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Volume 48(6); December 2010
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Research Support, Non-U.S. Gov'ts
Assessment of Genetic and Functional Relationship of Antagonistic Fluorescent Pseudomonads of Rice Rhizosphere by Repetitive Sequence, Protein Coding Sequence and Functional Gene Analyses
Jayakumar Pathma , Niraikulam Ayyadurai , Natarajan Sakthivel
J. Microbiol. 2010;48(6):715-727.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0064-3
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AbstractAbstract PDF
Antagonistic fluorescent pseudomonads isolated from rice rhizospheric soil were characterized using biochemical, taxonomical and molecular tools. Production of cyclopropane fatty acid (CFA) was correlated with their antagonistic potential. Strains were grouped into 18 different genotypes on the basis of amplified ribosomal DNA restriction analysis (ARDRA) and repetitive (rep)-PCR based genotypic fingerprinting analyses. High phylogenetic resolution among antagonistic fluorescent pseudomonad strains was obtained based on the DNA gyrase B subunit (gyrB) and RNA polymerase sigma factor 70 (rpoD) gene sequence analyses. Combined gyrB and rpoD sequence analysis resulted in the accurate estimation of molecular phylogeny and provided a significant correlation between the genetic distances among strains. Present study demonstrated the genetic and functional relationship of fluorescent pseudomonads. The knowledge on genetic and functional potential of fluorescent pseudomonads associated with rice rhizosphere is useful to understand their ecological role and for their utilization in sustainable agriculture.

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    Jayakumar Pathma, Natarajan Sakthivel
    Applied Soil Ecology.2013; 70: 33.     CrossRef
  • Microbial diversity of vermicompost bacteria that exhibit useful agricultural traits and waste management potential
    Jayakumar Pathma, Natarajan Sakthivel
    SpringerPlus.2012;[Epub]     CrossRef
An Improved Method for Extracting Bacteria from Soil for High Molecular Weight DNA Recovery and BAC Library Construction
Juan Liu , Jingquan Li , Li Feng , Hui Cao , Zhongli Cui
J. Microbiol. 2010;48(6):728-733.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0139-1
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AbstractAbstract PDF
Separation of bacterial cells from soil is a key step in the construction of metagenomic BAC libraries with large DNA inserts. Our results showed that when combined with sodium pyro-phosphate and homogenization for soil dispersion, sucrose density gradient centrifugation (SDGC) was more effective at separating bacteria from soil than was low speed centrifugation (LSC). More than 70% of the cells, along with some soil colloids, were recovered with one round of centrifugation. A solution of 0.8% NaCl was used to resuspend these cell and soil pellets for purification with nycodenz density gradient centrifugation (NDGC). After purification, more than 30% of the bacterial cells in the primary soil were extracted. This procedure effectively removed soil contamination and yielded sufficient cells for high molecular weight (HMW) DNA isolation. Ribosomal intergenic spacer analysis (RISA) showed that the microbial community structure of the extracted cells was similar to that of the primary soil, suggesting that this extraction procedure did not significantly change the the soil bacteria community structure. HMW DNA was isolated from bacterial cells extracted from red soil for metagenomic BAC library construction. This library contained DNA inserts of more than 200 Mb with an average size of 75 kb.

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Differentiation of Acremonium chrysogenum M35 in Submerged Culture with Glass Beads or Silicone Rubbers
Hwan Hyo Lee , Hyun Yong Shin , Eun Ji Kim , Seung Wook Kim
J. Microbiol. 2010;48(6):734-738.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0108-8
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AbstractAbstract PDF
In this study, we investigated the effects of glass beads and silicone rubbers on the differentiation and morphological changes of A. chrysogenum M35 in submerged culture. Differentiation in the center of the cell pellets was improved by the addition of glass beads or silicone rubbers to the primary medium. The fragmentation rate constant (kfrag), which is used to estimate the tensile strength of fungal hyphae, was increased by more than 40% in baffled flasks containing glass beads. The maximum fragmentation rate was also increased by 48% when silicone rubbers were added to a 5 L bioreactor containing the culture. During the cultivation in the main medium with 6 glass beads, the value of the fractal dimension increased by about 8% when it was compared with baffled flasks without glass beads. Additionally, the number of arthrospores and the dry cell weight were increased by more than 10% in baffled flasks containing beads. The degree of roundness, which is the ratio of the object area to the longest Feret diameter, was decreased from 0.85 at day 1 to 0.77 at day 5. The differentiation of A. chrysogenum M35 was also supposedly closely related with the enlargement of the cell surfaces. Taken together, these results indicate that complex changes in morphology resulted in increased cell growth and differentiation in the culture broth containing glass beads and silicone rubbers.

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  • Concept for sustainable biorefinery process utilizing corn cobs as feedstock: Conversion to cephalosporin C via dilute acid hydrolysis and detoxification
    Chan Kyum Kim, Seunghee Kim, Jeongho Lee, Kang Hyun Lee, Hah Young Yoo, Chun-Woong Park
    Journal of Industrial and Engineering Chemistry.2025;[Epub]     CrossRef
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    PRATAP R. PATNAIK
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    Hyun Yong Shin, Jin Young Lee, Han Suk Choi, Ja Hyun Lee, Seung Wook Kim
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Metagenomic Assessment of a Sulfur-Oxidizing Enrichment Culture Derived from Marine Sediment
Man-Young Jung , VinhHoa Pham , Soo-Je Park , So-Jeong Kim , Jong-Chan Chae , Yul Roh , Sung-Keun Rhee
J. Microbiol. 2010;48(6):739-747.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0257-9
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AbstractAbstract PDF
The biological oxidation of reduced sulfur compounds is a critically important process in global sulfur biogeochemistry. In this study, we enriched from marine sediments under denitrifying conditions, chemolithotrophic sulfur oxidizers that could oxidize a variety of reduced sulfur compounds: thiosulfate, tetrathionate, sulfide, and polysulfide. Two major phylotypes of 16S rRNA gene (>99% identity in each phylotype) were detected in this enrichment culture. In order to characterize sulfide oxidation, we sequenced and characterized one fosmid clone (43.6 kb) containing the group I sulfide-quinone reductase (sqr) gene. Interestingly, four putative rhodanese genes were found in this clone. Furthermore, comparative alignment with the closest genome of Thiomicrospira crunogena XCL2 revealed that three homologous genes were located within the vicinity of the sqr gene. Fosmid clones harboring carbon fixation (cbbL and cbbM) and denitrification (narG) genes were screened, and the phylogeny of the functional genes was analyzed. Along with the comparison between the sqr-containing fosmid clones and the relevant gamma-proteobacteria, our phylogenetic study based on the 16S rRNA gene and carbon fixation genes suggest the prevalence of chemolithotrophic gamma-proteobacteria in the denitrifying cultures. The findings of this study imply that a combination of cultivation and metagenomic approaches might provide us with a glimpse into the characteristics of sulfur oxidizers in marine sediments.

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The First Report of Two Species of Polyporus (Polyporaceae, Basidiomycota) from South Korea
Jin Sung Lee , Eun Ju Woo , Kyoung Hee Oh , Jae-Jin Kim , Young Woon Lim
J. Microbiol. 2010;48(6):748-753.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0105-y
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AbstractAbstract PDF
Based on morphological examination, two species of Polyporus, P. dictyopus, and P. tuberaster, were identified, which constitutes the first record of these species in South Korea. To confirm their affinity within the genus Polyporus, the phylogenetic relationships of Polyporus and allied genera were established from nuclear large subunit ribosomal DNA (nLSU rDNA) sequences, and a morphological diagnostic key is presented to clarify the Korean species of Polyporus.

Citations

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Acinetobacter kyonggiensis sp. nov., a beta-Glucosidase-Producing Bacterium, Isolated from Sewage Treatment Plant
Hye-Jung Lee , Sang-Seob Lee
J. Microbiol. 2010;48(6):754-759.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0355-8
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AbstractAbstract PDF
A Gram-negative, non-motile bacterium, designated KSL5401-037T, was isolated from a sewage treatment plant in Gwangju in the Republic of Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain KSL5401-037T belonged to the genus Acinetobacter in the family Moraxellaceae of the Gammaproteobacteria (Brisou and Prevot, 1954). According to a 16S rRNA gene sequence analysis, it was closely related to Acinetobacter johnsonii ATCC 17909T (97.3%), A. bouvetii 4B02T (97.2%), and A. beijerinckii 58aT (96.8%). Chemotaxonomic data revealed that strain KSL5401- 037T possesses an ubiquinone system with Q-8 as the predominant compound and C16:0 (19.2%), C18:1 w9c (19.5%), and summed feature 3 (C16:1 w6c / C16:1 w7c, 34.1%) as the predominant cellular fatty acids. The major polar lipids detected in strain KSL5401-037T were diphosphatidylglycerol (DPG) and, phosphatidylethanolamine (PE), followed by phosphatidylglycerol (PG) and moderate amounts of phosphatidylcholine and phosphatidylserine. The G+C content of the genomic DNA was 41.2-42.1 mol%. Strain KSL5401-037T exhibited relatively low levels of DNA-DNA relatedness with respect to A. johnsonii DSM 6963T (17.7%) and A. bouvetii 4B02T (9.3%). The DNA-DNA relatedness values, biochemical, and physiological characteristics of strain KSL5401-037T strongly support its genotypic and phenotypic differentiation from other recognized type strains of the genus Acinetobacter. Based on these data, strain KSL5401-037T (JCM 17071T =KEMC 5401- 037T) should be classified in the genus Acinetobacter as a type strain of novel species, for which the name Acinetobacter kyonggiensis sp. nov. is proposed.

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Sphingomonas ginsenosidimutans sp. nov., with Ginsenoside Converting Activity
Tae-Eun Choi , Qing-Mei Liu , Jung-Eun Yang , Siyi Sun , Se-Young Kim , Tae-Hoo Yi , Wan-Taek Im
J. Microbiol. 2010;48(6):760-766.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0469-z
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AbstractAbstract PDF
The Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming, and rod-shaped bacterial strain designated Gsoil 1429T was isolated from the soil of ginseng cultivating field of Pocheon province in South Korea. This bacterium was characterized in order to determine its taxonomic position by using the polyphasic approach. Strain Gsoil 1429T grew well at 25-37°C and at pH 7.0 on R2A and nutrient agar without NaCl supplement. Strain Gsoil 1429T had beta-glucosidase activity, which was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to F2 via gypenoside XVII. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 1429T was shown to belong to the family Sphingomonadaceae and to be related to Sphingomonas yunnanensis YIM 003T (98.2% sequence similarity), S. phyllosphaerae FA2T (97.5%), S. koreensis JSS26T (97.3%), and S. asaccharolytica IFO 15499T (97.1%). The G+C content of the genomic DNA was 65.6%. The major respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (comprising C18:1 w7c/w9t/w12t), C16:0 and C14:0 2OH. DNA and chemotaxonomic data supported the affiliation of strain Gsoil 1429T to the genus Sphingomonas. The DNA-DNA relatedness values between strain Gsoil 1429T and its closest phylogenetically neighbours were below 28%. Strain Gsoil 1429T could be differentiated genotypically and phenotypically from the recognized species of the genus Sphingomonas. The isolate therefore represents a novel species, for which the name Sphingomonas ginsenosidimutans sp. nov. is proposed, with the type strain Gsoil 1429T (=KACC 14949T =JCM 17074T =LMG 25799T).
Sporulation of Several Biocontrol Fungi as Affected by Carbon and Nitrogen Sources in a Two-Stage Cultivation System
Li Gao , Xingzhong Liu
J. Microbiol. 2010;48(6):767-770.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0049-2
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AbstractAbstract PDF
The development of fungal biopesticides requires the efficient production of large numbers spores or other propagules. The current study used published information concerning carbon concentrations and C:N ratios to evaluate the effects of carbon and nitrogen sources on sporulation of Paecilomyces lilacinus (IPC-P and M- 14) and Metarhizium anisopliae (SQZ-1-21 and RS-4-1) in a two-stage cultivation system. For P. lilacinus IPCP, the optimal sporulation medium contained urea as the nitrogen source, dextrin as the carbon source at 1 g/L, a C:N ratio of 5:1, with ZnSO4·7H2O at 10 mg/L and CaCl2 at 3 g/L. The optimal sporulation medium for P. lilacinus M-14 contained soy peptone as the nitrogen source and maltose as the carbon source at 2 g/L, a C:N ratio of 10:1, with ZnSO4·7H2O at 250 mg/L, CuSO4·5H2O at 10 mg/L, H3BO4 at 5 mg/L, and Na2MoO4·2H2O at 5 mg/L. The optimum sporulation medium for M. anisopliae SQZ-1-21 contained urea as the nitrogen source, sucrose as the carbon source at 16 g/ L, a C:N ratio of 80:1, with ZnSO4·7H2O at 50 mg/L, CuSO4·5H2O at 50 mg/L, H3BO4 at 5 mg/L, and MnSO4·H2O at 10 mg/L. The optimum sporulation medium for M. anisopliae RS-4-1 contained soy peptone as the nitrogen source, sucrose as the carbon source at 4 g/L, a C:N ratio of 5:1, with ZnSO4·7H2O at 50 mg/L and H3BO4 at 50 mg/L. All sporulation media contained 17 g/L agar. While these results were empirically derived, they provide a first step toward low-cost mass production of these biocontrol agents.

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    Yi-Ping Gao, De-Xiang Shi, Yuan-Hao Li, Xiong Zhao He, Xiao-Yun Wang, Kai Lin, Xia-Lin Zheng
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    Veterinary Parasitology.2025; 340: 110613.     CrossRef
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    Raymyson R. S. Queiroz, Thais B. P. Teodoro, Aline T. Carolino, Ricardo O. B. Bitencourt, Willians G. Souza, Marcela S. B. Boechat, Roberto R. Sobrinho, Gerson A. Silva, Richard I. Samuels
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    Ling Xie, Ji Hee Han, Jeong Jun Kim, Sang Yeob Lee
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    Gutierr eacute z Rojas Ivonne, Tibasosa Rodr iacute guez Geraldine, Moreno Sarmiento Nubia, Ximena Rodr iacute guez Bocanegra Mar iacute a, Montoya Dolly
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Comparative Proteome Analysis of Bacillus anthracis with pXO1 Plasmid Content
Sudipto Shahid , Ji Hyun Park , Hyung Tae Lee , Seong-Joo Kim , Ji Cheon Kim , Sang Hoon Kim , Dal Mu Ri Han , Dong In Jeon , Kyoung Hwa Jung , Young Gyu Chai
J. Microbiol. 2010;48(6):771-777.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0136-4
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AbstractAbstract PDF
Bacillus anthracis the causative agent of anthrax, is an important pathogen among the Bacillus cereus group of species because of its physiological characteristics and its importance as a biological warfare agent. Tripartite anthrax toxin proteins and a poly-D-glutamic acid capsule are produced by B. anthracis vegetative cells during mammalian hosts infection and when cultured in conditions that are thought to mimic the host environment. To identify the factors regulating virulence in B. anthracis the whole cell proteins were extracted from two B. anthracis strains and separated by narrow range immobilized pH gradient (IPG) strips (pH 4-7), followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins that were differentially expressed were identified by the peptide fingerprinting using matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS). A total of 23 proteins were identified as being either upregulated or downregulated in the presence or absence of the virulence plasmid pXO1. Two plasmid encoded proteins and 12 cellular proteins were identified and documented as potential virulence factors.

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Role of Hydrogen Generation by Klebsiella pneumoniae in the Oral Cavity
Tomoko Kanazuru , Eisuke F. Sato , Kumiko Nagata , Hiroshi Matsui , Kunihiko Watanabe , Emiko Kasahara , Mika Jikumaru , June Inoue , Masayasu Inoue
J. Microbiol. 2010;48(6):778-783.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0149-z
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AbstractAbstract PDF
Some gastrointestinal bacteria synthesize hydrogen (H2) by fermentation. Despite the presence of bactericidal factors in human saliva, a large number of bacteria also live in the oral cavity. It has never been shown that oral bacteria also produce H2 or what role H2 might play in the oral cavity. It was found that a significant amount of H2 is synthesized in the oral cavity of healthy human subjects, and that its generation is enhanced by the presence of glucose but inhibited by either teeth brushing or sterilization with povidone iodine. These observations suggest the presence of H2-generating bacteria in the oral cavity. The screening of commensal bacteria in the oral cavity revealed that a variety of anaerobic bacteria generate H2. Among them, Klebsiella pneumoniae (K. pneumoniae) generated significantly large amounts of H2 in the presence of glucose. Biochemical analysis revealed that various proteins in K. pneumoniae are carbonylated under standard culture conditions, and that oxidative stress induced by the presence of Fe++ and H2O2 increases the number of carbonylated proteins, particularly when their hydrogenase activity is inhibited by KCN. Inhibition of H2 generation markedly suppresses the growth of K. pneumoniae. These observations suggest that H2 generation and/or the reduction of oxidative stress is important for the survival and growth of K. pneumoniae in the oral cavity.

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Endophytic Fungus Trichothecium roseum LZ93 Antagonizing Pathogenic Fungi In Vitro and Its Secondary Metabolites
XiaoMei Zhang , GuoHong Li , Juan Ma , Ying Zeng , WeiGuang Ma , PeiJi Zhao
J. Microbiol. 2010;48(6):784-790.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0173-z
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AbstractAbstract PDF
The endophytic fungus Trichothecium roseum LZ93 from Maytenus hookeri was found to antagonize other pathogenic fungi in vitro. To identify which compound contributed substantially to the antagonism, we fermented the strain and purified its fermentation products. Eleven compounds were obtained, including two trichothecenes, five rosenonolactones, two cardiotonic cyclodepsipeptides, and two sterols. Compound 11β-hydroxyrosenonolactone (1) was assigned according to 1D and 2D-NMR data for the first time. At the same time, the 1H and 13C-NMR assignments for 6β-hydroxyrosenonolactone (2) were revised. Of all of them, only trichothecin (6) showed strong antifungal activity. Based on our observations of the antagonistic activity and the other experimental results, we suggest that the antifungal compound trichothecin was the main contributor to the antagonistic action of T. roseum LZ93.

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Isolation and Characterization of Antifungal Peptides Produced by Bacillus amyloliquefaciens LBM5006
Lisianne Brittes Benitez , Renata Voltolini Velho , Marcia Pagno Lisboa , Luis Fernando da Costa Medina , Adriano Brandelli
J. Microbiol. 2010;48(6):791-797.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0164-0
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AbstractAbstract PDF
Bacillus amyloliquefaciens LBM 5006 produces antagonistic activity against pathogenic bacteria and phytopathogenic fungi, including Aspergillus spp., Fusarium spp., and Bipolaris sorokiniana. PCR analysis revealed the presence of ituD, but not sfp genes, coding for iturin and surfactin, respectively. The antimicrobial substance produced by this strain was isolated by ammonium sulfate precipitation, gel filtration chromatography and 1-butanol extraction. The ultraviolet spectrum was typical of a polypeptide and the infrared spectrum indicates the presence of peptide bonds and acyl group(s). The antimicrobial substance was resistant to proteolytic enzymes and heat treatment, and was reactive with ninhydrin. Mass spectroscopy analysis indicated that B. amyloliquefaciens LBM 5006 produces two antimicrobial peptides, with main peaks at m/z 1,058 Da and 1,464 Da, corresponding to iturin-like and fengycin-like peptides, respectively. B. amyloliquefaciens LBM 5006 showed significant activity against phytopatogenic fungi, showing potential for use as a biocontrol agent or production of antifungal preparations.

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Rescue of a Cold-Sensitive Mutant at Low Temperatures by Cold Shock Proteins from Polaribacter irgensii KOPRI 22228
Ji-hyun Uh , Youn Hong Jung , Yoo Kyung Lee , Hong Kum Lee , Hana Im
J. Microbiol. 2010;48(6):798-802.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0402-5
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AbstractAbstract PDF
Exposure to low temperatures induces the biosynthesis of specific sets of proteins, including cold shock proteins (Csps). Since many of the specific functions of pychrophilic Csps are unknown, the roles of Csps from an Arctic bacterium, Polaribacter irgensii KOPRI 22228, were examined. The genes encoding CspA and CspC of P. irgensii were cloned in this study. Sequence analysis showed that these proteins have cold shock domains containing two RNA-binding motifs, RNP1 and RNP2. Both proteins bound oligo(dT)-cellulose resins, suggesting single-stranded nucleic acid-binding activity. When the P. irgensii Csps were overexpressed in Escherichia coli, the cold-resistance of the host was increased by more than five-fold. The P. irgensii Csps also rescued a cold-sensitive E. coli csp-quadruple deletion strain, BX04, at low temperatures. These results suggest that Csps from P. irgensii play a role in survival in polar environments.
Characterization of Hyperthermostable Fructose-1,6-Bisphosphatase from Thermococcus onnurineus NA1
Yeol Gyun Lee , Sung Gyun Kang , Jung-Hyun Lee , Seung Il Kim , Young-Ho Chung
J. Microbiol. 2010;48(6):803-807.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0377-2
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AbstractAbstract PDF
To understand the physiological functions of thermostable fructose-1,6-bisphosphatase (TNA1-Fbp) from Thermococcus onnurineus NA1, its recombinant enzyme was overexpressed in Escherichia coli, purified, and the enzymatic properties were characterized. The enzyme showed maximal activity for fructose-1,6- bisphosphate at 95°C and pH 8.0 with a half-life (t1/2) of about 8 h. TNA1-Fbp had broad substrate specificities for fructose-1,6-bisphosphate and its analogues including fructose-1-phosphate, glucose-1-phosphate, and phosphoenolpyruvate. In addition, its enzyme activity was increased five-fold by addition of 1 mM Mg2+, while Li+ did not enhance enzymatic activity. TNA1-Fbp activity was inhibited by ATP, ADP, and phosphoenolpyruvate, but AMP up to 100 mM did not have any effect. TNA1-Fbp is currently defined as a class V fructose-1,6-bisphosphatase (FBPase) because it is very similar to FBPase of Thermococcus kodakaraensis KOD1 based on sequence homology. However, this enzyme shows a different range of substrate specificities. These results suggest that TNA1-Fbp can establish new criterion for class V FBPases.

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  • Pcal_0111, a highly thermostable bifunctional fructose-1,6-bisphosphate aldolase/phosphatase from Pyrobaculum calidifontis
    Iram Aziz, Naeem Rashid, Raza Ashraf, Qamar Bashir, Tadayuki Imanaka, Muhammad Akhtar
    Extremophiles.2017; 21(3): 513.     CrossRef
  • Identification of a novel ligand binding site in phosphoserine phosphatase from the hyperthermophilic archaeon Thermococcus onnurineus
    Tae‐Yang Jung, Yae‐Sel Kim, Byoung‐Ha Oh, Euijeon Woo
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  • Proteome Analyses of Hydrogen-producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1 in Different One-carbon Substrate Culture Conditions
    Yoon-Jung Moon, Joseph Kwon, Sung-Ho Yun, Hye Li Lim, Min-Sik Kim, Sung Gyun Kang, Jung-Hyun Lee, Jong-Soon Choi, Seung Il Kim, Young-Ho Chung
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Identification and Functional Analysis of a Gene Encoding β-Glucosidase from the Brown-Rot Basidiomycete Fomitopsis palustris
Hwang-Woo Ji , Chang-Jun Cha
J. Microbiol. 2010;48(6):808-813.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0482-2
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AbstractAbstract PDF
The brown-rot basidiomycete Fomitopsis palustris is known to degrade crystalline cellulose (Avicel) and produce three major cellulases, exoglucanases, endoglucanases, and β-glucosidases. A novel β-glucosidase designated as Cel3A was identified from F. palustris grown at the expense of Avicel. The deduced amino acid sequence of Cel3A showed high homology with those of other fungal β-glucosidases that belong to glycosyl hydrolase (GH) family 3. The sequence analysis also indicated that Cel3A contains the N- and C-terminal domains of GH family 3 and Asp-209 was conserved as a catalytic nucleophile. The cloned gene was successfully expressed in the yeast Pichia pastoris and the recombinant protein exhibited β-glucosidase activity with cellobiose and some degree of thermostability. Considering the size and sequence of the protein, the β-glucosidase identified in this study is different from the protein purified directly from F. palustris in the previous study. Our results suggest that the fungus possesses at least two β-glucosidase genes.
Virulence Determinants in Vancomycin-Resistant Enterococcus faecium vanA Isolated from Different Sources at University Hospital of Londrina, Paraná, Brazil
Flávia Imanishi Ruzon , Suelen Balero de Paula , Renata Lumi Kanoshiki , Jussevania Pereira-Santos , Gilselena Kerbauy , Renata Katsuko Takayama Kobayashi , Lucy Megumi Yamauchi , Márcia Regina Eches Perugini , Sueli Fumie Yamada-Ogatta
J. Microbiol. 2010;48(6):814-821.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0099-5
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AbstractAbstract PDF
Enterococcus faecium, especially those showing multidrug resistance, has emerged as a significant cause of healthcare-associated infections worldwide. However, relatively little is known about the virulence and pathogenesis of this species. The aim of this study was to determine the occurrence of four putative virulence determinants of E. faecium and to correlate them with phenotypic traits. Using forty E. faecium vanA-type isolates from hospitalized patients and their environmental vicinity, we determined the following: the antimicrobial susceptibility profile, occurrence of the genes cylA, efaA, esp, and gelE, hemolytic and gelatinase activities, capacity to form biofilm and in vitro adhesion to epithelial cells. All isolates were shown to be resistant to vancomycin and teicoplanin, as well as to two or more other antimicrobials. All isolates harbored at least one putative virulence marker, and the prevalence was as follows: esp, 87.5%; efaA, 82.5%; gelE, 70%; and cylA, 65%. The presence of 4 genes was observed in 32.5% isolates. The presence of the efaA was associated with the presence of esp, regardless of the source of the isolates. A positive association with the presence of cylA and hemolytic activity in the sheep blood agar assay was observed. No association was found for gelE and gelatinase production in the agar plate assay, for efaA and LLC-MK2 cell adhesion, and for esp and biofilm formation on polystyrene surface. These results show the presence of putative virulence genes in multiple antimicrobial resistant E. faecium isolates from different sources in a hospital setting.

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  • Assessing the pollution and ecotoxicological status of the Iguaçu River, southern Brazil: A review
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  • Analysis Of Selected Genetic Traits, Phenotypes, And The Epidemiological Threat Of Enterococcus Bacteria Resistant To Vancomycin
    Wojciech Rogóż, Daniel Sypniewski, Ilona Bednarek
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    Andrey G. Sacramento, Rosemeire C. Zanella, Fernanda Esposito, Emanuela A.S. Costa, Lara M. de Almeida, Carlos Pires, Artemir C. de Brito, Elsa M. Mamizuka, Louise T. Cerdeira, Nilton Lincopan
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    Andressa Blainski, Barbara Gionco, Admilton G. Oliveira, Galdino Andrade, Ieda S. Scarminio, Denise B. Silva, Norberto P. Lopes, João C.P. Mello
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    Dalèle Elhani, Naouel Klibi, Raoudha Dziri, Meriem Ben Hassan, Selim Asli Mohamed, Laila Ben Said, Aouini Mahjoub, Karim Ben Slama, Boutheina Jemli, Ridha Bellaj, Farouk Barguellil, Carmen Torres
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    Paola A. Campos, Deivid W. F. Batistão, Paulo P. Gontijo-Filho, Rosineide M. Ribas
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  • Vancomycin-dependent Enterococcus faecium vanA: characterization of the first case isolated in a university hospital in Brazil
    G. Kerbauy, M.R.E. Perugini, L.M. Yamauchi, S.F. Yamada-Ogatta
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The Inter-generic Fungicidal Activity of Xanthophyllomyces dendrorhous
Marcelo Baeza , Oriana Flores , Mario Carrasco , Juan Manuel Rozas , Vicente Oviedo , Salvador Barahona , Víctor Cifuentes
J. Microbiol. 2010;48(6):822-828.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0180-0
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AbstractAbstract PDF
In this study, the existence of intra-specific and inter-generic fungicidal activity in Xanthophyllomyces dendrorhous and Phaffia rhodozyma strains isolated from different regions of the earth was examined. Assays were performed under several culture conditions, showing that all the analyzed X. dendrorhous and P. rhodozyma strains have killing activity against Kloeckera apiculata, Rhodotorula sloffiae, and R. minuta. This activity was greater in rich media at a pH from 4.6 to 5.0. Extracellular protein extracts with fungicidal activity were obtained from cultures of all strains, and their characterization suggested that a protein of ∼33 kDa is the antifungal factor. According to peptide mass fingerprinting and an analysis of the results with the MASCOT search engine, this protein was identified as an aspartic protease. Additionally, extrachromosomal double-stranded DNA elements (dsDNAs) were observed in all X. dendrorhous and P. rhodozyma strains. Although there is a high variability, two dsDNAs of 5.4 and 6.8 kb are present in all strains.
Periplasmic Domain of CusA in an Escherichia coli Cu+/Ag+ Transporter Has Metal Binding Sites
Bo-Young Yun , Yongbin Xu , Shunfu Piao , Nahee Kim , Jeong-Hyun Yoon , Hyun-Soo Cho , Kangseok Lee , Nam-Chul Ha
J. Microbiol. 2010;48(6):829-835.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0339-8
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  • 6 Scopus
AbstractAbstract PDF
The resistance nodulation division (RND)-type efflux systems are utilized in Gram-negative bacteria to export a variety of substrates. The CusCFBA system is the Cu+ and Ag+ efflux system in Escherichia coli, conferring resistance to lethal concentrations of Cu+ and Ag+. The periplasmic component, CusB, which is essential for the assembly of the protein complex, has Cu+ or Ag+ binding sites. The twelve-span membrane protein CusA is a homotrimeric transporter, and has a relatively large periplasmic domain. Here, we constructed the periplasmic domain of CusA by joining two DNA segments and then successfully expressed and purified the protein. Isothermal titration calorimetry experiments revealed Ag+ binding sites with Kds of 10-6-10-5 M. Our findings suggest that the metal binding in the periplasmic domain of CusA might play an important role in the function of the efflux pump.
Purification and Biochemical Characterization of a 17 kDa Fibrinolytic Enzyme from Schizophyllum commune
In Suk Park , Jeong Uck Park , Min Jeong Seo , Min Jeong Kim , Hye Hyeon Lee , Sung Ryeal Kim , Byoung Won Kang , Yung Hyun Choi , Woo Hong Joo , Yong Kee Jeong
J. Microbiol. 2010;48(6):836-841.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0384-3
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AbstractAbstract PDF
A fibrinolytic enzyme of the mushroom, Schizophyllum commune was purified with chromatographic methods, including a DEAE-Sephadex A-50 ion-exchange column and gel filtrations with Sephadex G-75 and Sephadex G-50 columns. The analysis of fibrin-zymography and SDS-PAGE showed that the enzyme was a monomeric subunit that was estimated to be approximately 17 kDa in size. The fibrinolytic activity of the enzyme in plasminogen-rich and plasminogen-free fibrin plates was 1.25 and 0.44 U/ml, respectively. The N-terminal amino acid sequence of the purified enzyme was identified as HYNIXNSWSSFID, which was highly distinguished from known fibrinolytic enzymes. The relative activity of the purified enzyme with an addition of 5 mM EDTA, Phosphoramidon, and Bestatin was about 76, 64, and 52%, respectively, indicating that it is a metalloprotease. The optimum temperature for the purified enzyme was approximately 45°C, and over 87% of the enzymatic activity was maintained as a stable state in a pH range from 4.0 to 6.0. Therefore, our results suggest that the potential thrombolytic agent from S. commune is a unique type of fibrinolytic enzyme.

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    AMANDA EMMANUELLE S. CONNIFF, THIAGO P. NASCIMENTO, ROMERO MARCOS P.B. COSTA, LEONID BREYDO, CAMILA S. PORTO, ATTILIO CONVERTI, JOYCE G.W. SIQUEIRA, JOSE ANTONIO TEIXEIRA, GALBA MARIA DE CAMPOS-TAKAKI, VLADIMIR N. UVERSKY, ANA LÚCIA F. PORTO, TATIANA S. P
    Anais da Academia Brasileira de Ciências.2024;[Epub]     CrossRef
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    Jinyu Wang, Xiaolan Liu, Yan Jing, Xiqun Zheng
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    Nur Amalina Amirullah, Nurhayati Zainal Abidin, Noorlidah Abdullah
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    Xiaolan Liu, Narasimha-kumar Kopparapu, Yao Li, Yongping Deng, Xiqun Zheng
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    Xiaolan Liu, Narasimha-kumar Kopparapu, Xi Shi, Yongping Deng, Xiqun Zheng, Jianping Wu
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    Amanda Emmanuelle Sales, Fabiana América Silva Dantas de Souza, José Antônio Teixeira, Tatiana Souza Porto, Ana Lúcia Figueiredo Porto
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  • Biochemical analysis of a fibrinolytic enzyme purified from Bacillus subtilis strain A1
    Won Sik Yeo, Min Jeong Seo, Min Jeong Kim, Hye Hyeon Lee, Byoung Won Kang, Jeong Uck Park, Yung Hyun Choi, Yong Kee Jeong
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Asc1p, a Ribosomal Protein, Plays a Pivotal Role in Cellular Adhesion and Virulence in Candida albicans
Se Woong Kim , Yoo Jin Joo , Joon Kim
J. Microbiol. 2010;48(6):842-848.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0422-1
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AbstractAbstract PDF
Candida albicans, the common human fungal pathogen, can switch morphology from yeast to pseudohyphal or hyphal form upon various environmental cues. It is well-known that the ability of morphological conversion and adhesive growth renders C. albicans virulent. It is noteworthy that every factor involved in the morphogenesis is known to be important for the virulence of this pathogen. To examine a functional relevance of Asc1p, a ribosomal protein, in morphogenesis and virulence, an asc1 homozygous null mutant was generated. Although a normal morphological transition of the asc1 deletion strain in liquid media was found, it did not change its morphology on solid media. Moreover, the adhesion activity and hyphal-specific gene expression were defective due to ASC1 deletion. Finally, it was found that the asc1 null mutant was avirulent in a mouse model. These results strongly suggested that Asc1p a component of the 40S ribosomal subunit and a signal transducer, plays a pivotal role in cellular adhesion and virulence through regulation of specific gene expression in C. albicans.

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    Se Woong Kim, Yoo Jin Joo, Yu Jin Chun, Young Kwang Park, Joon Kim
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Multilocus Sequence Typing and Virulence Factors Analysis of Escherichia coli O157 Strains in China
Xiao W. Ji , Ya L. Liao , Ye F. Zhu , Hai G. Wang , Ling Gu , Jiang Gu , Chen Dong , Hong L. Ding , Xu H. Mao , Feng C. Zhu , Quan M. Zou
J. Microbiol. 2010;48(6):849-855.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0132-8
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AbstractAbstract PDF
Escherichia coli O157:H7, an important food-borne pathogen, has become a major public health concern worldwide. The aim of this study was to investigate the molecular epidemiologic feature of E. coli O157:H7 strains in China. 105 E. coli O157:H7 isolates were collected from various hosts and places over 9 years. A multilocus sequence typing scheme (MLST) was applied for bacteria genotyping and polymerase chain reaction (PCR) was used for virulence factor identification. Seven new MLST sequence types (STs), namely ST836, ST837, ST838, ST839, ST840, ST841, and ST842 were identified, which grouped into two lineages. Phylogenetic analysis suggested that the most two frequent STs in China, ST837 and ST836, may be the derivatives of E. coli O157:H7 Sakai or E. coli O157:H7 EDL933. Geographical diversity and host variety of E. coli O157:H7 were observed in China. In addition, the different distribution of tccp was detected. The data presented herein provide new insights into the molecular epidemiologic feature of E. coli O157:H7, and aid in the investigation of the transmission regularity and evolutionary mechanism of E. coli O157:H7.

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    Margot Ventura, Rosario Oporto-Llerena, Kathya Espinoza, Fernando Guibert, Antonio M. Quispe, Nidia Vilar, María López, Beatriz Rojo-Bezares, Yolanda Sáenz, Joaquim Ruiz, Maria J. Pons
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The Role of Carbohydrate-Binding Module (CBM) Repeat of a Multimodular Xylanase (XynX) from Clostridium thermocellum in Cellulose and Xylan Binding
Thangaswamy Selvaraj , Sung Kyum Kim , Yong Ho Kim , Yu Seok Jeong , Yu-Jeong Kim , Nguyen Dinh Phuong , Kyung Hwa Jung , Jungho Kim , Han Dae Yun , Hoon Kim
J. Microbiol. 2010;48(6):856-861.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0285-5
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AbstractAbstract PDF
A non-cellulosomal xylanase from Clostridium thermocellum, XynX, consists of a family-22 carbohydratebinding module (CBM22), a family-10 glycoside hydrolase (GH10) catalytic module, two family-9 carbohydrate-binding modules (CBM9-I and CBM9-II), and an S-layer homology (SLH) module. E. coli BL21(DE3) (pKM29), a transformant carrying xynX', produced several truncated forms of the enzyme. Among them, three major active species were purified by SDS-PAGE, activity staining, gel-slicing, and diffusion from the gel. The truncated xylanases were different from each other only in their C-terminal regions. In addition to the CBM22 and GH10 catalytic modules, XynX1 had the CBM9-I and most of the CBM9-II, XynX2 had the CBM9-I and about 40% of the CBM9-II, and XynX3 had about 75% of the CBM9-I. The truncated xylanases showed higher binding capacities toward Avicel than those toward insoluble xylan. XynX1 showed a higher affinity toward Avicel (70.5%) than XynX2 (46.0%) and XynX3 (42.1%); however, there were no significant differences in the affinities toward insoluble xylan. It is suggested that the CBM9 repeat, especially CBM9-II, of XynX plays a role in xylan degradation in nature by strengthening cellulose binding rather than by enhancing xylan binding.

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NOTE] Oceanobacillus kimchii sp. nov. Isolated from a Traditional Korean Fermented Food
Tae Woong Whon , Mi-Ja Jung , Seong Woon Roh , Young-Do Nam , Eun-Jin Park , Kee-Sun Shin , Jin-Woo Bae
J. Microbiol. 2010;48(6):862-866.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0214-7
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AbstractAbstract PDF
A moderate halophile, strain X50T, was isolated from mustard kimchi, a traditional Korean fermented food. The organism grew under conditions ranging from 0-15.0% (w/v) NaCl (optimum: 3.0%), pH 7.0-10.0 (optimum: pH 9.0) and 15-45°C (optimum: 37°C). The morphological, physiological, and biochemical features and the 16S rRNA gene sequences of strain X50T were characterized. Colonies of the isolate were creamcolored and the cells were rod-shaped. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain X50T belongs to the genus Oceanobacillus and is closely related phylogenetically to the type strain O. iheyensis HTE831T (98.9%) and O. oncorhynchi subsp. oncorhynchi R-2T (97.0%). The cellular fatty acid profiles predominately included anteiso-C15:0 and iso-C15:0. The G+C content of the genomic DNA of the isolate was 37.9 mol% and the major isoprenoid quinone was MK-7. Analysis of the 16S rRNA gene sequences, DNA-DNA relatedness and physiological and biochemical tests indicated genotypic and phenotypic differences among strain X50T and reference species in the genus Oceanobacillus. Therefore, strain X50T was proposed as a novel species and named Oceanobacillus kimchii. The type strain of the new species is X50T (=JCM 16803T =KACC 14914T =DSM 23341T).

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NOTE] Bacillus gaemokensis sp. nov., Isolated from Foreshore Tidal Flat Sediment from the Yellow Sea
Min-Young Jung , Woon Kee Paek , In-Soon Park , Jeong-Ran Han , Yeseul Sin , Jayoung Paek , Moon-Soo Rhee , Hongik Kim , Hong Seok Song , Young-Hyo Chang
J. Microbiol. 2010;48(6):867-871.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0148-0
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AbstractAbstract PDF
A Gram-positive, rod-shaped, endospore-forming organism, strain BL3-6T, was isolated from tidal flat sediments of the Yellow Sea in the region of Tae-An. A 16S rRNA gene sequence analysis demonstrated that this isolate belongs to the Bacillus cereus group, and is closely related to Bacillus mycoides (99.0% similarity), Bacillus thuringiensis (99.0%), Bacillus weihenstephanensis (99.0%), Bacillus cereus (98.9%), Bacillus anthracis (98.8%), and Bacillus pseudomycoides (98.1%). The phylogenetic distance from any validly described Bacillus species outside the Bacillus cereus group was less than 95.6%. The DNA G+C content of the strain was 39.4 mol% and the major respiratory quinone was menaquinone-7. The major cellular fatty acids were iso-C14:0 (17.8%), iso-C16:0 (15.8%), and iso-C12:0 (11.3%). The diagnostic amino acid of the cell wall was mesodiaminopimelic acid and the major cell wall sugar was galactose. The results of DNA-DNA hybridization (<55.6%) and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain BL3-6T from the published Bacillus species. BL3-6T therefore represents a new species, for which the name Bacillus gaemokensis sp. nov. is proposed, with the type strain BL3-6T (=KCTC 13318T =JCM 15801T).

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NOTE] Analysis of Cytoplasmic Membrane Proteome of Streptococcus pneumoniae by Shotgun Proteomic Approach
Chi-Won Choi , Sung-Ho Yun , Sang-Oh Kwon , Sun-Hee Leem , Jong-Soon Choi , Chi-Young Yun , Seung Il Kim
J. Microbiol. 2010;48(6):872-876.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0220-9
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AbstractAbstract PDF
In this study, cytoplasmic membrane proteins of S. pneumoniae strain R6 (ATCC BBA-255) were effectively separated from cell wall or extracellular proteins by sodium carbonate precipitation (SCP) and ultracentrifugation. Forty seven proteins were analyzed as cytoplasmic membrane proteins from the 260 proteins identified by the shotgun proteomic method using SDS-PAGE/LC/MS-MS. ABC transporters for metabolites such as metals, oligopeptides, phosphate, sugar, and amino acids, and membrane proteins involved in phosphotransferse systems, were identified as the predominant and abundant, cytoplasmic membrane proteins that would be essential for nutrient uptake, antibiotic resistance and virulence mechanisms. Our result supports that gel-based shotgun proteomics combined with sodium carbonate precipitation and ultracentrifugation is an effective method for analysis of cytoplasmic membrane proteins of S. pneumoniae.

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NOTE] The Presence of Borrelia valaisiana-Related Genospecies in Ticks and a Rodent in Taiwan
Chun-Man Huang , Hsi-Chieh Wang , Ying-Chun Lin , Shih-Hui Chiu , Ying-Shun Kao , Pei-Lung Lee , Hsiu-I Wang , Ruei-Chen Hung , Huang-I Chan , Ho-Sheng Wu , Chuen-Sheue Chiang , Jung-Jung Mu
J. Microbiol. 2010;48(6):877-880.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0331-3
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AbstractAbstract PDF
A field survey was conducted to investigate the presence of Borrelia burgdorferi sensu lato (s.l.) in six counties of Taiwan. Spirochetes were successfully isolated from one rodent ear sample out of 485 rodent ears and 53 live, fed tick (Ixodes granulatus) samples. The spirochetes were confirmed to be B. burgdorferi s.l. by real-time PCR. In addition, 23 of 113 tick samples were tested positive for Borrelia DNA according to real-time PCR. The Borrelia isolate from the rodent and the 23 Borrelia DNA samples from the ticks were identified as B. valaisiana-related genospecies by phylogenetic analysis based on flagellin gene sequences. These findings suggest that the Borrelia valaisiana-related strains are maintained in a zoonotic cycle between tick vectors and reservoir hosts in Taiwan.
NOTE] Initial Acidic pH Is Critical for Mycelial Cultures and Functional Exopolysaccharide Production of an Edible Mushroom, Laetiporus sulphureus var. miniatus JM 27
Min Jeong Seo , Min Jeong Kim , Hye Hyeon Lee , Sung Ryeal Kim , Byoung Won Kang , Jeong Uck Park , En Ju Rhu , Yung Hyun Choi , Yong Kee Jeong
J. Microbiol. 2010;48(6):881-884.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0410-5
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AbstractAbstract PDF
We conducted a time course experiment on mycelial cultures of Laetiporus sulphureus var. miniatus. The strain showed significant survival in an initial pH range of 2.0 to 7.0 for 24 days, during which time oxalic acid was accumulated. A structural analysis of purified exopolysaccharide suggested that it contained 96.1% glucose, and the mode of linkage was mainly-4-Glcp-(1-units, with branches at the C-6 position consisting of a Glcp-(1-4) linked side chain. An exopolysaccharide purified from the acidophilic strain was added to cultured U937 cells, resulting in significantly increased transcription levels of p53 and p21 genes.

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NOTE] Simple Identification of veA1 Mutation in Aspergillus nidulans
Kap-Hoon Han , Jae-Sin Park , Keon Sang Chae , Dong-Min Han
J. Microbiol. 2010;48(6):885-887.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0506-y
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AbstractAbstract PDF
The veA gene plays an important role in development of a homothallic filamentous fungus Aspergillus nidulans. The veA1 phenotype can be difficult to distinguish from the wild-type veA. Despite the importance of the veA allele, no efficient identification method has been reported besides DNA sequencing. Here, we present simple physiological and molecular biological ways to distinguish between the veA wild-type and veA1 allele. The novel approaches, which involve incubation in the presence of oxalic acid, polymerase chain reaction using double mismatched primers, and BstXI enzyme digestion, are simpler, faster and more cost-efficient than genome sequencing.

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