Search results for "Research and analysis methods"
showing 10 items of 584 documents
Recombinant laccase from Pediococcus acidilactici CECT 5930 with ability to degrade tyramine
2017
Biogenic amines degradation by bacterial laccases is little known, so we have cloned and heterologously expressed, in E. coli, a new laccase from Pediococcus acidilactici CECT 5930 (Lpa5930), a lactic acid bacterium commonly found in foods able to degrade tyramine. The recombinant enzyme has been characterized by physical and biochemical assays. Here we report the optimization of expression and purification procedures of this laccase. DNA encoding sequence of laccase from P. acidilactici was amplified by PCR and cloned into the expression plasmid pET28a for induction by isopropyl-β-D-thiogalactoipyranoside. Protein expression was performed in E. coli BL21(DE3) harboring pGro7 plasmid expres…
Ocean acidification at a coastal CO2 vent induces expression of stress-related transcripts and transposable elements in the sea anemone Anemonia viri…
2019
Published version, available at: https://doi.org/10.1371/journal.pone.0210358 Ocean acidification threatens to disrupt interactions between organisms throughout marine ecosystems. The diversity of reef-building organisms decreases as seawater CO2 increases along natural gradients, yet soft-bodied animals, such as sea anemones, are often resilient. We sequenced the polyA-enriched transcriptome of adult sea anemone Anemonia viridis and its dinoflagellate symbiont sampled along a natural CO2 gradient in Italy to assess stress levels in these organisms. We found that about 1.4% of the anemone transcripts, but only ~0.5% of the Symbiodinium sp. transcripts were differentially expressed. Processe…
Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species.
2018
International audience; Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast …
Comparative Mitogenomics of Leeches (Annelida: Clitellata): Genome Conservation and Placobdella-Specific trnD Gene Duplication.
2015
Mitochondrial DNA sequences, often in combination with nuclear markers and morphological data, are frequently used to unravel the phylogenetic relationships, population dynamics and biogeographic histories of a plethora of organisms. The information provided by examining complete mitochondrial genomes also enables investigation of other evolutionary events such as gene rearrangements, gene duplication and gene loss. Despite efforts to generate information to represent most of the currently recognized groups, some taxa are underrepresented in mitochondrial genomic databases. One such group is leeches (Annelida: Hirudinea: Clitellata). Herein, we expand our knowledge concerning leech mitochon…
Long-Distance Travellers: Phylogeography of a Generalist Parasite, Pholeter gastrophilus, from Cetaceans
2017
We studied the phylogeography and historical demography of the most generalist digenean from cetaceans, Pholeter gastrophilus, exploring the effects of isolation by distance, ecological barriers and hosts' dispersal ability on the population structure of this parasite. The ITS2 rDNA, and the mitochondrial COI and ND1 from 68 individual parasites were analysed. Worms were collected from seven oceanic and coastal cetacean species from the south western Atlantic (SWA), central eastern Atlantic, north eastern Atlantic (NEA), and Mediterranean Sea. Pholeter gastrophilus was considered a single lineage because reciprocal monophyly was not detected in the ML cladogram of all individuals, and seque…
Co-infection with iflaviruses influences the insecticidal properties of Spodoptera exigua multiple nucleopolyhedrovirus occlusion bodies: Implication…
2017
Biological insecticides based on Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) can efficiently control S. exigua larvae on field and greenhouse crops in many parts of the world. Spanish wild populations and laboratory colonies of S. exigua are infected by two iflaviruses (SeIV-1 and SeIV-2). Here we evaluated the effect of iflavirus co-infection on the insecticidal characteristics of SeMNPV occlusion bodies (OBs). Overall, iflavirus co-inoculation consistently reduced median lethal concentrations (LC50) for SeMNPV OBs compared to larvae infected with SeMNPV alone. However, the speed of kill of SeMNPV was similar in the presence or absence of the iflaviruses. A reduction of the we…
The role of the Strait of Gibraltar in shaping the genetic structure of the Mediterranean Grenadier, Coryphaenoides mediterraneus, between the Atlant…
2017
24 pages, 4 figures, 4 tables, supplementary information https://dx.doi.org/10.1371/journal.pone.0174988.-- Data Availability: The mtDNA COI sequences can be accessed at BOLD systems through the sample ID: ME-9911; ME-11972; ME-13727; GLF011. New mtDNA COI sequences can be accessed at GenBank by the accession numbers KY345206 - KY345398. GenBank accession numbers for close related species of C. mediterraneus are: Coryphaenoides striaturus - KX656427.1, KX656428.1; Coryphaenoides murray - KX656411.1, KX656410.1; Coryphaenoides carapinus - KX656382.1, KX656381.1; Coryphaenoides brevibarbis - KX656377.1, KX656376.1, KX656375.1. An alignment in fasta with all the haplotypes and respective frequ…
Response to formal comment on Myhrvold (2016) submitted by Griebeler and Werner (2017)
2018
In his 2016 paper, Myhrvold criticized ours from 2014 on maximum growth rates (Gmax, maximum gain in body mass observed within a time unit throughout an individual’s ontogeny) and thermoregulation strategies (ectothermy, endothermy) of 17 dinosaurs. In our paper, we showed that Gmax values of similar-sized extant ectothermic and endothermic vertebrates overlap. This strongly questions a correct assignment of a thermoregulation strategy to a dinosaur only based on its Gmax and (adult) body mass (M). Contrary, Gmax separated similar-sized extant reptiles and birds (Sauropsida) and Gmax values of our studied dinosaurs were similar to those seen in extant similar-sized (if necessary scaled-up) …
Dinosaur Metabolism and the Allometry of Maximum Growth Rate
2016
In his 2016 paper, Myhrvold criticized ours from 2014 on maximum growth rates (Gmax, maximum gain in body mass observed within a time unit throughout an individual’s ontogeny) and thermoregulation strategies (ectothermy, endothermy) of 17 dinosaurs. In our paper, we showed that Gmax values of similar-sized extant ectothermic and endothermic vertebrates overlap. This strongly questions a correct assignment of a thermoregulation strategy to a dinosaur only based on its Gmax and (adult) body mass (M). Contrary, Gmax separated similar-sized extant reptiles and birds (Sauropsida) and Gmax values of our studied dinosaurs were similar to those seen in extant similar-sized (if necessary scaled-up) …
Molecular signatures of silencing suppression degeneracy from a complex RNA virus
2021
As genomic architectures become more complex, they begin to accumulate degenerate and redundant elements. However, analyses of the molecular mechanisms underlying these genetic architecture features remain scarce, especially in compact but sufficiently complex genomes. In the present study, we followed a proteomic approach together with a computational network analysis to reveal molecular signatures of protein function degeneracy from a plant virus (as virus-host protein-protein interactions). We employed affinity purification coupled to mass spectrometry to detect several host factors interacting with two proteins of Citrus tristeza virus (p20 and p25) that are known to function as RNA sil…