 16S rRNA gene sequence with Rhodoferax ferrireducens. Although a major clone belonging to Clostridium spp. was found, possible IRB candidates could not be unambiguously determined at the B1 (18 m) site. Acanonical correspondence analysis demonstrated that, among potential IRB, only the Geobacteraceae were well correlated with Fe(II) and As concentrations. Our results indicate high environmental heterogeneity, and thus high spatial variability, in thedistribution of potential IRB in the riverine alluvial aquifersnear the Mankyeong River.

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Microbial Fingerprinting Detects Unique Bacterial Communities in the Faecal Microbiota of Rats with Experimentally-Induced Colitis
Ashis K. Samanta , Valeria A. Torok , Nigel J. Percy , Suzanne M. Abimosleh , Gordon S. Howarth
J. Microbiol. 2012;50(2):218-225.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1362-8
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AbstractAbstract PDF
An abnormal composition of the gut microbiota is believed to be associated with the pathogenesis of inflammatory bowel disease (IBD). We utilized terminal restriction fragment length polymorphism (T-RFLP) analysis to quantify faecal bacterial communities from rats with experimental colitis. Male Sprague Dawley rats (n=10/group) ingested 2% dextran sulfate sodium (DSS) or water for up to 7 days. Rats were killed and colonic tissues collected for histological analysis. Damage severity score in the distal colon was significantly greater (P<0.001) following DSS consumption compared to controls. T-RFLP faecal bacterial profiles generated with either MspI or CfoI revealed a significant difference (P<0.001) in community composition between healthy and colitic rats, with bacterial composition in healthy rats more variable than in rats with colitis. Operational taxonomic units (OTU: taxonomically related groups of bacteria) associated with either the healthy or colitic state were identified. OTU (116, 226, 360, and 948; CfoI) and (118 and 188; MspI) were strongly associated with untreated healthy rats, while OTU (94, 98, 174, and 384; CfoI) and (94 and 914; MspI) were predominantly associated with DSS-treated colitic rats. Phylogenetic OTU assignment suggested that Bacteroidales and Lactobacillus sp. were predominantly associated with the colitic and healthy rats, respectively. These
results
show that faecal bacterial profiling is a rapid, sensitive and non-invasive tool for detecting and identifying changes in gut microbiota associated with colitis. Restoring microbial homeostasis by targeting colitis-associated OTU through specific microbiological interventions could form the basis of novel therapeutic strategies for IBD.

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Effect of Natural Mediators on the Stability of Trametes trogii Laccase during the Decolourization of Textile Wastewaters
Rim Khlifi-Slama , Tahar Mechichi , Sami Sayadi , Abdelhafidh Dhouib
J. Microbiol. 2012;50(2):226-234.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1421-1
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AbstractAbstract PDF
The purpose of the present study was to determine the effect of natural mediators on the stability of the Trametes trogii crude laccase in the process of decolourization of textile effluents. Acetosyringone allowed the highest wastewaters decolourization rate of 25%. At higher concentrations of acetosyringone, the relative activity of laccase decreased approximately by between 38% and 88% after 5 days of incubation. T. trogii laccase was strongly inactivated at 3 mM syringaldehyde, after 3 days of incubation. However, laccase activity is more stable in the presence of the vanillin and m-coumarate. The T. trogii growth on solid effluentbased- medium was examined and evaluated by measuring the colony diameter in cm. T. trogii was completely inhibited on 100:0 and 80:20 effluent:water solid medium, however, colony diameter reached 5 cm on 60:40 effluent:water solid medium after 13–14 days incubation. When the textile effluent was pre-treated with laccase and laccase-acetosyringone system, the colony diameter of 2 cm of T. trogii on 80:20 effluent:water solid medium was reached after 14 and 10 days of incubation respectively.

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Purification and Structure Analysis of Mycolic Acids in Corynebacterium glutamicum
Yang Yang , Feng Shi , Guanjun Tao , Xiaoyuan Wang
J. Microbiol. 2012;50(2):235-240.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1459-0
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AbstractAbstract PDF
Corynebacterium glutamicum is widely used for producing amino acids. Mycolic acids, the major components in the cell wall of C. glutamicum might be closely related to the secretion of amino acids. In this study, mycolic acids were extracted from 5 strains of C. glutamicum, including ATCC 13032, ATCC 13869, ATCC 14067, L-isoleucine producing strain IWJ-1, and L-valine producing strain VWJ-1. Structures of these mycolic acids were analyzed using thin layer chromatography and electrospray ionization mass spectrometry. More than twenty molecular species of mycolic acid were observed in all 5 strains. They differ in the length (20–40 carbons) and saturation (0–3 double bonds) of their constituent fatty acids. The dominant species of mycolic acid in every strain was different, but their two hydrocarbon chains were similar in length (14–18 carbons), and the meromycolate chain usually contained double bonds. As the growth temperature of cells increased from 30°C to 34°C, the proportion of mycolic acid species containing unsaturated and shorter hydrocarbon chains increased. These results provide new information on mycolic acids in C. glutamicum, and could be useful for modifying the cell wall to increase the production of amino acids.

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Effects of Exopolysaccharide Production on Liquid Vegetative Growth, Stress Survival, and Stationary Phase Recovery in Myxococcus xanthus
Wei Hu , Jing Wang , Ian McHardy , Renate Lux , Zhe Yang , Yuezhong Li , Wenyuan Shi
J. Microbiol. 2012;50(2):241-248.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1349-5
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AbstractAbstract PDF
Exopolysaccharide (EPS) of Myxococcus xanthus is a wellregulated cell surface component. In addition to its known functions for social motility and fruiting body formation on solid surfaces, EPS has also been proposed to play a role in multi-cellular clumping in liquid medium, though this phenomenon has not been well studied. In this report, we confirmed that M. xanthus clumps formed in liquid were correlated with EPS levels and demonstrated that the EPS encased cell clumps exhibited biofilm-like structures. The clumps protected the cells at physiologically relevant EPS concentrations, while cells lacking EPS exhibited significant reduction in long-term viability and resistance to stressful conditions. However, excess EPS production was counterproductive to vegetative growth and viable cell recovery declined in extended late stationary phase as cells became trapped in the matrix of clumps. Therefore, optimal EPS production by M. xanthus is important for normal physiological functions in liquid.
Development of a Suicidal Vector-Cloning System Based on Butanal Susceptibility Due to an Expression of YqhD Aldehyde Reductase
Changhan Lee , Chankyu Park
J. Microbiol. 2012;50(2):249-255.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1438-5
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AbstractAbstract PDF
Previously, we observed butanal/propanal sensitivity of Escherichia coli K-12 when cells overexpress YqhD protein, a NADPH dependent aldehyde reductase, possibly due to an accumulation of butanol/propanol in vivo as the reaction products. Based on this finding, we developed a suicidal vector-cloning system derived from pUC19, in which lacZ was substituted with the yqhD gene. As a result, when foreign DNA was inserted into its multiple cloning sites by disrupting an expression of YqhD, the recombinants survived on butanal/propanal containing plate, whereas cells containing the YqhD vector died because of the alcohol production by YqhD. The cloning efficiency, estimated based on colony PCR and enzyme digestion, was achieved more than 90% when the suicidal vector system was used. Moreover, the plasmid vector itself was stably maintained in the cell, presumably due to its ability to remove toxic aldehydes being accumulated in E. coli cell by metabolic stress.
Effects of Mutations in the WD40 Domain of α-COP on Its Interaction with the COPI Coatomer in Saccharomyces cerevisiae
Ki-Hyun Kim , Eun Kyung Kim , Ki Young Jeong , Yun-Hee Park , Hee-Moon Park
J. Microbiol. 2012;50(2):256-262.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1326-z
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AbstractAbstract PDF
Replacement of glycine 227 in the fifth WD40 motif of α-COP/Ret1p/Soo1p by charged or aromatic amino acids is responsible for the temperature-dependent osmo-sensitivity of Saccharomyces cerevisiae, while truncations of WD40 motifs exerted a reduction in cell growth rate and impairment in assembly of cell-wall associated proteins such as enolase and Gas1p. Yeast two-hybrid analysis revealed that the ret1-1/soo1-1 mutation of α-COP abolished the interaction with β- and ε-COP, respectively, and that the interaction between α-COP and β-COP relied on the WD40 domain of α-COP. Furthermore, although the WD40 domain is dispensable for interaction of α-COP with ε-COP, structural alterations in the WD40 domain could impair the interaction.

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  • Dissecting the essential role of N-glycosylation in catalytic performance of xanthan lyase
    Jingjing Zhao, Qian Wang, Xin Ni, Shaonian Shen, Chenchen Nan, Xianzhen Li, Xiaoyi Chen, Fan Yang
    Bioresources and Bioprocessing.2022;[Epub]     CrossRef
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    Eun-Hye Kang, Eun-Jung Song, Jun Ho Kook, Hwan-Hee Lee, Bo-Ri Jeong, Hee-Moon Park
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    Eun-Jung Song, Ki-Hyun Kim, Hwan-Hee Lee, Jeong-Seok Park, Eun-Hye Kang, Hee-Moon Park
    The Korean Journal of Mycology.2012; 40(4): 224.     CrossRef
Morphological Structure of Propagules and Electrophoretic Karyotype Analysis of False Smut Villosiclava virens in Rice
Rongtao Fu , Lei Ding , Jun Zhu , Ping Li , Ai-ping Zheng
J. Microbiol. 2012;50(2):263-269.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1456-3
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AbstractAbstract PDF
The target pathogen Villosiclava virens (teleomorph: claviceps oryzae-sativae) was isolated from the infected rice, where it caused false smut. In our study, the forming processes of the chlamydospores, chlamydospore balls, conidiospores, and secondary conidiospores during the asexual reproduction were observed more precisely and in greater detail than previous descriptions. The microstructure of the infected rice kernel showed that the outer dense chlamydospores piled around the false smut balls grown on XBZ medium; moreover the sclerotia consisting of dense mycelium were found. The different morphology was observed across the different growing conditions. In addition, we observed the nuclear numbers of both the conidiospores and hyphae using 4′,6-diamidino-2-phenylindole (DAPI) staining. Because the fungus has small chromosomes and the numbers were not previously known, we analyzed the electrophoretic karyotype using a pulsed field gel electrophoresis (PFGE) technique. The results showed that V. virens has at least 10 chromosomes ranging in size from 0.6 kb to 6 Mb. The V. virens genome size is estimated to be 23 Mb. Here, we report the morphological characteristics of the fungus and the process of asexual spores forming asexual propagules, along with the first analyze the molecular karyotype of V. virens. These
results
supply a foundation for further study of the pathogenicity and biology of this devastating pathogen.
Protein-Protein Interactions between Histidine Kinases and Response Regulators of Mycobacterium tuberculosis H37Rv
Ha-Na Lee , Kwang-Eun Jung , In-Jeong Ko , Hyung Suk Baik , Jeong-Il Oh
J. Microbiol. 2012;50(2):270-277.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-2050-4
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AbstractAbstract PDF
Using yeast two-hybrid assay, we investigated protein-protein interactions between all orthologous histidine kinase (HK)/response regulator (RR) pairs of M. tuberculosis H37Rv and identified potential protein-protein interactions between a noncognate HK/RR pair, DosT/NarL. The protein interaction between DosT and NarL was verified by phosphotransfer reaction from DosT to NarL. Furthermore, we found that the DosT and DosS HKs, which share considerable sequence similarities to each other and form a twocomponent system with the DosR RR, have different crossinteraction capabilities with NarL: DosT interacted with NarL, while DosS did not. The dimerization domains of DosT and DosS were shown to be sufficient to confer specificity for DosR, and the different cross-interaction abilities of DosS and DosT with NarL were demonstrated to be attributable to variations in the amino acid sequences of the α2-helices of their dimerization domains.

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Research Support, U.S. Gov't, Non-P.H.S.
Shedding of Viral Hemorrhagic Septicemia Virus (Genotype IVb) by Experimentally Infected Muskellunge (Esox masquinongy)
Robert K. Kim , Mohamed Faisal
J. Microbiol. 2012;50(2):278-284.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1145-2
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AbstractAbstract PDF
Previous experimental infection demonstrated that juvenile muskellunge (Esox masquinongy) can survive experimental infection of viral hemorrhagic septicemia virus, Genotype IVb (VHSV IVb) at a low concentration of exposure. Herein we report that survivors of experimental infection with VHSV IVb shed the virus into the surrounding environment for an extended period of time. When muskellunge were exposed to VHSV IVb by immersion at a concentration of 1,400 plaque forming units (PFU)/ml, VHSV IVb was detected in the water of surviving fish for up to 15 weeks postexposure (p.e.) with the highest levels of shedding occurring between weeks 1 and 5 p.e. We estimated that each juvenile muskellunge can shed upwards of 1.36×105 PFU/fish/h after initial exposure signifying the uptake and amplification of VHSV to several orders of magnitude above the original exposure concentration. Muskellunge surviving low concentration exposure were re-infected with VHSV IVb by immersion at week 22 p.e. at concentrations ranging from 0 to 106 PFU/ml. Viral shedding was detected in all re-exposed fish, including mock rechallenged controls up to 15 consecutive weeks. Rates of viral shedding were substantially higher following rechallenge in the first 5 weeks. The highest rate of viral shedding was approximately 4.6×106 PFU/fish/h and shedding did not necessarily correspond to the re-exposure VHSV concentration. The results of this study shed new light into the dynamics of VHSV IVb shedding in a highly susceptible host and provide useful insights to fishery managers to design effective control strategies to this deadly virus.
Research Support, Non-U.S. Gov'ts
KSHV Infection of B-Cell Lymphoma Using a Modified KSHV BAC36 and Coculturing System
Hyosun Cho , Hyojeung Kang
J. Microbiol. 2012;50(2):285-292.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1495-9
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AbstractAbstract PDF
Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of two B cell lymphoproliferative diseases, namely primary effusion lymphoma (PEL) and multicentric Castleman’s disease (MCD). KSHV infection of B cell lymphoma in vitro has been a long-standing battle in advancing human KSHV biology. In this study, a modified form of KSHV BAC36 named BAC36A significantly increased the fidelity of gene-targeted site-directed mutagenesis in the KSHV genome. This modification eliminates tedious screening steps required to obtain mutant clones when a KSHV BAC36 reverse genetic system is used. Coculturing B-cell lymphoma BJAB cells with KSHV BAC36A stably transfected 293T cells enabled us to infect BJAB cells with a KSHV virion derived from the KSHV BAC36A. The coculture system produced substantial amounts of KSHV infection to BJAB, meaning that KSHV virions were released from 293T cells and then infected neighboring BJAB cells. Owing to our success with the KSHV BAC36A and coculture system, we propose a new genetic system for the study of KSHV gene expression and regulation in B-cell lymphoma.

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Antiviral Activities of Flavonoids Isolated from the Bark of Rhus verniciflua Stokes against Fish Pathogenic Viruses In Vitro
So Young Kang , Ji-Young Kang , Myung-Joo Oh
J. Microbiol. 2012;50(2):293-300.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-2068-7
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AbstractAbstract PDF
An 80% methanolic extract of Rhus verniciflua Stokes bark showed significant anti-viral activity against fish pathogenic infectious hematopoietic necrosis virus (IHNV) and viral hemorrhagic septicemia virus (VHSV) in a cell-based assay measuring virus-induced cytopathic effect (CPE). Activity-guided fractionation and isolation for the 80% methanolic extract of R. verniciflua yielded the most active ethyl acetate fraction, and methyl gallate (1) and four flavonoids: fustin (2), fisetin (3), butin (4) and sulfuretin (5). Among them, fisetin (3) exhibited high antiviral activities against both IHNV and VHSV showing EC50 values of 27.1 and 33.3 μM with selective indices (SI = CC50/EC50) more than 15, respectively. Fustin (2) and sulfuretin (5) displayed significant antiviral activities showing EC50 values of 91.2– 197.3 μM against IHNV and VHSV. In addition, the antiviral activity of fisetin against IHNV and VHSV occurred up to 5 hr post-infection and was not associated with direct virucidal effects in a timed addition study using a plaque reduction assay. These results suggested that the bark of R. verniciflua and isolated flavonoids have significant anti-viral activity against IHNV and VHSV, and also have potential to be used as anti-viral therapeutics against fish viral diseases.

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    International Immunopharmacology.2018; 54: 366.     CrossRef
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    Jinfeng Yang, Yong Soo Kwon, Myong Jo Kim
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  • Heartwood extract of Rhus verniciflua Stokes and its active constituent fisetin attenuate vasoconstriction through calcium-dependent mechanism in rat aorta
    Jung-Min Park, Jun-Hyeong Lee, Chun-Soo Na, Dongho Lee, Jin-Yong Lee, Masahiko Satoh, Moo-Yeol Lee
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    Romana Sokolová, Šárka Ramešová, Jana Kocábová, Viliam Kolivoška, Ilaria Degano, Emanuela Pitzalis
    Monatshefte für Chemie - Chemical Monthly.2016; 147(8): 1375.     CrossRef
  • Fisetin-Rich Extracts ofRhus vernicifluaStokes Improve Blood Flow Rates in Mice Fed Both Normal and High-Fat Diets
    Won Kyun Im, Hyun Jung Park, Kwang Soo Lee, Jung Hoon Lee, Young Dong Kim, Kyeong-Hee Kim, Sang-Jae Park, Seokmann Hong, Sung Ho Jeon
    Journal of Medicinal Food.2016; 19(2): 120.     CrossRef
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    Jianjun Pei, Ping Dong, Tao Wu, Linguo Zhao, Xianying Fang, Fuliang Cao, Feng Tang, Yongde Yue
    Journal of Agricultural and Food Chemistry.2016; 64(42): 7966.     CrossRef
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    Šárka Ramešová, Romana Sokolová, Ilaria Degano
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  • Comparison of the Flavonoid and Urushiol Content in Different Parts of Rhus verniciflua Stokes Grown in Wonju and Okcheon
    Won-Jae Lee, Ji-Eun Kang, Ji-Ho Choi, Seok-Tae Jeong, Myung-Kon Kim, Han-Seok Choi
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    Jun-Hyeong Lee, Mikyung Kim, Kyung-Hwa Chang, Cheol Yi Hong, Chun-Soo Na, Mi-Sook Dong, Dongho Lee, Moo-Yeol Lee
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    Canhui Yi, Yong Zhang, Zhenlong Yu, Yao Xiao, Jingshu Wang, Huijuan Qiu, Wendan Yu, Ranran Tang, Yuhui Yuan, Wei Guo, Wuguo Deng, Chunhong Yan
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    Ji Hye Kim, Yong Cheol Shin, Seong-Gyu Ko
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  • Phenolic extractives in the trunk of Toxicodendron vernicifluum: chemical characteristics, contents and radial distribution
    Koh Hashida, Masanobu Tabata, Katsushi Kuroda, Yuichiro Otsuka, Satoshi Kubo, Rei Makino, Yoshitaka Kubojima, Mario Tonosaki, Seiji Ohara
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Modulation of Immune Response by Interleukin-10 in Systemic Corynebacterium kutscheri Infection in Mice
Eui-Suk Jeong , Kyoung-Sun Lee , Seung-Ho Heo , Jin-Hee Seo , Yang-Kyu Choi
J. Microbiol. 2012;50(2):301-310.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1298-z
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AbstractAbstract PDF
Interleukin (IL)-10 is an anti-inflammatory cytokine that modulates sepsis by decreasing pro-inflammatory cytokine production and chemokine expression. In this study, IL- 10-deficient and wild-type (WT) mice were infected with Corynebacterium kutscheri to determine if the absence of IL-10 altered the protective immunity and pathogenesis. After infection, IL-10 knockout (KO) mice had a higher survival rate than WT mice. The decrease of body weight and the increased weight of organs such as liver and spleen were greater in WT mice. Bacterial counts were significantly increased after inoculation in WT mice over those in IL-10 KO mice. WT mice had more granulomatous inflammation and coagulative necrosis in the liver and spleen, lymphocyte depletion in lymphoid follicles, and apoptosis of immune cells in the spleen. WT mice had significantly higher plasma concentrations of aspartate aminotransferase and alanine aminotransferase. Furthermore, more upregulation of tumor necrosis factor-α and IL-4 in the plasma, macrophage inflammatory protein-2, keratinocyte-derived chemokine, inducible nitric oxide synthase, and interferoninducible protein 10 mRNA in the spleen were observed in WT mice after inoculation. These results suggest that the lack of IL-10 contributes to an increase in the systemic clearance of C. kutscheri, and that IL-10 plays a detrimental role in controlling systemic C. kutscheri infection.
Journal Article
Porphyromonas gingivalis-Derived Lipopolysaccharide-Mediated Activation of MAPK Signaling Regulates Inflammatory Response and Differentiation in Human Periodontal Ligament Fibroblasts
Taegun Seo , Seho Cha , Tae-Il Kim , Hee-Jung Park , Jeong-Soon Lee , Kyung Mi Woo
J. Microbiol. 2012;50(2):311-319.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-2146-x
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AbstractAbstract PDF
Porphyromonas gingivalis (P.g.), which is a potential pathogen for periodontal diseases, contains lipopolysaccharide (LPS), and this endotoxin stimulates a variety of cellular responses. At present, P.g.-derived LPS-induced cellular responses in human periodontal ligament fibroblasts (PDLFs) are not well characterized. Here, we demonstrate that P.gderived LPS regulates inflammatory responses, apoptosis and differentiation in PDLFs. Interleukin-6 (IL-6) and -8 (IL-8) were effectively upregulated by treatment of P.g.-derived LPS, and we confirmed apoptosis markers including elevated cytochrome c levels, active caspase-3 and morphological change in the presence of P.g.-derived LPS. Moreover, when PDLFs were cultured with differentiation media, P.g.- derived LPS reduced the expression of differentiation marker genes, as well as reducing alkaline phosphatase (ALP) activity and mineralization. P.g.-derived LPS-mediated these cellular responses were effectively abolished by treatment of mitogen-activated protein kinase (MAPK) inhibitors. Taken together, our results suggest that P.g.-derived LPS regulates several cellular responses via activation of MAPK signaling pathways in PDLFs.

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Research Support, Non-U.S. Gov'ts
Cyclic AMP-Receptor Protein Activates Aerobactin Receptor IutA Expression in Vibrio vulnificus
Choon-Mee Kim , Seong-Jung Kim , Sung-Heui Shin
J. Microbiol. 2012;50(2):320-325.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-2056-y
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AbstractAbstract PDF
The ferrophilic bacterium Vibrio vulnificus can utilize the siderophore aerobactin of Escherichia coli for iron acquisition via its specific receptor IutA. This siderophore piracy by V. vulnificus may contribute to its survival and proliferation, especially in mixed bacterial environments. In this study, we examined the effects of glucose, cyclic AMP (cAMP), and cAMP-receptor protein (Crp) on iutA expression in V. vulnificus. Glucose dose-dependently repressed iutA expression. A mutation in cya encoding adenylate cyclase required for cAMP synthesis severely repressed iutA expression, and this change was recovered by in trans complementing cya or the addition of exogenous cAMP. Furthermore, a mutation in crp encoding Crp severely repressed iutA expression, and this change was recovered by complementing crp. Accordingly, glucose deprivation under iron-limited conditions is an environmental signal for iutA expression, and Crp functions as an activator that regulates iutA expression in response to glucose availability.
Expression and Purification of Lacticin Q by Small Ubiquitin-Related Modifier Fusion in Escherichia coli
Qingshan Ma , Zhanqiao Yu , Bing Han , Qing Wang , Rijun Zhang
J. Microbiol. 2012;50(2):326-331.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1425-x
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AbstractAbstract PDF
Lacticin Q is a broad-spectrum class II bacteriocin with potential as an alternative to conventional antibiotics. The objective of this study was to produce recombinant lacticin Q using a small ubiquitin-related modifier (SUMO) fusion protein expression system. The 168-bp lacticin Q gene was cloned into the expression vector pET SUMO and transformed into Escherichia coli BL21(DE3). The soluble fusion protein was recovered with a Ni-NTA Sepharose column (95% purity); 130 mg protein was obtained per liter of fermentation culture. The SUMO tag was then proteolytically cleaved from the protein, which was re-applied to the column. Finally, about 32 mg lacticin Q (≥96% purity) was obtained. The recombinant protein exhibited antimicrobial properties similar to that of the native protein, demonstrating that lacticin Q had been successfully expressed by the SUMO fusion system.
Heterologous Expression of Polygalacturonase Genes Isolated from Galactomyces citri-aurantii IJ-1 in Pichia pastoris
Il Jae Cho , In-Cheol Yeo , Nam Keun Lee , Suk Hee Jung , Young Tae Hahm
J. Microbiol. 2012;50(2):332-340.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1290-7
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AbstractAbstract PDF
The objective of this work was to isolate the polygalacturonase genes of Galactomyces citri-aurantii IJ-1 harvested from rotten citrus peels and to heterologously express these genes in Pichia pastoris. Two polygalacturonase (PG) genes from G. citri-aurantii IJ-1 were obtained and tentatively named PG1 and PG2. The genes were cloned into pPICZαC, and expressed in Pichia pastoris strain GS115 with a native signal peptide or the α-factor secretion signal peptide of Saccharomyces cerevisiae. All of the recombinant proteins were successfully secreted into the culture media and confirmed as a single band with a molecular weight of 35 to 38 kDa by SDS-PAGE. The specific enzyme activities of recombinant PG1 and PG2 purified by His-tag affinity resin were 4,749 and 6,719 U/mg, respectively, with an optimal pH and temperature of pH 4.0 and 50°C. The Michaelis- Menten kinetic constants for PG1 and PG2, Km, were confirmed to be 0.94 and 0.84 mM, respectively. In the presence of Mn2+, the activity of PG1 and PG2 were increased to 160.8 and 146.4% of normal levels, respectively. In contrast, Cu2+ and Fe3+ acted as strong inhibitors to the PGs.

Citations

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  • Integrated in vitro fermentation, transcriptomics and enzymatic property analyses uncover interaction between polysaccharide from the fruits of Lycium barbarum and Bacteroides ovatus
    Jinghong Wei, Wangting Zhou, Wei Yi, Jiameng Shi, Yamei Yan, Jia Mi, Lu Lu, Youlong Cao, Xiaoxiong Zeng
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Remodeling of the Glycosylation Pathway in the Methylotrophic Yeast Hansenula polymorpha to Produce Human Hybrid-Type N-Glycans
Seon Ah Cheon , Hyunah Kim , Doo-Byoung Oh , Ohsuk Kwon , Hyun Ah Kang
J. Microbiol. 2012;50(2):341-348.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-2097-2
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AbstractAbstract PDF
As a step forward to achieve the generation of human complex- type N-glycans in the methylotrophic yeast Hansenula polymorpha, we here report the modification of the yeast glycosylation pathway by heterologous expression of the human gene encoding β-1,2-N-acetylglucosaminyltransferase I (GnTI). For the optimal expression of human GnTI in the yeast Golgi compartment, the catalytic domain of the GnTI was fused to various N-terminal leader sequences derived from the yeast type II membrane proteins. The vectors containing GnTI fusion constructs were introduced into the H. polymorpha och1Δ single and och1Δalg3Δ double mutant strains expressing the ER-targeted Aspergillus saitoi α-1,2 mannosidase, respectively. Both of the glycoengineered Hpoch1Δ and Hpoch1ΔHpalg3Δ strains were shown to produce successfully the hybrid-type glycans with a monoantennary N-acetylglucosamine (GlcNAc1Man5GlcNAc2 and GlcNAc1Man3GlcNAc2, respectively) by N-glycan profile analysis of cell wall proteins. Furthermore, by comparative analysis of byproduct formation and the glycosylation site occupancy, we propose that the Hpoch1Δ strain would be more suitable than the Hpoch1ΔHpalg3Δ strain as a host for the production of recombinant proteins with humanized glycans.

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NOTE] Phycicoccus ochangensis sp. nov., Isolated from Soil of a Potato Cultivation Field
Hyangmi Kim , Hyun-Woo Oh , Doo-Sang Park , Kang Hyun Lee , Sung Uk Kim , Hee-Moon Park , Kyung Sook Bae
J. Microbiol. 2012;50(2):349-353.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1206-6
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AbstractAbstract PDF
Two novel, Gram-positive, motile, coccal bacteria, strains L1b-b9T and B5a-b5, were isolated from a potato cultivation field in Ochang, Korea. These isolates grew at 10–45°C, pH 5.0–10.0, and in the presence of 8% (w/v) NaCl. The diagnostic diamino acid in the cell-wall peptidoglycan was mesodiaminopimelic acid. The major menaquinone was MK-8(H4) and the main cellular fatty acids were iso-C14:0, iso-C15:0, and anteiso-C15:0. Polar lipids in strain L1b-b9T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and an unknown glyco-amino lipid. The G+C content of genomic DNA was 73.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strains L1b-b9T and B5a-b5 shared 99.36% similarity and formed a robust clade with the type species of the genus Phycicoccus. Strain L1b-b9T is related most closely to Phycicoccus cremeus V2M29T (97.52% 16S rRNA gene sequence similarity). On the basis of phylogenetic characteristics, the name Phycicoccus ochangensis sp. nov. is proposed for strain LIb-b9T (=KCTC 19694T =JCM 17595T).

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  • Phycicoccus sonneraticus sp. nov., a Novel Endophytic Actinobacterium Isolated from the Bark of Sonneratia apetala
    Huiling Tang, Xiaohui Chen, Mingsheng Chen, Xiaohong Li, Jianjing Jiang, Li Tuo, Feina Li
    Current Microbiology.2023;[Epub]     CrossRef
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    Jong-Pyo Kang, Yeon-Ju Kim, Ngoc-Lan Nguyen, Van-An Hoang, Mohamed El-Agamy Farh, Sung-Chul Joo, Lin-Hu Quan, Deok-Chun Yang
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    Hina Singh, KyungHwa Won, Hien T. T. Ngo, Juan Du, MooChang Kook, Tae-Hoo Yi
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Journal Article
NOTE] Arenimonas aquaticum sp. nov., a Member of the Gammaproteobacterium, Isolated from a Freshwater Reservoir
A-Ram Kim , Siwon Lee , Kyudong Han , Tae-Young Ahn
J. Microbiol. 2012;50(2):354-358.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1301-8
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AbstractAbstract PDF
A novel bacterial strain, designated NA-09T, was isolated from a freshwater sample collected from the Cheonho reservoir, Republic of Korea. Colonies were creamy-white pigmented, translucent, and circular with convex shape. The isolate was Gram-staining negative, strictly aerobic, motile, and rod-shaped. The 16S rRNA gene sequence analysis revealed that strain NA-09T belonged to the genus Arenimonas and showed the highest sequence similarities with Arenimonas malthae CC-JY-1T (95.4%), A. oryziterrae YC6267T (94.9%), A. composti P2-12-1T (94.8%), and A. donghaensis H03-R19T (94.1%). The major fatty acids were iso-C16:0 (20.8%), iso-C15:0 (16.9%), summed feature 1 (13.2%), and iso-C16:1ω7c alcohol (10.2%). The major isoprenoid quinone of the isolate was ubiquionone-8. On the basis of the data from the polyphasic characterization, the strain NA-09T represents a novel species, for which the name Arenimonas aquaticum sp. nov. is proposed (type strain NA-09T =KACC 14663T =NBRC 106550T).
Research Support, Non-U.S. Gov't
NOTE] GFP-Expressing Influenza A Virus for Evaluation of the Efficacy of Antiviral Agents
Jin Il Kim , Sehee Park , Ilseob Lee , Sangmoo Lee , Saem Shin , Yongkwan Won , Min-Woong Hwang , Joon-Yong Bae , Jun Heo , Hye-Eun Hyun , Hyejin Jun , Soon Sung Lim , Man-Seong Park
J. Microbiol. 2012;50(2):359-362.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-2163-9
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AbstractAbstract PDF
To address its value as a screening tool in the development of antiviral drugs, a recombinant influenza virus expressing green fluorescent protein (rPR8-GFP virus) was investigated in vitro and in vivo. The inhibition of viral growth by a neuraminidase inhibitor in the cells or lower respiratory tracts of mice could be visualized by the level of fluorescence. In addition, the rPR8-GFP virus exhibited high pathogenicity in mice. Taken together, these results suggest that the rPR8-GFP virus can be a useful tool for the rapid identification of antiviral drugs active against influenza viruses.

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    Sangmoo Lee, Jin Il Kim, Jun Heo, Ilseob Lee, Sehee Park, Min-Woong Hwang, Joon-Yong Bae, Mee Sook Park, Hyoung Jin Park, Man-Seong Park
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    Sehee Park, Jin Il Kim, Ilseob Lee, Sangmoo Lee, Min-Woong Hwang, Joon-Yong Bae, Jun Heo, Donghwan Kim, Sang-Zin Han, Man-Seong Park
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ERRATUM] Neutralization Potential of the Plasma of HIV-1 Infected Indian Patients in the Context of Anti-V3 Antibody Content and Antiretroviral Theraphy
Alok Kumar Choudhary , Raiees Andrabi , Somi Sankaran Prakash , Rajesh Kumar , Shubhasree Dutta Choudhury , Naveet Wig , Ashutosh Biswas , Anjali Hazarika , Kalpana Luthra
J. Microbiol. 2012;50(2):363-363.
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In the article by Choudhary et al. that appears in the Journal of Microbiology 2012; 50, 149-154. Page 149, on journal title ‘Theraphy’ should read ‘Therapy’.

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