1,720,963 research outputs found
First high-quality draft genome of Ochrobactrum haematophilum P6BS-III, a highly glyphosate-tolerant strain isolated from agricultural soil in Argentina
No full textWe report here on a high-quality draft genome sequence of Ochrobactrum haematophilum strain P6BS-III (DSM 106071), a Gram negative, non-sporulating bacterium isolated from a pastureland (Buenos Aires province, Argentina) which had been chronically exposed to the herbicide glyphosate. The genome of 5.25 Mb with a DNA G+C content of 56.63% size was estimated to contain 5,291 protein coding genes and 57 RNA genes. Genome analysis revealed the presence of the phn operon, which is involved in the phosphonate degradation pathway, and a class II 5-enolpyruvylshikimate-3-phosphate synthase (EPSP) that confers tolerance to glyphosate. Genes related to plant growth promotion traits are also present, and include genes for phosphorus metabolism, calcium phosphate and phytate solubilization, siderophore production, organic acid biosynthesis and indole acetic acid (IAA) production.Fil: Massot, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; Argentina. Hasselt University; BélgicaFil: Gkorezis, Panagiotis. Hasselt University; BélgicaFil: McAmmond, Breanne. Thompson Rivers University; CanadáFil: d´Haen, Jan. Hasselt University; BélgicaFil: Van Hamme, Jonathan. Thompson Rivers University; CanadáFil: Merini, Luciano Jose. Instituto Nacional de Tecnología Agropecuaria. Centro Regional La Pampa-San Luis. Estación Experimental Agropecuaria Anguil; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vangronsveld, Jaco. Hasselt University; BélgicaFil: Thijs, Sofie. Hasselt University; Bélgic
Impact of host physiology and external stressors on the bacterial community of Schmidtea mediterranea
No full textTo fully comprehend host-microorganism interactions, it is crucial to understand the composition and diversity of the microbiome, as well as the factors that shape these characteristics. We investigated microbiome variation using the freshwater planarian Schmidtea mediterranea, an invertebrate model in regeneration biology and (eco-)toxicology, by exposing the organisms to various controlled conditions. The microbiome composition exhibited high variability, with most of the bacteria belonging to the Betaproteobacteria. Among the diverse microbial communities, a few genera, such as Curvibacter, were consistently present, but exhibited significant alterations in response to changing conditions. The relative abundance of Curvibacter fluctuated during the regeneration process, initially increasing before returning to a composition similar to the beginning situation. After applying external stress, the relative abundance of Curvibacter and other genera decreased. Variation over time, between different origin laboratories and between individuals, showed that additional, yet to-be-identified, factors of variation are present. Taking all results together, our study provides a solid basis for future research focusing on bacterial functionality in planarians and other invertebrates.This work was supported by the Research Foundation Flanders (FWO) (G.0B83.17 N and N152219), the Bijzonder OnderzoeksFonds of Hasselt University (BOF16NI03) and the Hasselt University Methusalem project (08M03VGRJ). The research leading to results presented in this publication was carried out with infrastructure funded by EMBRC Belgium - FWO project GOH3817N. Bioinformatics analyses were made possible thanks to the Flemish Supercomputer Centre (VSC) infrastructure, supported by the FWO.
Acknowledgements
We thank dr. Pieter Samyn of the Innovations in Chemical Materials Analysis Group at Hasselt University for kindly providing access to the scanning electron microscope. The authors thank Natascha Steffanie, Ria Vanderspikken and Julie Claes for their skillful technical assistance
Differential effect of silver nanoparticles on the microbiome of adult and developing planaria
No full textSilver nanoparticles (AgNPs) are widely incorporated in household, consumer and medical products. Their unintentional release via wastewaters raises concerns on their environmental impact, particularly for aquatic organisms and their associated bacterial communities. It is known that the microbiome plays an important role in its host's health and physiology, e.g. by producing essential nutrients and providing protection against pathogens. A thorough understanding of the effects of AgNPs on bacterial communities and on their interactions with the host is crucial to fully assess AgNP toxicity on aquatic organisms. Our results indicate that the microbiome of the invertebrate Schmidtea mediterranea, a freshwater planarian, is affected by AgNP exposure at the tested 10 μg/ml concentration. Using targeted amplification of the bacterial 16S rRNA gene V3-V4 region, two independent experiments on the microbiomes of adult worms revealed a consistent decrease in Betaproteobacteriales after AgNP exposure, mainly attributed to a decrease in Curvibacter and Undibacterium. Although developing tissues and organisms are known to be more sensitive to toxic compounds, three independent experiments in regenerating worms showed a less pronounced effect of AgNP exposure on the microbiome, possibly because underlying bacterial community changes during development mask the AgNP induced effect. The presence of a polyvinyl-pyrrolidone (PVP) coating did not significantly alter the outcome of the experiments compared to those with uncoated particles. The observed variation between the different experiments underlines the highly variable nature of microbiomes and emphasises the need to repeat microbiome experiments, within and between physiological states of the animal.This work was supported by the Research Foundation Flanders (FWO) (G.0B83.17N,N1522719 and 1522015N), the Bijzonder OnderzoeksFonds of Hasselt University (BOF16NI03) and the Hasselt University Methusalem project (08M03VGRJ). The research leading to results presented in this publication was carried out with infrastructure funded by The European Marine Biological Resource Centre (EMBRC) Belgium - FWO projectGOH3817N. Bioinformatics analyses were made possible thanks to the Flemish Supercomputer Centre (VSC) infrastructure, supported by the FWO.
The authors thank Natascha Steffanie and Ria Vanderspikken for their skillful technical assistanc
Evaluating the Effectiveness of Metagenome Plasmid Enrichment by Bioinformatically Comparing a Metagenome and Plasmidome from a Mine Reclamation Site
No full textMetagenomic analysis of environmental DNA tells us a great deal about the metabolic capacity of the resident microorganisms; however, assembling environmental metagenomes is time consuming, and requires a high level of sequencing commitment. In the context of tracking bacterial pathogens and monitoring antimicrobial and metal resistance genes, a more efficient method might be to enrich plasmids from metagenomes and sequence them, allowing for higher sample throughput. To put this idea to the test, metagenomic DNA isolated from samples originating from a mine reclamation site historically treated with biosolids was treated with plasmid-safe DNase to remove non-circular DNA and generate a “plasmidome”. Both the metagenome and plasmidome were sequenced using Ion Torrent S5 XL sequencing technology, generating 6.91 Gb and 5.89 Gb, respectively. Data were annotated in MG-RAST, and the proportion of antibiotic resistance, metal resistance, and pathogenesis genes in both the metagenome and plasmidome was determined. The plasmidome was found to have over 7.1 million identified protein features and over 5.8 million identified functional categories. From here, methods to assemble the plasmids from the metagenome and plasmidome will be developed to determine if small circular plasmids were in fact enriched using DNase treatments
The Effect of Biological Properties and Sequencer Performance on \u3cem\u3eDe novo\u3c/em\u3e Assembly of Microbial Genomes
No full textCurrent genome sequencing technologies rely on first physically or chemically fragmenting an organism’s genome into small, machine-readable fragments prior to shotgun, or bulk, sequencing. The sequenced fragments must then be assembled into the correct order, a computationally expensive task that requires bioinformatics assembly software driven by mathematical algorithms. Different algorithms have been developed for this task, but generally fragments are joined to one other by matching overlapping reads. Groups of joined fragments are called contigs, and if insufficient data are available, contigs cannot be joined to reveal the true nature of each chromosome and plasmid in the original genome. When resequencing a genome, reference data can be provided to order sequencing reads, but for de novo sequencing of novel organisms, one relies heavily on assembly software models of a genome. The overreaching goal of this project is to determine how biological properties of genomes and sequencing performance affects genome assembly. Since the summer of 2016, I have sequenced a total of 15 bacterial genomes and one yeast genome. All draft genomes were prepared using SPAdes, a graph-based assembler, and statistical analyses were carried out to determine the effect of genome GC content, the presence of plasmids, predicted genome size, mean sequencing read length and the amount of sequencing data available on both the number of contigs in draft assemblies and the size of the contig at which half of the genome was captured. By understanding what factors affect the accuracy of genome assembly, we can use sequencing data with confidence
Interactome of Two Fermenting Yeast Species During Beer Production
No full textParallel 49 Brewing Company opened in East Vancouver in 2012 and has become an award-winning microbrewery central to the growing beer culture in British Columbia. One of their most successful beers is brewed with a co-culture of Saccharomyces cerevisiae and Brettanomyces claussenii using a fairly complex and laborious process to achieve a unique flavour profile; however, due to the time and energy expenses required to produce this beer, production has been halted. At present, Parallel 49 critically needs information regarding this unique brew in order to: understand the genetic makeup of these two strains; characterize the metabolites produced by the individual strains in relation to their gene expression profiles; and understand how yeast strains genetically and metabolically interact during mixed-strain fermentations. To achieve these goals, the genomic, transcriptomic, proteomic, and metabolomic profiles of each yeast species are being characterized independently and in co-culture during fermentation of wort into beer. Measures of fermentation progress, specifically decreasing oxygen, pH and specific gravity, as well as increasing ethanol content, show that Brettanomyces works at a much slower rate than Saccharomyces cerevisiae or co-cultures of the two. The rate of flavour compound production, as measured by headspace gas chromatography coupled to a flame ionization detector, differed in each yeast culture. By gaining an understanding of underlying biological processes, Parallel 49 will be able to identify key biochemical pathways that lead to the flavour profile of this popular brew. As advances in brewing sciences are made, the company will hopefully be able to tailor their brewing process to allow for use a single yeast species to make a similar product more efficiently
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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