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https://www.readbyqxmd.com/read/29338795/the-first-report-of-xenorhabdus-indica-from-steinernema-pakistanense-co-phylogenetic-study-suggests-co-speciation-between-x-indica-and-its-steinernematid-nematodes
#1
A H Bhat, A K Chaubey, V Půža
During a survey in agricultural fields of the sub-humid region of Meerut district, India, two strains of entomopathogenic nematodes, labelled CS31 and CS32, were isolated using the Galleria baiting technique. Based on morphological and morphometric studies, and molecular data, the nematodes were identified as Steinernema pakistanense, making this finding the first report of this species from India. For the first time, we performed a molecular and biochemical characterization of the bacterial symbiont of S. pakistanense...
January 17, 2018: Journal of Helminthology
https://www.readbyqxmd.com/read/29336852/brazilian-species-of-calliandra-benth-tribe-ingeae-are-nodulated-by-diverse-strains-of-paraburkholderia
#2
Verônica Cordeiro Silva, Patricia Alves Casaes Alves, Mariana Ferreira Kruschewsky Rhem, José Miguel Ferreira Dos Santos, Euan K James, Eduardo Gross
The Chapada Diamantina in NE of Brazil is a biodiversity hotspot and a center of radiation for many Neotropical legume genera, such as Calliandra and Mimosa. The present study aimed to evaluate nodulation in Calliandra species endemic to various environments, and to characterize the diversity of their symbiotic rhizobia using housekeeping (16S rRNA, recA) and plasmid-borne, symbiosis-related (nifH and nodC) genes. The nodulation ability of selected isolates was assessed. All of the 126 bacterial isolates from 18 Calliandra species collected in six different vegetation types were identified as Paraburkholderia according to their housekeeping and symbiosis gene phylogenies...
January 5, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29331569/salinivibrio-kushneri-sp-nov-a-moderately-halophilic-bacterium-isolated-from-salterns
#3
Clara López-Hermoso, Rafael R de la Haba, Cristina Sánchez-Porro, Antonio Ventosa
Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29325987/transfer-of-pectobacterium-carotovorum-subsp-carotovorum-strains-isolated-from-potatoes-grown-at-high-altitudes-to-pectobacterium-peruviense-sp-nov
#4
Malgorzata Waleron, Agnieszka Misztak, Michal Waleron, Martyna Franczuk, Bartosz Wielgomas, Krzysztof Waleron
Seven Gram-negative, rod-shaped pectinolytic bacteria strains designated as IFB5227, IFB5228, IFB5229, IFB5230, IFB5231, IFB5232, IFB5636, isolated from potato tubers cultivated in Peru at high altitude (2400-3800m) were subjected to polyphasic analyses that revealed their distinctiveness from the other Pectobacterium species. Phylogenetic analyses based on five housekeeping genes (gyrA, recA, recN, rpoA and rpoS) clearly showed strains separateness, simultaneously indicating Pectobacterium atrosepticum, Pectobacterium wasabiae, Pectobacterium parmentieri and Pectobacterium betavasculorum as the closest relatives...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29321563/probiotic-activities-of-rhizobium-laguerreae-on-growth-and-quality-of-spinach
#5
Alejandro Jiménez-Gómez, José David Flores-Félix, Paula García-Fraile, Pedro F Mateos, Esther Menéndez, Encarna Velázquez, Raúl Rivas
The growing interest in a healthy lifestyle and in environmental protection is changing habits regarding food consumption and agricultural practices. Good agricultural practice is indispensable, particularly for raw vegetables, and can include the use of plant probiotic bacteria for the purpose of biofertilization. In this work we analysed the probiotic potential of the rhizobial strain PEPV40, identified as Rhizobium laguerreae through the analysis of the recA and atpD genes, on the growth of spinach plants...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29316866/the-first-high-frequency-of-recombination-like-conjugal-transfer-from-an-integrated-origin-of-transfer-sequence-in-bacillus-subtilis-168
#6
Mitsuhiro Itaya, Miki Hasegawa, Masaru Tomita, Mitsuru Sato
Bacillus subtilis 168 was developed as a genome vector to manipulate large DNA fragments. The system is based on the inherent natural transformation (TF) activity. However, DNA size transferred by TF is limited up to approximately 100 kb. A conjugal transfer system capable of transferring DNA fragments considerably larger than those transferred by TF was developed. A well-defined oriT110 sequence and a cognate relaxase gene from the pUB110 plasmid were inserted into the xkdE gene of the B. subtilis genome...
January 10, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29310897/vicia-faba-l-in-the-bejaia-region-of-algeria-is-nodulated-by-rhizobium-leguminosarum-sv-viciae-rhizobium-laguerreae-and-two-new-genospecies
#7
Djellali Belhadi, Philippe de Lajudie, Nacer Ramdani, Christine Le Roux, Farida Boulila, Pierre Tisseyre, Abdelghani Boulila, Amar Benguedouar, Yahia Kaci, Gisèle Laguerre
Fifty-eight rhizobial strains were isolated from root nodules of Vicia faba cv. Equina and Vicia faba cv. Minor by the host-trapping method in soils collected from eleven sites in Bejaia, Eastern Algeria. Eleven genotypic groups were distinguished based on the combined PCR/RFLP of 16S rRNA, 16S-23S rRNA intergenic spacer and symbiotic (nodC and nodD-F) genes and further confirmed by multilocus sequence analysis (MLSA) of three housekeeping genes (recA, atpD and rpoB), the 16S rRNA gene and the nodulation genes nodC and nodD...
December 27, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29299771/vibrio-coralliirubri-sp-nov-a-new-species-isolated-from-mucus-of-red-coral-corallium-rubrum-collected-at-procida-island-italy
#8
Annarita Poli, Ida Romano, Vincenza Mastascusa, Lorena Buono, Pierangelo Orlando, Barbara Nicolaus, Luigi Leone, Kar Wai Hong, Kok-Gan Chan, Kian Mau Goh, Javier Pascual
Strain Corallo1T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic...
January 3, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29286386/investigating-the-detrimental-effects-of-low-pressure-plasma-sterilization-on-the-survival-of-bacillus-subtilis-spores-using-live-cell-microscopy
#9
Felix M Fuchs, Marina Raguse, Marcel Fiebrandt, Kazimierz Madela, Peter Awakowicz, Michael Laue, Katharina Stapelmann, Ralf Moeller
Plasma sterilization is a promising alternative to conventional sterilization methods for industrial, clinical, and spaceflight purposes. Low pressure plasma (LPP) discharges contain a broad spectrum of active species, which lead to rapid microbial inactivation. To study the efficiency and mechanisms of sterilization by LPP, we use spores of the test organism Bacillus subtilis because of their extraordinary resistance against conventional sterilization procedures. We describe the production of B. subtilis spore monolayers, the sterilization process by low pressure plasma in a double inductively coupled plasma reactor, the characterization of spore morphology using scanning electron microscopy (SEM), and the analysis of germination and outgrowth of spores by live cell microscopy...
November 30, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29279139/photobacterium-carnosum-sp-nov-isolated-from-spoiled-modified-atmosphere-packaged-poultry-meat
#10
Maik Hilgarth, Sandra Fuertes, Matthias Ehrmann, Rudi F Vogel
Analysis of spoilage-associated microbiota of modified-atmosphere packaged poultry meat revealed four different bacterial isolates that could not be assigned to known species. They showed a Gram-negative staining behavior, were facultatively aerobic, non-motile with variable cell morphology. Phylogenetic analysis of 16S rDNA and gyrB, rpoD and recA revealed a distinct lineage within the genus Photobacterium with Photobacterium (P.) iliopiscarium DSM 9896T, P. phosphoreum DSM 15556T, P. kishitanii DSM 19954T, P...
December 19, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29275629/inhibitors-of-lexa-autoproteolysis-and-the-bacterial-sos-response-discovered-by-an-academic-industry-partnership
#11
Charlie Y Mo, Matthew J Culyba, Trevor Selwood, Jeffrey M Kubiak, Zachary M Hostetler, Anthony J Jurewicz, Paul M Keller, Andrew J Pope, Amy Quinn, Jessica L Schneck, Katherine L Widdowson, Rahul M Kohli
The RecA/LexA axis of the bacterial DNA damage (SOS) response is a promising, yet non-traditional drug target. The SOS response is initiated upon genotoxic stress, when RecA, a DNA damage sensor, induces LexA, the SOS repressor, to undergo autoproteolysis, thereby de-repressing downstream genes that can mediate DNA repair and accelerate mutagenesis. As genetic inhibition of the SOS response sensitizes bacteria to DNA damaging antibiotics and decreases acquired resistance, inhibitors of the RecA/LexA axis could potentiate our current antibiotic arsenal...
December 24, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29238335/treatment-with-cefotaxime-affects-expression-of-conjugation-associated-proteins-and-conjugation-transfer-frequency-of-an-inci1-plasmid-in-escherichia-coli
#12
Thea S B Møller, Gang Liu, Anders Boysen, Line E Thomsen, Freja L Lüthje, Sisse Mortensen, Jakob Møller-Jensen, John E Olsen
Horizontal gene transfer (HGT) is the major mechanism responsible for spread of antibiotic resistance. Antibiotic treatment has been suggested to promote HGT, either by directly affecting the conjugation process itself or by selecting for conjugations subsequent to DNA transfer. However, recent research suggests that the effect of antibiotic treatment on plasmid conjugation frequencies, and hence the spread of resistance plasmids, may have been overestimated. We addressed the question by quantifying transfer proteins and conjugation frequencies of a blaCTX-M-1 encoding IncI1 resistance plasmid in Escherichia coli MG1655 in the presence and absence of therapeutically relevant concentrations of cefotaxime (CTX)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29233227/dna-partitions-into-triplets-under-tension-in-the-presence-of-organic-cations-with-sequence-evolutionary-age-predicting-the-stability-of-the-triplet-phase
#13
Amirhossein Taghavi, Paul van der Schoot, Joshua T Berryman
Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure-function relationship in Σ DNA...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29233223/a-stretched-conformation-of-dna-with-a-biological-role
#14
Niklas Bosaeus, Anna Reymer, Tamás Beke-Somfai, Tom Brown, Masayuki Takahashi, Pernilla Wittung-Stafshede, Sandra Rocha, Bengt Nordén
We have discovered a well-defined extended conformation of double-stranded DNA, which we call Σ-DNA, using laser-tweezers force-spectroscopy experiments. At a transition force corresponding to free energy change ΔG = 1·57 ± 0·12 kcal (mol base pair)-1 60 or 122 base-pair long synthetic GC-rich sequences, when pulled by the 3'-3' strands, undergo a sharp transition to the 1·52 ± 0·04 times longer Σ-DNA. Intriguingly, the same degree of extension is also found in DNA complexes with recombinase proteins, such as bacterial RecA and eukaryotic Rad51...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29229555/reduced-cerebrovascular-reactivity-and-increased-resting-cerebral-perfusion-in-rats-exposed-to-a-cafeteria-diet
#15
Mariana Gomez-Smith, Rafal Janik, Evelyn M Lake, Lynsie A M Thomason, Conner Adams, Matthew S Jeffers, Bojana Stefanovic, Dale Corbett
To better understand the effects of a diet high in fat, sugar, and sodium on cerebrovascular function, Sprague Dawley rats were chronically exposed to a Cafeteria diet. Resting cerebral perfusion and cerebrovascular reactivity were quantified using continuous arterial spin labeling (CASL) magnetic resonance imaging (MRI). In addition, structural changes to the cerebrovasculature and susceptibility to ischemic lesion were examined. Compared to control animals fed standard chow (SD), Cafeteria diet (CAF) rats exhibited increased resting brain perfusion in the hippocampus and reduced cerebrovascular reactivity in response to 10% inspired CO2 challenges in both the hippocampus and the neocortex...
December 8, 2017: Neuroscience
https://www.readbyqxmd.com/read/29214235/kinetics-and-thermodynamics-of-dbpa-protein-s-c-terminal-domain-interaction-with-rna
#16
Aliana López de Victoria, Anthony F T Moore, Apostolos G Gittis, Eda Koculi
DbpA is an Escherichia coli DEAD-box RNA helicase implicated in RNA structural isomerization in the peptide bond formation site. In addition to the RecA-like catalytic core conserved in all of the members of DEAD-box family, DbpA contains a structured C-terminal domain, which is responsible for anchoring DbpA to hairpin 92 of 23S ribosomal RNA during the ribosome assembly process. Here, surface plasmon resonance was used to determine the equilibrium dissociation constant and the microscopic rate constants of the DbpA C-terminal domain association and dissociation to a fragment of 23S ribosomal RNA containing hairpin 92...
November 30, 2017: ACS Omega
https://www.readbyqxmd.com/read/29202219/direct-single-molecule-observation-of-mode-and-geometry-of-reca-mediated-homology-search
#17
Andrew James Lee, Masayuki Endo, Jamie Kayne Hobbs, Christoph Walti
Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous Recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging...
December 4, 2017: ACS Nano
https://www.readbyqxmd.com/read/29198596/phenotypic-and-genetic-diversity-of-moroccan-rhizobia-isolated-from-vicia-faba-and-study-of-genes-that-are-likely-to-be-involved-in-their-osmotolerance
#18
Loubna Benidire, Majida Lahrouni, Khalid Daoui, Zain El Abidine Fatemi, Ricardo Gomez Carmona, Michael Göttfert, Khalid Oufdou
Rhizobia are symbiotic nitrogen-fixing bacteria in root nodules of legumes. In Morocco, faba bean (Vicia faba L.), which is the main legume crop cultivated in the country, is often grown in marginal soils of arid and semi-arid regions. This study examines the phenotypic diversity of rhizobia nodulating V. faba isolated from different regions in Morocco for tolerance to some abiotic stresses. A total of 106 rhizobia strains isolated from nodules were identified at the species level by analysing 16S rDNA. Additionally, for selected strains recA, otsA, kup and nodA fragments were sequenced...
November 3, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29196271/gibson-assembly-facilitates-bacterial-allelic-exchange-mutagenesis
#19
Oleksandra Silayeva, Andrew C Barnes
Allelic exchange mutagenesis that relies on RecA-mediated homologous recombination up- and downstream from the targeted gene is a generalizable method of site-specific bacterial gene knock-out and knock-in. However, generation of a mutagenic DNA construct (alternative allele flanked by regions surrounding the gene target) and subsequent mutant selection are laborious procedures. Here we demonstrate allelic exchange knock-out facilitated by Gibson Assembly in Streptococcus iniae. Gibson Assembly allows rapid construction of a mutagenic DNA sequence simultaneous with cloning, as well as rapid reconstruction of complete recombinant vector sequence when required...
November 28, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29189891/coralloluteibacterium-stylophorae-gen-nov-sp-nov-a-new-member-of-the-family-lysobacteraceae-isolated-from-the-reef-building-coral-stylophora-sp
#20
Wen-Ming Chen, Pei-Bei Xie, Sen-Lin Tang, Shih-Yi Sheu
A bacterial strain, designated Sty a-1T, was isolated from a reef-building coral Stylophora sp., collected off coast of Southern Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain Sty a-1T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate accumulating, motile by means of flagella, non-spore forming, straight rod-shaped and colonies were yellow and circular. Growth occurred at 15-40 °C (optimum, 30-35 °C), at pH 6-10 (optimum, pH 6.5-8) and with 0-7% NaCl (optimum, 2-3%)...
November 30, 2017: Archives of Microbiology
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