Unique Features of Odorant-Binding Proteins of the Parasitoid Wasp Nasonia vitripennis Revealed by Genome Annotation and Comparative Analyses

Insects are the most diverse group of animals on the planet, comprising over 90% of all metazoan life forms, and have adapted to a wide diversity of ecosystems in nearly all environments. They have evolved highly sensitive chemical senses that are central to their interaction with their environment and to communication between individuals. Understanding the molecular bases of insect olfaction is therefore of great importance from both a basic and applied perspective. Odorant binding proteins (OBPs) are some of most abundant proteins found in insect olfactory organs, where they are the first component of the olfactory transduction cascade, carrying odorant molecules to the olfactory receptors. We carried out a search for OBPs in the genome of the parasitoid wasp Nasonia vitripennis and identified 90 sequences encoding putative OBPs. This is the largest OBP family so far reported in insects. We report unique features of the N. vitripennis OBPs, including the presence and evolutionary origin of a new subfamily of double-domain OBPs (consisting of two concatenated OBP domains), the loss of conserved cysteine residues and the expression of pseudogenes. This study also demonstrates the extremely dynamic evolution of the insect OBP family: (i) the number of different OBPs can vary greatly between species; (ii) the sequences are highly diverse, sometimes as a result of positive selection pressure with even the canonical cysteines being lost; (iii) new lineage specific domain arrangements can arise, such as the double domain OBP subfamily of wasps and mosquitoes.Rothamsted Research receives grant-aided support from the BBSRC of the UK. The authors thank Prof. David M. Shuker, University of Edinburgh, UK, who provided us with N. vitripennis. FGV was supported by a predoctoral fellowship SFRH/BD/22360/2005 from the ‘Fundac¸a˜o para a Cieˆncia e a Tecnologı´a’ (Portugal). This work was funded by grants BFU2007-62927 and BFU2010-15484 from the ‘Direccio´n General de Investigacio´n Cientı´fica y Te´cnica’ (Spain) to JR. JR was partially supported by ICREA Academia (Generalitat de Catalunya). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

BadiRate Software

Podeu consultar l'article relacionat a: http://hdl.handle.net/2445/53350Podeu consultar la pàgina de desenvolupament del programari: http://www.ub.edu/softevol/badirate/BadiRate is a software package to estimate, within a phylogenetic context and by likelihood-based methods (or parsimony): (1) the gain, birth, death and innovation family turnover rates (2) most likely number of family members in internal nodes (3) families with turnover rates higher or lower than that estimated for the whole dat

Mycobacterial Phylogenomics: An Enhanced Method for Gene Turnover Analysis Reveals Uneven Levels of Gene Gain and Loss among Species and Gene Families

Species of the genus Mycobacterium differ in several features, from geographic ranges, and degree of pathogenicity, to ecological and host preferences. The recent availability of several fully sequenced genomes for a number of these species enabled the comparative study of the genetic determinants of this wide lifestyle diversity. Here, we applied two complementary phylogenetic-based approaches using information from 19 Mycobacterium genomes to obtain a more comprehensive view of the evolution of this genus. First, we inferred the phylogenetic relationships using two new approaches, one based on a Mycobacterium-specific amino acid substitution matrix and the other on a gene content dissimilarity matrix. Then, we utilized our recently developed gain-and-death stochastic models to study gene turnover dynamics in this genus in a maximum-likelihood framework. We uncovered a scenario that differs markedly from traditional 16S rRNA data and improves upon recent phylogenomic approaches. We also found that the rates of gene gain and death are high and unevenly distributed both across species and across gene families, further supporting the utility of the new models of rate heterogeneity applied in a phylogenetic context. Finally, the functional annotation of the most expanded or contracted gene families revealed that the transposable elements and the fatty acid metabolism-related gene families are the most important drivers of gene content evolution in Mycobacterium

Surveillance of non-indigenous invertebrate species through DNA metabarcoding in recreational marinas in the North and Center of Portugal

DNA metabarcoding has been widely used in biodiversity assessments as a complement to traditional morphology-based techniques. This technique is useful for the early detection and surveillance of non-indigenous species (NIS) in aquatic ecosystems. When introduced to new locations, NIS can establish, and become invasive, which may cause severe alterations to native ecosystems and biodiversity. As most introductions in coastal ecosystems occur by transport in ships (through ballast waters discharges and biofouling), ports and marinas are priority hubs for the early detection of NIS. The aim of this study was to survey marine invertebrate NIS in four marinas in the north and center of Portugal using (e)DNA metabarcoding and different sampling methodologies. We sampled four marinas in three locations in Portugal spanning a distance of ca. 150 km: one in Viana do Castelo (VC), one in Porto (L), inside the port of Leixões, and two in Aveiro (Av1: Costa Nova and Av2: Oudinot). Viana do Castelo, Porto, and Oudinot marinas are more sheltered, located near the coast, with a lower current flow, while Costa Nova marina is located inside a channel, more exposed to the passage of ships and to a higher current flow. Samples were taken of the organisms colonizing the marinas’ hard substrates (e.g. pontoons, buoys, ropes), as well as from water, for environmental DNA (eDNA) analysis, and zooplankton, collected using a 55-µm mesh net. We used two molecular markers: the mitochondrial cytochrome c oxidase gene (COI) and the small subunit ribosomal RNA gene (18S) to produce amplicon libraries for each sample, which were high throughput sequenced in an Illumina MiSeq platform. mBRAVE and SILVAngs were then used to process the sequence data and to generate species-level assignments for COI and 18S data, respectively. A total of 23 NIS was detected in this study: 13 using each molecular marker. Only 3 NIS were detected using both markers. The highest number of NIS was detected in the Av1 marina with COI (11), whereas in the other marinas this number ranged from 5-9 NIS depending on the molecular marker. Six NIS were common to all the marinas, amongst which Amphibalanus amphitrite and Amphibalanus eburneus , two invasive barnacle species and Eriocheir sinensis, the Chinese mitten crab, a very well-known species with invasive behavior that causes severe ecological and economic damages. Fifty percent of NIS belonged to the phyla Arthropoda: Crustacea and Chordata: Ascidiacea. The sampling method that registered the highest number of NIS (9) was the eDNA from water in Av1, using COI. Overall, 18S detected approximately 1,6 times higher numbers of OTUs (237-267), phyla (16-21) and species (179-210) than COI, and only 5-6% of species were detected using both markers. Regarding the type of sampling method, the zooplankton samples retrieved the highest number of phyla (20 in VC; COI: 12 and 18S: 20) and more species (40 to 155; COI: 90 and 18S: 155), namely from Mollusca and Annelida. Between the three methods, there were only 21 (COI) to 28% (18S) of shared species. Crustacea dominated most samples collected from hard substrates. As for marinas, VC had the highest number of recovered OTUs (267), phyla (21) and species (210), when analyzed with the 18S marker, and the lowest number of OTUs (94) and species (86) was recovered in Av1 with COI. Coincidently, this was also the marina with the highest number of NIS probably due to its more exposed location. These results show the efficiency of NIS detection using (e)DNA metabarcoding but reveal the need to employ different molecular markers and sampling methodologies to guarantee a more comprehensive surveillance and detection of NIS in these environmentsNIS-DNA: Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools (PTDC/BIA-BMA/29754/2017). Ana S. Lavrador was supported by grant UI/BD/150871/202

Spatial modelling and mapping of urban fire occurrence in Portugal

Funding Information: This work is funded by national funds through the FCT - Fundação para a Ciência e a Tecnologia , I.P., under the scope of the project DSAIPA/DS/0088/2019 and research and development units UNIDEMI (project UIDB/00667/2020 ) and NOVAMath (projects UIDB/00297/2020 and UIDP/00297/2020 ). Publisher Copyright: © 2023 The Author(s)Fires in urban areas typically carry severe consequences. High population density together with the complexity of urban network potentially imply significant impacts in property loss, physical damage and life losses. However, despite the impact that fires may have in urban areas, research in urban fire prediction remains limited. In this study, we modelled urban fire occurrences while making a comparative analysis of different strategies to account for spatial autocorrelation. Considering space dependence in addition to a range of social-economic explanatory variables has proven to strengthen the validity of the fitted models. The spatial Durbin error model, including population density, degraded buildings density and buying power, was selected as having the best fit. This model allowed to map the estimated probability of fire occurrence across Portugal, revealing a spatial pattern with clusters centred on the two main Portuguese city districts (Lisboa and Porto). Ultimately, the analysis of the relation between the observed urban fire incidence and the actual number of fire stations in each municipality allowed to underline the need for planning the spatial configuration of fire stations, both in number and location, at a regional scale.publishersversionpublishe

can a rapid local cooling intervention help young soccer players?

The effects of a cooling strategy following repeated high-intensity running (RHIR) on soccer kicking performance in a hot environment (>30ºC) were investigated in youth soccer players. Fifteen academy under-17 players participated. In Experiment 1, players completed an all-out RHIR protocol (10×30 m, with 30s intervals). In Experiment 2 (cross-over design), participants performed this running protocol under two conditions: (1) following RHIR 5 minutes of cooling where ice packs were applied to the quadriceps/hamstrings, (2) a control condition involving passive resting. Perceptual measures [ratings of perceived exertion (RPE), pain and recovery], thigh temperature and kick-derived video three-dimensional kinematics (lower limb) and performance (ball speed and two-dimensional placement indices) were collected at baseline, post-exercise and intervention. In Experiment 1, RHIR led to small- to-large impairments (p < 0.03;d = −0.42–-1.83) across perceptual, kinematic and performance measures. In experiment 2, RPE (p < 0.01; Kendall’s W = 0.30) and mean radial error (p = 0.057; η2 = 0.234) increased only post-control. Significant small declines in ball speed were also observed post-control (p < 0.05; d = 0.35). Post-intervention foot centre-of-mass velocity was moderately faster in the cooling compared to control condition (p = 0.04; d = 0.60). In youth soccer players, a short cooling period was beneficial in counteracting declines in kicking performance, in particular ball placement, following intense running activity in the heat.9E1A-F9DD-3EB8 | Filipe Manuel ClementeN/

The BINGO Project IV: Simulations for mission performance assessment and preliminary component separation steps

The large-scale distribution of neutral hydrogen (HI) in the Universe is luminous through its 21 cm emission. The goal of the Baryon Acoustic Oscillations from Integrated Neutral Gas Observations -- BINGO -- radio telescope is to detect baryon acoustic oscillations (BAOs) at radio frequencies through 21 cm intensity mapping (IM). The telescope will span the redshift range 0.127 $< z <$ 0.449 with an instantaneous field-of-view of $14.75^{\circ} \times 6.0^{\circ}$. In this work we investigate different constructive and operational scenarios of the instrument by generating sky maps as they would be produced by the instrument. In doing this we use a set of end-to-end IM mission simulations. The maps will additionally be used to evaluate the efficiency of a component separation method (GNILC). We have simulated the kind of data that would be produced in a single-dish IM experiment such as BINGO. According to the results obtained, we have optimized the focal plane design of the telescope. In addition, the application of the GNILC method on simulated data shows that it is feasible to extract the cosmological signal across a wide range of multipoles and redshifts. The results are comparable with the standard principal component analysis method.Comment: 16 pages. Version to appear in A&

The BINGO Project IX: Search for Fast Radio Bursts -- A Forecast for the BINGO Interferometry System

The Baryon Acoustic Oscillations (BAO) from Integrated Neutral Gas Observations (BINGO) radio telescope will use the neutral Hydrogen emission line to map the Universe in the redshift range $0.127 \le z \le 0.449$, with the main goal of probing BAO. In addition, the instrument optical design and hardware configuration support the search for Fast Radio Bursts (FRBs). In this work, we propose the use of a BINGO Interferometry System (BIS) including new auxiliary, smaller, radio telescopes (hereafter \emph{outriggers}). The interferometric approach makes it possible to pinpoint the FRB sources in the sky. We present here the results of several BIS configurations combining BINGO horns with and without mirrors ($4$ m, $5$ m, and $6$ m) and 5, 7, 9, or 10 for single horns. We developed a new {\tt Python} package, the {\tt FRBlip}, which generates synthetic FRB mock catalogs and computes, based on a telescope model, the observed signal-to-noise ratio (S/N) that we used to compute numerically the detection rates of the telescopes and how many interferometry pairs of telescopes (\emph{baselines}) can observe an FRB. FRBs observed by more than one baseline are the ones whose location can be determined. We thus evaluate the performance of BIS regarding FRB localization. We found that BIS will be able to localize 23 FRBs yearly with single horn outriggers in the best configuration (using 10 outriggers of 6 m mirrors), with redshift $z \leq 0.96$; the full localization capability depends on the number and the type of the outriggers. Wider beams are best to pinpoint FRB sources because potential candidates will be observed by more baselines, while narrow beams look deep in redshift. The BIS can be a powerful extension of the regular BINGO telescope, dedicated to observe hundreds of FRBs during Phase 1. Many of them will be well localized with a single horn + 6 m dish as outriggers.(Abridged)Comment: 12 pages, 9 figures, 5 tables, submitted to A&

Parallel adaptation of rabbit populations to myxoma virus.

In the 1950s the myxoma virus was released into European rabbit populations in Australia and Europe, decimating populations and resulting in the rapid evolution of resistance. We investigated the genetic basis of resistance by comparing the exomes of rabbits collected before and after the pandemic. We found a strong pattern of parallel evolution, with selection on standing genetic variation favoring the same alleles in Australia, France, and the United Kingdom. Many of these changes occurred in immunity-related genes, supporting a polygenic basis of resistance. We experimentally validated the role of several genes in viral replication and showed that selection acting on an interferon protein has increased the protein's antiviral effect.This work was supported by grants from the Programa Operacional Potencial Humano–Quadro de Referência Estratégica Nacional funds from the European Social Fund and Portuguese Ministério da Ciência, Tecnologia e Ensino Superior to M.C. (IF/00283/2014/CP1256/CT0012), to P.J.E. (IF/00376/2015) and to J.M.A. (SFRH/BD/72381/2010). AM was supported by the European Research Council (grant 647787-LocalAdaptation). FJ was supported by the European Research Council (grant 281668). LL was supported by the European Research Council grant (339941-ADAPT). McFadden Lab is supported by National Institute of Health (NIH) grant R01 AI080607. S.C.G. holds a Sir Henry Dale Fellowship, co-funded by the Wellcome Trust and the Royal Society (098406/Z/12/Z)