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https://www.readbyqxmd.com/read/27931748/lentil-lens-culinaris-medik-nodulates-with-genotypically-and-phenotypically-diverse-rhizobia-in-ethiopian-soils
#1
Wondwosen Tena, Endalkachew Wolde-Meskel, Tulu Degefu, Fran Walley
Forty-eight lentil-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations in Ethiopia, and characterized based on 76 phenotypic traits. Furthermore, 26 representative strains were selected and characterized using multilocus sequence analyses (MLSA) of core (16S rRNA, recA, atpD, glnII and gyrB) and symbiotic (nodA and nifH) genes. Numerical analysis of phenotypic characteristics showed that the 48 test strains fell into three major distinct clusters. The phylogenetic trees based on 16S rRNA genes showed that they belong to the Rhizobium genus...
November 24, 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27930272/dyella-acidisoli-sp-nov-dyella-flagellata-sp-nov-and-dyella-nitratireducens-sp-nov-isolated-from-forest-soil
#2
Mei-Hong Chen, Fan Xia, Ying-Ying Lv, Xiang-Yue Zhou, Li-Hong Qiu
Bacterial strains 4M-Z03T, 4M-K16T and DHG59T were isolated from forest soil samples collected from the Dinghushan Biosphere Reserve, Guangdong Province, PR China (112º 31' E 23º 10' N). The three strains grew well at 28 °C, pH 5.0-6.0 on R2A medium. On the basis of 16S rRNA gene sequence analysis, the three strains, together with D. humi DHG40T, formed a distinct phyletic clade within the genus Dyella, and the sequence similarities between any strains of the clade ranged from 97.8 to 98.5 %. Sequence analysis of concatenated partial gyrB, lepA and recA gene sequences also strongly suggested that the three strains represented three novel species of the genus Dyella...
December 8, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27919072/structure-and-regulation-of-the-chromatin-remodeller-iswi
#3
Lijuan Yan, Li Wang, Yuanyuan Tian, Xian Xia, Zhucheng Chen
ISWI is a member of the SWI2/SNF2 family of chromatin remodellers, which also includes Snf2, Chd1, and Ino80. ISWI is the catalytic subunit of several chromatin remodelling complexes, which mobilize nucleosomes along genomic DNA, promoting replication progression, transcription repression, heterochromatin formation, and many other nuclear processes. The ATPase motor of ISWI is an autonomous remodelling machine, whereas its carboxy (C)-terminal HAND-SAND-SLIDE (HSS) domain functions in binding extranucleosomal linker DNA...
December 5, 2016: Nature
https://www.readbyqxmd.com/read/27902438/dna-double-strand-break-repair-is-involved-in-desiccation-resistance-of-sinorhizobium-meliloti-but-is-not-essential-for-its-symbiotic-interaction-with-medicago-truncatula
#4
Pierre Dupuy, Benjamin Gourion, Laurent Sauviac, Claude Bruand
The soil bacterium Sinorhizobium meliloti, a nitrogen-fixing symbiont of legume plants, is exposed to numerous stress conditions in nature, some of which cause the formation of harmful DNA double strand breaks (DSB). In particular, the reactive oxygen (ROS) and nitrogen (RNS) species produced during symbiosis, and the desiccation occurring in dry soils, are conditions which induce DSB. Two major systems of DSB repair are known in S. meliloti: homologous recombination (HR) and non-homologous end-joining (NHEJ)...
November 23, 2016: Microbiology
https://www.readbyqxmd.com/read/27902304/pseudomonas-canadensis-sp-nov-a-biological-control-agent-isolated-from-a-field-plot-under-long-term-mineral-fertilization
#5
James T Tambong, Renin Xu, Eden Bromfield
The bacterial strain 2-92T isolated from a field plot under long-term (>40 years) mineral fertilization exhibited in vitro antagonistic properties against fungal pathogens. A polyphasic approach was undertaken to verify its taxonomic status. Strain 2-92T is gram-negative, aerobic, non-spore-forming, motile by one or more flagella, and oxidase-, catalase- and urease-positive. Optimal growth temperature of strain 2-92T is 30 °C. 16S rRNA gene sequence analysis demonstrated that the strain is related to species of the genus Pseudomonas...
November 28, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902301/isolation-of-vibrio-tapetis-from-two-native-fish-species-genypterus-chilensis-and-paralichthys-adspersus-reared-in-chile-and-description-of-vibrio-tapetis-subsp-quintayensis-subsp-nov
#6
Arturo Levican, Aide Lasa, Rute Irgang, Jesús L Romalde, Matías Poblete-Morales, Ruben Avendaño-Herrera
Seven isolates recovered from diseased fine flounders (Paralichthys adspersus) and red conger eel (Genypterus chilensis) experimentally reared in Quintay (Chile) were confirmed as V. tapetis on the basis of the MALDI-TOF MS, 16S rRNA gene, DNA-DNA hybridization values and G+C content. The ERIC-PCR and REP-PCR patterns were homogeneous among those isolates recovered from a same host, but distinct to the type strains V. tapetis subsp. tapetis CECT 4600T and V. tapetis subsp. britannicus CECT 8161T. On the basis of atpA, rpoA, rpoD, recA and pyrH gene similarities (99...
November 30, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902255/paraburkholderia-piptadeniae-sp-nov-and-paraburkholderia-ribeironis-sp-nov-two-root-nodulating-symbiotic-species-of-piptadenia-gonoacantha-in-brazil
#7
Caroline Bournaud, Lionel Moulin, Margo Cnockaert, Sergio Miana de Faria, Yves Prin, Dany Severac, Peter Vandamme
During a survey of root-nodulating symbionts of Mimosoid species in South-east region of Brazil, eight Paraburkholderia isolates were obtained from nodules of the legume species Piptadenia gonoacantha, either from the field or following a soil trapping method with the same plant host. 16S rRNA as well as recA and gyrB phylogenetic markers placed these strains in two new clades within the genus Burkholderia sensu lato. DNA-DNA hybridization values and analyses of the whole genome sequence of selected strains in each clade showed that the two clades represented novel Paraburkholderia species...
November 9, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902217/microvirga-ossetica-sp-nov-a-new-species-of-rhizobia-isolated-from-root-nodules-of-the-legume-species-vicia-alpestris-steven-originated-from-north-ossetia-region-in-the-caucasus
#8
Vera Safronova, Irina Kuznetsova, Anna Sazanova, Andrey Belimov, Evgeny Andronov, Elizaveta Chirak, Yuri Osledkin, Olga Onishchuk, Oksana Kurchak, Alexander Shaposhnikov, Anne Willems, Igor Tikhonovich
Gram-negative, rod-shaped strains V5/3MT, V5/5K, V5/5M and V5/13 with a medium growth rate were isolated from root nodules of Vicia alpestris plants growing in the North Ossetia region (Caucasus). The sequencing of the partial 16S rDNA gene (rrs) and four housekeeping genes (dnaK, gyrB, recA and rpoB ) showed that the isolates from V. alpestris were most closely related to the species Microvirga zambiemsis (order Rhizobiales, family Methylobacteriaceae) which was described for the single isolate from root nodule of Listia angolensis growing in Zambia...
October 16, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27899634/homologous-recombination-mediated-by-the-mycobacterial-adnab-helicase-without-end-resection-by-the-adnab-nucleases
#9
Richa Gupta, Mihaela-Carmen Unciuleac, Stewart Shuman, Michael S Glickman
Current models of bacterial homologous recombination (HR) posit that extensive resection of a DNA double-strand break (DSB) by a multisubunit helicase-nuclease machine (e.g. RecBCD, AddAB or AdnAB) generates the requisite 3' single-strand DNA substrate for RecA-mediated strand invasion. AdnAB, the helicase-nuclease implicated in mycobacterial HR, consists of two subunits, AdnA and AdnB, each composed of an N-terminal ATPase domain and a C-terminal nuclease domain. DSB unwinding by AdnAB in vitro is stringently dependent on the ATPase activity of the 'lead' AdnB motor translocating on the 3' ssDNA strand, but not on the putative 'lagging' AdnA ATPase...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27881980/comparative-genomics-of-dna-recombination-and-repair-in-cyanobacteria-biotechnological-implications
#10
REVIEW
Corinne Cassier-Chauvat, Théo Veaudor, Franck Chauvat
Cyanobacteria are fascinating photosynthetic prokaryotes that are regarded as the ancestors of the plant chloroplast; the purveyors of oxygen and biomass for the food chain; and promising cell factories for an environmentally friendly production of chemicals. In colonizing most waters and soils of our planet, cyanobacteria are inevitably challenged by environmental stresses that generate DNA damages. Furthermore, many strains engineered for biotechnological purposes can use DNA recombination to stop synthesizing the biotechnological product...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27875752/toxicity-evaluation-of-e-juice-and-its-soluble-aerosols-generated-by-electronic-cigarettes-using-recombinant-bioluminescent-bacteria-responsive-to-specific-cellular-damages
#11
Shiv Bharadwaj, Robert J Mitchell, Anjum Qureshi, Javed H Niazi
Electronic-cigarettes (e-cigarette) are widely used as an alternative to traditional cigarettes but their safety is not well established. Herein, we demonstrate and validate an analytical method to discriminate the deleterious effects of e-cigarette refills (e-juice) and soluble e-juice aerosol (SEA) by employing stress-specific bioluminescent recombinant bacterial cells (RBCs) as whole-cell biosensors. These RBCs carry luxCDABE-operon tightly controlled by promoters that specifically induced to DNA damage (recA), superoxide radicals (sodA), heavy metals (copA) and membrane damage (oprF)...
November 12, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27871138/high-genetic-diversity-of-vibrio-cholerae-in-the-european-lake-neusiedler-see-is-associated-with-intensive-recombination-in-the-reed-habitat-and-the-long-distance-transfer-of-strains
#12
Carina Pretzer, Irina S Druzhinina, Carmen Amaro, Eva Benediktsdóttir, Ingela Hedenström, Dominique Hervio-Heath, Steliana Huhulescu, Franciska M Schets, Andreas H Farnleitner, Alexander K T Kirschner
Coastal marine Vibrio cholerae populations usually exhibit high genetic diversity. To assess the genetic diversity of abundant V. cholerae non-O1/non-O139 populations in the Central European lake Neusiedler See we performed a phylogenetic analysis based on recA, toxR, gyrB and pyrH loci sequenced for 472 strains. The strains were isolated from three ecologically different habitats in a lake that is a hot-spot of migrating birds and an important bathing water. We also analysed 76 environmental and human V. cholerae non-O1/non-O139 isolates from Austria and other European countries and added sequences of seven genome-sequenced strains...
November 21, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27864174/multilocus-sequence-analysis-of-phylogroup-1-and-2-oral-treponeme-strains
#13
Yong-Biao Huo, Yuki Chan, Donnabella C Lacap-Bugler, Sisu Mo, Patrick C Y Woo, W Keung Leung, Rory M Watt
: More than 75 'species-level' phylotypes of spirochete bacteria belonging to the genus Treponema reside within the human oral cavity. The majority of these oral treponeme phylotypes correspond to as-yet uncultivated taxa, or strains of uncertain standing in taxonomy. Here, we analyze phylogenetic and taxonomic relationships between oral treponeme strains using a multilocus sequence analysis (MLSA) scheme based on the highly-conserved 16S rRNA, pyrH, recA and flaA genes. We utilize this MLSA scheme to analyze genetic data from a curated collection of oral treponeme strains (n=71) of diverse geographical origins...
November 18, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27833912/sacb-sacr-gene-cassette-as-the-negative-selection-marker-to-suppress-agrobacterium-overgrowth-in-agrobacterium-mediated-plant-transformation
#14
Yiming Liu, Jiamin Miao, Sy Traore, Danyu Kong, Yi Liu, Xunzhong Zhang, Zachary L Nimchuk, Zongrang Liu, Bingyu Zhao
Agrobacterium overgrowth is a common problem in Agrobacterium-mediated plant transformation. To suppress the Agrobacterium overgrowth, various antibiotics have been used during plant tissue culture steps. The antibiotics are expensive and may adversely affect plant cell differentiation and reduce plant transformation efficiency. The SacB-SacR proteins are toxic to most Agrobacterium tumefaciens strains when they are grown on culture medium supplemented with sucrose. Therefore, SacB-SacR genes can be used as negative selection markers to suppress the overgrowth of A...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27813083/dbpa-is-a-region-specific-rna-helicase
#15
Anthony F T Moore, Riley C Gentry, Eda Koculi
DbpA is a DEAD-box RNA helicase implicated in RNA structural rearrangements in the peptidyl transferase center. DbpA contains an RNA binding domain, responsible for tight binding of DbpA to hairpin 92 of 23S ribosomal RNA, and a RecA-like catalytic core responsible for double-helix unwinding. It is not known if DbpA unwinds only the RNA helices that are part of a specific RNA structure, or if DbpA unwinds any RNA helices within the catalytic core's grasp. In other words, it is not known if DbpA is a site-specific enzyme or region-specific enzyme...
November 4, 2016: Biopolymers
https://www.readbyqxmd.com/read/27794044/rad51-and-reca-juxtapose-dsdna-ends-ready-for-dna-ligase-catalyzed-end-joining-under-recombinase-suppressive-conditions
#16
Naoto Konomura, Naoto Arai, Takeshi Shinohara, Jun Kobayashi, Wakana Iwasaki, Shukuko Ikawa, Kohji Kusano, Takehiko Shibata
RecA-family recombinase-catalyzed ATP-dependent homologous joint formation is critical for homologous recombination, in which RecA or Rad51 binds first to single-stranded (ss)DNA and then interacts with double-stranded (ds)DNA. However, when RecA or Rad51 interacts with dsDNA before binding to ssDNA, the homologous joint-forming activity of RecA or Rad51 is quickly suppressed. We found that under these and adenosine diphosphate (ADP)-generating suppressive conditions for the recombinase activity, RecA or Rad51 at similar optimal concentrations enhances the DNA ligase-catalyzed dsDNA end-joining (DNA ligation) about 30- to 40-fold...
October 27, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27789781/the-dnae-polymerase-from-deinococcus-radiodurans-features-reca-dependent-dna-polymerase-activity
#17
Lorenzo Randi, Alessandro Perrone, Mirko Maturi, Fabrizio Dal Piaz, Michela Camerani, Alejandro Hochkoeppler
We report in the present study on the catalytic properties of the Deinococcus radiodurans DNA polymerase III α subunit (αDr). The αDr enzyme was overexpressed in Escherichia coli, both in soluble form and as inclusion bodies. When purified from soluble protein extracts, αDr was found to be tightly associated with E. coli RNA polymerase, from which αDr could not be dissociated. On the contrary, when refolded from inclusion bodies, αDr was devoid of E. coli RNA polymerase and was purified to homogeneity...
December 2016: Bioscience Reports
https://www.readbyqxmd.com/read/27785661/isolation-of-a-novel-atypical-brucella-strain-from-a-bluespotted-ribbontail-ray-taeniura-lymma
#18
Tobias Eisenberg, Karin Riße, Nicole Schauerte, Christina Geiger, Jochen Blom, Holger C Scholz
A pleomorphic Gram-negative, motile coccobacillus was isolated from the gills of a wild-caught bluespotted ribbontail ray after its sudden death during quarantine. Strain 141012304 was observed to grow aerobically, to be clearly positive for cytochrome oxidase, catalase, urease and was initially identified as "Brucella melitensis" or "Ochrobactrum anthropi" by Matrix-assisted laser desorption/ionization-time of flight mass spectrometry and VITEK2-compact(®), respectively. Affiliation to the genus Brucella was confirmed by bcsp31 and IS711 PCR as well as by Brucella species-specific multiplex PCR, therein displaying a characteristic banding pattern recently described for Brucella strains obtained from amphibian hosts...
October 26, 2016: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/27780963/properties-of-a-fibrinolytic-enzyme-secreted-by-bacillus-amyloliquefaciens-rsb34-isolated-from-doenjang
#19
Zhuang Yao, Xiaoming Liu, Jae Min Shim, Kang Wook Lee, Hyun-Jin Kim, Jeong Hwan Kim
Nine bacilli with fibrinolytic activities were isolated from Doenjang, a traditional Korean fermented soy food. Among them, RSB 34 showed the strongest activity and identified as Bacillus amyloliquefaciens by 16S rRNA and recA genes sequencing. During growth on LB up to 96 h, RSB34 showed the highest fibrinolytic activity (83.23 mU/μl) at 48 h. Three bands of 23, 27, and 42 kDa in size were observed when culture supernatant was analyzed by SDS-PAGE and 27 and 42 kDa bands by fibrin zymography. A gene encoding the 27 kDa major fibrinolytic enzyme, AprE34, was cloned by PCR...
October 25, 2016: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27778377/dynamics-of-pdgfr%C3%AE-expression-in-different-cell-types-after-brain-injury
#20
Jenni Kyyriäinen, Xavier Ekolle Ndode-Ekane, Asla Pitkänen
Platelet-derived growth factor receptor β (PDGFRβ) is upregulated after brain injury and its depletion results in the blood-brain barrier (BBB) damage. We investigated the time-window and localization of PDGFRβ expression in mice with intrahippocampal kainic acid-induced status epilepticus (SE) and in rats with lateral fluid-percussion-induced traumatic brain injury (TBI). Tissue immunohistochemistry was evaluated at several time-points after SE and TBI. The distribution of PDGFRβ was analyzed, and its cell type-specific expression was verified with double/triple-labeling of astrocytes (GFAP), NG2 cells, and endothelial cells (RECA-1)...
October 25, 2016: Glia
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