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Volume 46(6); December 2008
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Journal Articles
Molecular Identification of Fecal Pollution Sources in Water Supplies by Host-Specific Fecal DNA Markers and Terminal Restriction Fragment Length Polymorphism Profiles of 16S rRNA Gene
Ju-Yong Jeong , Kyung-Ik Gil , Kyong-Hee Lee , Jong-Ok Ka
J. Microbiol. 2008;46(6):599-607.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0174-3
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AbstractAbstract PDF
Specific fecal DNA markers were investigated for major pollution sources, cow, human, and pig, and occurrence of the identified markers was analyzed in river waters using Terminal Restriction Fragment Length Polymorphism (T-RFLP) techniques and sequencing of 16S rDNA of Bacteroides-Prevotella. The unique and specific DNA markers for cow and human were identified as a 222 bp and 60 bp peak in HaeIII T-RFLP profiles, respectively, and the pig-specific marker was not identified but the unique T-RFLP profile of pig could be used as a substitution. Human-specific marker was detected in most of the river waters tested (92.1%) and T-RFLP profiles of river waters were shown to be similar to those of human feces. Cluster analysis of T-RFLP data showed that the fecal sources were multiple (human plus cow and human plus dairy cow) in most of the river waters. The phylogenetic analysis for the clones recovered from the fecal and water samples showed that the clones from cow formed a discreet cluster from those of other sources. The other clones from human, pig, and river water formed two groups all together. The results of this study could be used to identify and control the fecal pollution source in the bodies of water in Korea.

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  • Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing
    Ju-Yong Jeong, Hee-Deung Park, Kyong-Hee Lee, Hang-Yeon Weon, Jong-Ok Ka
    The Journal of Microbiology.2011; 49(4): 585.     CrossRef
  • Application of an Integrated Community Analysis Approach for Microbial Source Tracking in a Coastal Creek
    Yiping Cao, Laurie C. Van De Werfhorst, Bram Sercu, Jill L. S. Murray, Patricia A. Holden
    Environmental Science & Technology.2011; 45(17): 7195.     CrossRef
Targeting the rpoB Gene Using Nested PCR-Restriction Fragment Length Polymorphism for Identification of Nontuberculous Mycobacteria in Hospital Tap Water
Ji-Hyun Shin , Hae-Kyung Lee , Eun-Jin Cho , Jae-Yon Yu , Yeon-Ho Kang
J. Microbiol. 2008;46(6):608-614.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0102-6
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AbstractAbstract PDF
Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and can cause nosocomial infections in immunocompromised patients. Recently the presence of NTM in public drinking water and hospital water distribution systems has been reported. Their ability to form biofilms and their resistance to chlorine both contribute to their survival and colonization in water distribution systems. Here we analyzed thirty-two hospital tap water samples that were collected from different locations in three hospitals so as to evaluate the prevalence of NTM species. The water samples were concentrated by membrane filtration and then eluted with sterilized water following sonication. Two-step direct PCR targeting the rpoB gene, restriction fragment length polymorphism (RFLP) using the MspI restriction enzyme, and sequence analysis were performed for identification of NTM to the species level. The sequences of each PCR product were analyzed using BLASTN. Seven samples (7/32, 21.9%) were positive for NTM as determined by nested-PCR. The PCR-RFLP results indicated five different patterns among the seven positive PCR samples. The waterborn NTM were identified, including M. peregrinum, M. chelonae (2 cases), M. abscessus, M. gordonae (2 cases), and Mycobacterium sp. JLS. The direct two-step PCR-RFLP method targeting the rpoB gene was effective for the detection and the differentiation of NTM species from hospital tap water.

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  • Occurrence of opportunistic pathogens in private wells after major flooding events: A four state molecular survey
    Kris Mapili, William J. Rhoads, Mary Coughter, Kelsey J. Pieper, Marc A. Edwards, Amy Pruden
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    Chrislène Laurens, Geneviève Héry-Arnaud, Raphael Chiron, Eric Oziol, Hélène Jean-Pierre, Nicolas Bouzinbi, Philippe Vande Perre, Anne-Laure Bañuls, Sylvain Godreuil
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  • Mycobacterium abscessus Induces a Limited Pattern of Neutrophil Activation That Promotes Pathogen Survival
    Kenneth C. Malcolm, E. Michelle Nichols, Silvia M. Caceres, Jennifer E. Kret, Stacey L. Martiniano, Scott D. Sagel, Edward D. Chan, Lindsay Caverly, George M. Solomon, Paul Reynolds, Donna L. Bratton, Jennifer L. Taylor-Cousar, David P. Nichols, Milene T.
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    Song Yee Kim, Young Ae Kang, Il Kwon Bae, Jae-Joon Yim, Moo Suk Park, Young Sam Kim, Se Kyu Kim, Joon Chang, Seok Hoon Jeong
    Diagnostic Microbiology and Infectious Disease.2013; 77(2): 143.     CrossRef
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    Mohamed Sassi, Imen Ben Kahla, Michel Drancourt
    BMC Microbiology.2013;[Epub]     CrossRef
  • Diversity, Community Composition, and Dynamics of Nonpigmented and Late-Pigmenting Rapidly Growing Mycobacteria in an Urban Tap Water Production and Distribution System
    S. Dubrou, J. Konjek, E. Macheras, B. Welté, L. Guidicelli, E. Chignon, M. Joyeux, J. L. Gaillard, B. Heym, T. Tully, G. Sapriel
    Applied and Environmental Microbiology.2013; 79(18): 5498.     CrossRef
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    Gonca Erkose Genc, Elvira Richter, Zayre Erturan
    APMIS.2013; 121(12): 1192.     CrossRef
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    K. Hruska, M. Kaevska
    Veterinární medicína.2012; 57(12): 623.     CrossRef
  • Molecular Survey of the Occurrence of Legionella spp., Mycobacterium spp., Pseudomonas aeruginosa, and Amoeba Hosts in Two Chloraminated Drinking Water Distribution Systems
    Hong Wang, Marc Edwards, Joseph O. Falkinham, Amy Pruden
    Applied and Environmental Microbiology.2012; 78(17): 6285.     CrossRef
  • Multilocus Sequence Analysis and rpoB Sequencing of Mycobacterium abscessus (Sensu Lato) Strains
    Edouard Macheras, Anne-Laure Roux, Sylvaine Bastian, Sylvia Cardoso Leão, Moises Palaci, Valérie Sivadon-Tardy, Cristina Gutierrez, Elvira Richter, Sabine Rüsch-Gerdes, Gaby Pfyffer, Thomas Bodmer, Emmanuelle Cambau, Jean-Louis Gaillard, Beate Heym
    Journal of Clinical Microbiology.2011; 49(2): 491.     CrossRef
Monitoring Nutrient Impact on Bacterial Community Composition during Bioremediation of Anoxic PAH-Contaminated Sediment
Myungsu Kim , Seung Seob Bae , Mijin Seol , Jung-Hyun Lee , Young-Sook Oh
J. Microbiol. 2008;46(6):615-623.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0097-z
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AbstractAbstract PDF
Marine harbor sediments are frequently polluted with significant amount of polycyclic aromatic hydrocarbons (PAHs) some of which are naturally toxic, recalcitrant, mutagenic, and carcinogenic. To stimulate biodegradation of PAHs in PAH-contaminated sediments collected from near Gwangyang Bay, Korea, lactate was chosen as a supplementary carbonaceous substrate. Sediment packed into 600 ml air-tight jar was either under no treatment condition or lactate amended condition (1%, w/v). Microbial community composition was monitored by bacteria-specific and archaea-specific PCR-terminal restriction fragment length polymorphism (T-RFLP), in addition to measuring the residual PAH concentration. Results showed that lactate amendment enhanced biodegradation rate of PAHs in the sediment by 4 to 8 times, and caused a significant shift in archaebacterial community in terms of structure and diversity with time. Phylogenetic analysis of 23 archaeal clones with distinctive RFLP patterns among 288 archaeal clones indicated that majority of the archaeal members were closest to unculturable environmental rDNA clones from hydrocarbon-contaminated and/or methanogenesis-bearing sediments. Lactate amendment led to the enrichment of some clones that were most closely related to PAH-degrading Methanosarcina species. These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments.

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Research Support, Non-U.S. Gov'ts
Dark Septate Endophyte (DSE) Fungi Isolated from Metal Polluted Soils: Their Taxonomic Position, Tolerance, and Accumulation of Heavy Metals In Vitro
Yujie Zhang , Yan Zhang , Maojun Liu , Xiaodong Shi , Zhiwei Zhao
J. Microbiol. 2008;46(6):624-632.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0163-6
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AbstractAbstract PDF
To understand the possible role of the plant root associated fungi on metal tolerance, their role in the uptake of heavy metals and the potential transfer of these metal ions to the plant, three strains of dark septate endophytic (DSE) fungi were isolated from a waste smelter site in southwest China, and one strain was isolated from a non-contaminated site. According to molecular phylogenetic analysis of the ITS 1-5.8S rDNA-ITS 2 gene regions and morphological characteristics, one is identified as Exophiala pisciphila, and the other three are non-sporulating fungi under the experiment condition with the nearest phylogenetic affinities to the Thysanorea papuana strain EU041814. Tolerance and accumulation abilities of the three DSE strains for metals were investigated in liquid culture. Minimum inhibitory concentrations (MIC) of Pb, Zn, and Cd were determined. It was demonstrated that the tolerance of the DSE strains varied between metal species and strains. The E. pisciphila strain is able to accumulate lead and cadmium over 20% and 5% of dry weight of biomass, respectively. Partial of the sequestrated metals can be washed with CaCl2. Morphological and enzyme activity changes taking place in the presence of excessive Pb, Cd, and/or Zn also indicate that the mechanism of heavy metal tolerance and accumulation of the DSE strains would be a complex process. The findings indicated promising tolerance and accumulation of the DSE strains with potential values in metal cycling and restoration of soil and water system.

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Prevalence of Tetracycline Resistance Genes in Greek Seawater Habitats
Theodora L. Nikolakopoulou , Eleni P. Giannoutsou , Adamandia A. Karabatsou , Amalia D. Karagouni
J. Microbiol. 2008;46(6):633-640.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0080-8
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AbstractAbstract PDF
The presence of selected tetracycline resistance (TcR) genes was studied in different Greek seawater habitats, originated from wastewater treatment facilities, fishfarm, and coastal environments. The methods employed included assessment of the presence of twelve gene clusters by PCR, followed by hybridization with specific probes, in habitat extracted DNA, TcR bacteria, and exogenous isolated plasmids conferring TcR. The direct DNA-based analysis showed that tet(Α) and tet(K) genes were detected in all habitats, whilst tet(C) and tet(E) were present in fishfarm and wastewater effluent samples and tet(M) was detected in fishfarm and coastal samples. Resistance genes tet(A), tet(C), tet(K), and tet(M) were detected in 60 of the 89 isolates screened. These isolates were identified by fatty acid methyl ester analysis (FAME) as Stenotrophomonas, Acinetobacter, Pseudomonas, Bacillus, and Staphylococcus strains. The presence of the TcR genes in 15% of the bacterial isolates coincided with the presence of IncP plasmids. A habitat-specific dissemination of IncP alpha plasmids in wastewater effluent isolates and of IncP beta plasmids in fishfarm isolates was observed. Exogenous isolation demonstrated the presence of plasmids harbouring TcR genes in all the habitats tested. Plasmids were shown to carry tet(A), tet(C), tet(E), and tet(K) genes. It is concluded that TcR genes are widespread in the seawater habitats studied and often occur on broad host range plasmids that seem to be well disseminated in the bacterial communities.

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Enhancement of Growth and Yield of Tomato by Rhodopseudomonas sp. under Greenhouse Conditions
Kang-Hyeong Lee , Rae-Hyun Koh , Hong-Gyu Song
J. Microbiol. 2008;46(6):641-646.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0159-2
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AbstractAbstract PDF
A greenhouse test was carried out to examine the effects on tomato growth of application of purple nonsulfur bacterium Rhodopseudomonas sp. which had enhanced germination and growth of tomato seed under axenic conditions. The shoot length of tomato plant inoculated by Rhodopseudomonas sp. KL9 increased by 34.6% compared to that of control in 8 weeks of cultivation. During the same period, this strain increased 120.6 and 78.6% of dry weight of shoot and root of tomato plants, respectively. The formation ratio of tomato fruit from flower was also raised by inoculation of KL9. In addition, Rhodopseudomonas sp. KL9 treatment enhanced the fresh weight and lycopene content in the harvested tomato fruits by 98.3 and 48.3%, respectively compared to those of the uninoculated control. When the effect on the indigenous bacterial community and fate of the inoculated Rhodopseudomonas sp. KL9 were monitored by denaturing gradient gel electrophoresis analysis, its application did not affect the native bacterial community in tomato rhizosphere soil, but should be repeated to maintain its population size. This bacterial capability may be applied as an environment-friendly biofertilizer to cultivation of high quality tomato and other crops including lycopene-containing vegetables and fruits.

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    Vipin Kumar Singh, Amit Kishore Singh, Prem Pratap Singh, Ajay Kumar
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    Shao Shuang, Wang Dongdong, Zhu Dan
    Journal of Nutritional Therapeutics.2017; 6(3): 64.     CrossRef
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    Md. Yeakub Khan, Md. Manjurul Haque, Abul Hossain Molla, Md. Mizanur Rahman, Mohammad Zahangeer Alam
    Journal of Integrative Agriculture.2017; 16(3): 691.     CrossRef
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    Pin Su, Xinqiu Tan, Chenggang Li, Deyong Zhang, Ju'e Cheng, Songbai Zhang, Xuguo Zhou, Qingpin Yan, Jing Peng, Zhuo Zhang, Yong Liu, Xiangyang Lu
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    Jiangbing Xu, Youzhi Feng, Yanling Wang, Xiaosan Luo, Jianwu Tang, Xiangui Lin
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    B M Rubayet Bostami A, T Ahmed S, S Mun H, B Hong S, Yang Chul Ju
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    Pamela R. Bernabeu, Mariano Pistorio, Gonzalo Torres-Tejerizo, Paulina Estrada-De los Santos, María L. Galar, José L. Boiardi, María F. Luna
    Scientia Horticulturae.2015; 191: 113.     CrossRef
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    Hong-Lian Ge, Fu-Li Zhang
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    Satoshi Nagata, Keiko Yamaji, Nobuhiko Nomura, Hiroshi Ishimoto
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    M. Quambusch, A. M. Pirttila, M. V. Tejesvi, T. Winkelmann, M. Bartsch
    Tree Physiology.2014; 34(5): 524.     CrossRef
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    J. Xu, Y. Feng, Y. Wang, X. Lin
    Letters in Applied Microbiology.2013; 57(5): 420.     CrossRef
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    Jing Wu, Yiming Wang, Xiangui Lin, Gustavo Bonaventure
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    Agricultural Research.2012; 1(3): 265.     CrossRef
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    S.K. UPADHYAY, J.S. SINGH, D.P. SINGH
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    Youzhi Feng, Xiangui Lin, Yongchang Yu, Jianguo Zhu
    Microbial Ecology.2011; 62(4): 789.     CrossRef
  • Field Evidence for the Potential of Rhodobacter capsulatus as Biofertilizer for Flooded Rice
    Hosny Gamal-Eldin, Khaled Elbanna
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Diversity of Bacterial Community in Freshwater of Woopo Wetland
Keun Sik Baik , Seong Chan Park , Eun Mi Kim , Kyung Sook Bae , Jae-Hyung Ahn , Jong-Ok Ka , Jongsik Chun , Chi Nam Seong
J. Microbiol. 2008;46(6):647-655.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0135-x
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AbstractAbstract PDF
Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones. Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher than that of isolated bacteria.
Journal Article
Biologically Active and C-Amidated HinnavinII-38-Asn Produced from a Trx Fusion Construct in Escherichia coli
Chang Soo Kang , Seung-Yeol Son , In Seok Bang
J. Microbiol. 2008;46(6):656-661.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0214-z
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AbstractAbstract PDF
The cabbage butterfly (Artogeia rapae) antimicrobial peptide hinnavinII as a member of cecropin family is synthesized as 37 residues in size with an amidated lysine at C-terminus and shows the humoral immune response to a bacterial invasion. In this work, a synthetic gene for hinnavinII-38-Asn (HIN) with an additional amino acid asparagine residue containing amide group at C-terminus was cloned into pET-32a(+) vector to allow expression of HIN as a Trx fusion protein in Escherichia coli strain BL21 (DE3) pLysS. The resulting expression level of the fusion protein Trx-HIN could reach 15~20% of the total cell proteins and more than 70% of the target proteins were in soluble form. The fusion protein could be purified successfully by HiTrap Chelating HP column and a high yield of 15 mg purified fusion protein was obtained from 80 ml E. coli culture. Recombinant HIN was readily obtained by enterokinase cleavage of the fusion protein followed by FPLC chromatography, and 3.18 mg pure active recombinant HIN was obtained from 80 ml culture. The molecular mass of recombinant HIN determined by MALDI-TOF mass spectrometer is 4252.084 Da which matches the theoretical mass (4252.0 Da) of HIN. Comparing the antimicrobial activities of the recombinant hinnavinII with C-amidated terminus to that without an amidated C-terminus, we found that the amide of asparagine at C-terminus of hinnavinII improved its potency on certain microorganism such as E. coli, Enterobacter cloacae, Bacillus megaterium, and Staphylococcus aureus.
Research Support, Non-U.S. Gov'ts
Stable Expression and Secretion of Polyhydroxybutyrate Depolymerase of Paucimonas lemoignei in Escherichia coli
Se Whan Park , Moon Gyu Chung , Hwa Young Lee , Jeong Yoon Kim , Young Ha Rhee
J. Microbiol. 2008;46(6):662-669.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0283-z
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AbstractAbstract PDF
An efficient strategy for the expression and secretion of extracellular polyhydroxybutyrate depolymerase (PhaZ1) of Paucimonas lemoignei in Escherichia coli was developed by employing the signal peptide of PhaZ1 and a truncated ice nucleation protein anchoring motif (INPNC). Directly synthesized mature form of PhaZ1 was present in the cytoplasm of host cells as inclusion bodies, while a construct containing PhaZ1 and its own N-terminal signal peptide (PrePhaZ1) enabled the secretion of active PhaZ1 into the extracellular medium. However, the PrePhaZ1 construct was harmful to the host cell and resulted in atypical growth and instability of the plasmid during the cultivation. In contrast, INPNC-PhaZ1 and INPNCPrePhaZ1 fusion constructs did not affect growth of host cells. INPNC-PhaZ1 was successfully displayed on the cell surface with its fusion form, but did not retain PhaZ1 activity. In the case of INPNC-PrePhaZ1, the initially synthesized fusion form was separated by precise cleavage of the signal peptide, and active PhaZ1 was consequently released into the culture medium. The amount of PhaZ1 derived from E. coli (INPNC-PrePhaZ1) was almost twice as great as that directly expressed from E. coli (PrePhaZ1), and was predominantly (approximately 85%) located in the periplasm when cultivated at 22°C but was efficiently secreted into the extracellular medium when cultivated at 37°C.
Cys-92, Cys-95, and the C-Terminal 12 Residues of the Vibrio harveyi Ferric Uptake Regulator (Fur) are Functionally Inessential
Kun Sun , Shuang Cheng , Min Zhang , Fang Wang , Li Sun
J. Microbiol. 2008;46(6):670-680.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0113-3
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AbstractAbstract PDF
Ferric uptake regulator (Fur) is a global regulator involved in multiple aspects of bacterial life. The gene encoding the Vibrio harveyi Fur (FurVh) was cloned from a pathogenic V. harveyi strain isolated from diseased fish. FurVh shares 77% overall sequence identity with the Escherichia coli Fur (FurEc) and could complement a mutant of FurEc. Like FurEc, FurVh possesses two cysteine residues at positions 92 and 95, yet unlike FurEc, in which these cysteine residues constitute part of the metal ion coordination site and hence are vital to the repressor activity, C92 and C95 of FurVh proved to be functionally inessential. Further study identified a Vibrio Fur signature sequence, which is preserved in all the ten Vibrio Fur proteins that have been discovered to date but in none of the non-vibrio Fur proteins. Site-directed and random mutation analyses of the signature residues, the cysteine residues, and seven highly charged amino acid residues indicated that D9, H32, C137, and K138 of FurVh are functionally important but D9, C137, and K138 can be replaced by more than one functional substitutes. Systematic deletion analysis demonstrated that the C-terminal 12 residues of FurVh are functionally inessential. These results (i) indicated that the activation mechanism, or certain aspects of which, of FurVh is possibly different from that of FurEc; and (ii) suggested that it is not very likely that the C-terminal 12 residues play any significant role in the activation or stability of FurVh; and (iii) provided insights into the potential function of the local structure involving C137 and K138.

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  • Comparative analysis of the survival and gene expression of pathogenic strainsVibrio harveyiafter starvation
    Jingjing Sun, Xiaojian Gao, Jiang Qun, Xuedi Du, Keran Bi, Xiaojun Zhang, Li Lin, Alejandra Bravo
    FEMS Microbiology Letters.2016; 363(22): fnw250.     CrossRef
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    María F. Fillat
    Archives of Biochemistry and Biophysics.2014; 546: 41.     CrossRef
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    Kun Sun, Xu-dong Jiao, Min Zhang, Li Sun
    Veterinary Microbiology.2010; 141(1-2): 149.     CrossRef
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    Hege Lynum Pedersen, Rafi Ahmad, Ellen Kristin Riise, Hanna-Kirsti Schrøder Leiros, Stefan Hauglid, Sigrun Espelid, Bjøn Olav Brandsdal, Ingar Leiros, Nils-Peder Willassen, Peik Haugen
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    Shana Miles, Beth M. Carpenter, Hanan Gancz, D. Scott Merrell
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    Huan-ran Wang, Yong-hua Hu, Wei-wei Zhang, Li Sun
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    Md. Arif Sheikh, Garry L. Taylor
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Genus-Specific Distribution and Pathovar-Specific Variation of the Glycinecin R Gene Homologs in Xanthomonas genomes
Eunjung Roh , Sunggi Heu , Eunpyo Moon
J. Microbiol. 2008;46(6):681-686.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0209-9
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AbstractAbstract PDF
Xanthomonas axonopodis pv. glycines produces bacteriocins called glycinecin, and two glycinecin genes, glyA and glyR, were reported previously. In this paper, we describe genomic distribution and variation of the glyR gene revealed by extensive Southern hybridization analysis. In contrast to the glyA gene present only in X. axonopodis pv. glycines, the glyR gene was found to be distributed widely in all the pathovars of Xanthomas genus. It was also found that the glyR gene is a multigene family while the glyA is a single copy gene. Moreover, the copy number and the variation of the glyR multigene are unique to each pathovar of Xanthomonas. The uniqueness can be easily detected by the patterns resulted from Southern hybridization using the genomic digests. Thus, we suggest the glyR gene can serve as a useful genus-specific and pathovarspecific DNA marker for Xanthomonas. One of the glyR homologs was further isolated from X. axonopodis pv. glycines, and analyzed to be functional with strong inhibitory activity against several members of Xanthomonas.
Detection of Pseudomonas aeruginosa Carried a New Array of Gene Cassettes within Class 1 Integron Isolated from a Teaching Hospital in Nanjing, China
Yuan Wu† , Hui Li† , Jun Li , Zu Hu Huang
J. Microbiol. 2008;46(6):687-691.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0021-6
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AbstractAbstract PDF
We report here novel array of gene cassettes found in single variable region of class 1 integron disseminated in Pseudomonas aeruginosa isolated from a teaching hospital in Nanjing, Jiangsu Province, China. 29 of 47 (61%) P. aeruginosa strains were confirmed haboured class 1 integron, and all the positive strains have the same variable region confirmed by PCR and RFLP methods. The variable region contained an unreported order of four gene cassettes aac(6’)-II-aadA13-cmlA8-oxa 10. Of those, cmlA8 gene was a variant of cmlA5 encoding non-enzymatic protein which putatively confer resistance to chloramphenicol. Susceptibility testing revealed multidrug-resistant mechanisms were involved in the class 1 integron positive clinical isolates. And the class 1 integron located on an about 15 kb transferable plasmid was certified by conjugation experiment and plasmid DNA analysis. The macro restriction profile indicated those clinical strains were clonally related.

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  • Distribution and Molecular Characterization of Resistance Gene Cassettes Containing Class 1 Integrons in Multi-Drug Resistant (MDR) Clinical Isolates of Pseudomonas aeruginosa


    Leila Ahmadian, Mohammad Reza Haghshenas, Bahman Mirzaei, Zahra Norouzi Bazgir, Hamid Reza Goli
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    E. V. Starikova, N. A. Prianichnikov, E. Zdobnov, V. M. Govorun
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    Hamid Reza Goli, Mohammad Reza Nahaei, Mohammad Ahangarzadeh Rezaee, Alka Hasani, Hossein Samadi Kafil, Mohammad Aghazadeh, Vajihe Sheikhalizadeh
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    E.V. Starikova, N.A. Prianichnikov, E. Zdobnov, V.M. Govorun
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    Jing Zhang, Beiwen Zheng, Lina Zhao, Zeqing Wei, Jinru Ji, Lanjuan Li, Yonghong Xiao
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    Ke-Yu Hsiao, Mei-Feng Lee, Chien-Fang Peng
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    Bamidele T Odumosu, Bolanle A Adeniyi, Ram Chandra
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Journal Article
Carbon Source Dependent Dynamics of the Ccr4-Not Complex in Saccharomyces cerevisiae
Joakim Norbeck
J. Microbiol. 2008;46(6):692-696.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0122-2
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AbstractAbstract PDF
We have investigated the composition of the conserved Ccr4-Not complex during different physiological states of Saccharomyces cerevisiae. Major changes were found, most notably in the expression of the central scaffold protein Not1p, which was strongly reduced in the absence of glucose. The low expression of Not1p was also evident from the inability of Pop2p to co-purify Not1p in cells from cultures lacking glucose. However, Not1p was still essential under conditions of low expression. The downregulation of Not1p indicates that many of the Ccr4-Not complex components are likely to have roles outside of the complex. We suggest that the use of different carbon sources will be a good starting point to unravel these functions.

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  • HIPK family kinases bind and regulate the function of the CCR4-NOT complex
    Alfonso Rodriguez-Gil, Olesja Ritter, Juliane Hornung, Hilda Stekman, Marcus Krüger, Thomas Braun, Elisabeth Kremmer, Michael Kracht, M. Lienhard Schmitz, Anne Spang
    Molecular Biology of the Cell.2016; 27(12): 1969.     CrossRef
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    Jason E. Miller, Joseph C. Reese
    Critical Reviews in Biochemistry and Molecular Biology.2012; 47(4): 315.     CrossRef
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    Martine A. Collart, Olesya O. Panasenko
    Gene.2012; 492(1): 42.     CrossRef
Research Support, Non-U.S. Gov'ts
Organization of Three rRNA (rrn) Operons from Sphingobium chungbukense DJ77
Sun-Mi Yeon , Beom-Soon Choi , Young-Chang Kim
J. Microbiol. 2008;46(6):697-703.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0193-0
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AbstractAbstract PDF
The nucleotide sequences of all three rRNA operons (rrnA, rrnB, and rrnC) of Sphingobium chungbukense DJ77 were determined. The three rrn operons have the same gene order (16S rRNA-tRNAIle-tRNAAla-23S rRNA-5S rRNA-tRNAfMet). The nucleotide sequences were identical over a 5,468 bp region spanning the 16S rRNA gene to the 5S rRNA gene. Variability was observed in the 5S rRNA-tRNAfMet spacer sequence of rrnB. The tRNAfMet gene sequences were identical except for two bases (T5794 and A5871 in rrnB, T5942 and A5956 in rrnA, but C5942 and G5956 in rrnC). Comparative sequence analyses of ribosomal RNA operons from DJ77 with those of the class Alphaproteobacteria, to which the genus Sphingobium belongs, reveal close evolutionary relationships with other members of the order Sphingomonadales.
Molecular and Phylogenetic Characterization of Spodoptera litura Granulovirus
Yong Wang , Jae Young Choi , Jong Yul Roh , Soo Dong Woo , Byung Rae Jin , Yeon Ho Je
J. Microbiol. 2008;46(6):704-708.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0133-z
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AbstractAbstract PDF
Baculovirus, Spodoptera litura granulovirus (SlGV) was isolated from the infected S. litura larvae, and was characterized. The granule of SlGV was ovoidal shape with an approximate size of 240~340 nm×140~180 nm. Each granule contained one single rod-shape virion with a mean size of 180~200 nm×20~40 nm. Restriction endonuclease fragment analysis estimated that the total genome size of SlGV is about 115 kb. Necleotide sequence analysis of the granulin gene showed that the gene encodes 249 amino acids with a predicted molecular mass of 29 kDa. When the phylogenic relationship was analyzed using the nucleotide sequence of the granulin gene, SlGV was most closely related to Trichoplusia ni granulovirus (TnGV) and Xestia c-nigrum granulovirus (XcGV) which belong to Type I granulovirus.

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Molecular Characterization of ORFs 2 to 7 of Korean Porcine Reproductive and Respiratory Syndrome Virus (CA) and Its Protein Expression by Recombinant Baculoviruses
Hyun Na Koo , Jeong Mi Oh , Jae Kyung Lee , Jae Young Choi , Kwang Sik Lee , Jong Yul Roh , Yeon Ho Je , Byung Rae Jin , Sung Sik Yoo , Jae Su Kim , Young In Kim , In Joong Yoon , Soo Dong Woo
J. Microbiol. 2008;46(6):709-719.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0224-x
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AbstractAbstract PDF
To determine the characteristics of the Korean porcine reproductive and respiratory syndrome virus (PRRSV), CA, which was isolated from the serum of an infected pig in 2006, we investigated the nucleotide sequence and expression of the structural ORFs (ORFs 2 to 7) using the bApGOZA system. We found that the structural ORFs 2 to 7 of CA consisted of 3188 nucleotides that were the same as those formed from VR-2332. Comparison of the CA with the other strains revealed nucleotide sequence identity ranging from 89.8 to 99.5%. To better understand the genetic relationships between other strains, phylogenetic analyses were performed. The CA strain was closely related to the other North American genotype strains but formed a distinct branch with high bootstrap support. Additionally, expression levels of the PRRSV proteins in insect cells were strong or partially weak. The results of this study have implications for both the taxonomy of PRRSV and vaccine development.

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Journal Article
Proteomic Analysis of Outer Membrane Proteins from Acinetobacter baumannii DU202 in Tetracycline Stress Condition
Sung-Ho Yun , Chi-Won Choi , Soon-Ho Park , Je Chul Lee , Sun-Hee Leem , Jong-Soon Choi , Soohyun Kim , Seung Il Kim
J. Microbiol. 2008;46(6):720-727.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0202-3
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AbstractAbstract PDF
Acinetobacter baumannii readily developed antimicrobial resistance to clinically available antibiotics. A. baumannii DU202 is a multi-drug resistant strain, and is highly resistant to tetracycline (MIC>1,024μg/ml). The surface proteome of A. baumannii DU202 in response to the sub-minimal inhibitory concentration (subMIC) of tetracycline was analyzed by 2-DE/MS-MS and 1-DE/LC/MS-MS to understand the pathways that form barriers for tetracycline. Membrane expression of major outer membrane proteins (Omps) was significantly decreased in response to the subMIC of tetracycline. These Omps with sizes of 38, 32, 28, and 21 kDa were identified as OmpA38, OmpA32, CarO, and OmpW, respectively. However, transcription level of these Omps was not significantly changed. 1-DE/LC/MS-MS analysis of secreted proteins showed that OmpA38, CarO, OmpW, and other Omps were increasingly secreted at tetracycline condition. This result suggests that A. baumannii actively regulates the membrane expression and the secretion of Omps to overcome antibiotic stress condition.

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Research Support, Non-U.S. Gov'ts
Enhancement of Immunotherapeutic Effects of HPV16E7 on Cervical Cancer by Fusion with CTLA4 Extracellular Region
Yi Zheng , Yijuan Zhang , Jun Wan , Chaofan Shi , Laiqiang Huang
J. Microbiol. 2008;46(6):728-736.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0087-1
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AbstractAbstract PDF
Cervical cancer is caused by infection by high-risk human papillomavirus (HPV), especially HPV16. Limitations in current treatments of cervical cancers call for the development of new and improved immunotherapies. This study aims at investigating the efficacy of a novel vaccine consisting of modified HPV 16E7 fused with human cytotoxic T-lymphocyte antigen 4 (CTLA4). The regions in HPV16 E7 gene associated with its transformation and CTL-enhanced response were modified; the resultant HPV16mE7 was fused with extracellular region of CTLA4 to generate HPVm16E7-eCTLA4 fusion protein. Binding of this fusion protein to B7 molecules expressed on antigen presenting-cells (APCs) was demonstrated. C57BL/6 (H-2b) mice immunized with low dose of the fusion protein (10 μg) produced higher titer antibody and stronger specific CTL response, and expressed higher levels of IFN-γ and IL-12, compared with those immunized with HPVm16E7 only or admixture of HPVm16E7 and CTLA4, or PBS; and were protected from lethal dose tumor challenge. Tumor growth was retarded and survival prolonged in mouse models with the fusion protein treatment. Our results demonstrate that fusion of HPV16 E7 with eCTLA4 targeting APCs resulted in enhanced immunity, and that this fusion protein may be useful for improving the efficacy of immunotherapeutic treatments of cervical cancer and other HPV16 infection-associated tumors.

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Protective Effect of Polygoni Cuspidati Radix and Emodin on Vibrio vulnificus Cytotoxicity and Infection
Jong Ro Kim , Dool-Ri Oh , Mi Hye Cha , Byoung Sik Pyo , Joon Haeng Rhee , Hyon E. Choy , Won Keun Oh , Young Ran Kim
J. Microbiol. 2008;46(6):737-743.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0232-x
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AbstractAbstract PDF
Vibrio vulnificus, a good model organism of bacterial septicemia, causes fatal septicemia manifesting a fulminating course and a high mortality rate within days. In order to identify new natural substances preventing V. vulnificus infection, a plant library was screened for inhibiting cytotoxicity to host cells by using Trypan blue staining and LDH assay. We found that Polygoni Cuspidati Radix potently suppressed the acute death of HeLa and RAW264.7 cells in a dose dependent manner. Further studies revealed that Polygoni Cuspidati Radix inhibited V. vulnificus growth and survival in HI broth and seawater, respectively. We confirmed that Polygoni Cuspidati Radix contained high level of emodin by thin layer chromatography (TLC). Emodin showed direct antibacterial activity against V. vulnificus. In addition, emodin prevented the morphologic damages and acute death of HeLa cells caused from V. vulnificus. The safety of Polygoni Cuspidati Radix and emodin to host cells was confirmed by MTT assay. Polygoni Cuspidati Radix and emodin protected mice from V. vulnificus infection.

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Journal Article
Inhibitory Effect of Methyl Gallate and Gallic Acid on Oral Bacteria
Mi-Sun Kang , Jong-Suk Oh , In-Chol Kang , Suk-Jin Hong , Choong-Ho Choi
J. Microbiol. 2008;46(6):744-750.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0235-7
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AbstractAbstract PDF
This study examined the ability of methyl gallate (MG) and gallic acid (GA), the main compounds of gallotannins in Galla Rhois, to inhibit the proliferation of oral bacterial and the in vitro formation of Streptococcus mutans biofilms. The antimicrobial activities of these compounds were evaluated in vitro using the broth microdilution method and a beaker-wire test. Both MG and GA had inhibitory effects on the growth of cariogenic (MIC<8 mg/ml) and periodontopathic bacteria (MIC=1 mg/ml). Moreover, these compounds significantly inhibited the in vitro formation of S. mutans biofilms (MG, 1 mg/ml; GA, 4 mg/ml; P<0.05). MG was more effective in inhibiting bacterial growth and the formation of S. mutans biofilm than GA. In conclusion, MG and GA can inhibit the growth of oral pathogens and S. mutans biofilm formation, and may be used to prevent the formation of oral biofilms.

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