Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations

<p>Abstract</p> <p>Background</p> <p>Genome scans are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation, but on their own, they are often helpless at identifying the specific gene(s) or mutation(s) targeted by selection. This shortcoming is hopefully bound to disappear in the near future, thanks to the wealth of new genomic resources that are currently being developed for many species. In this article, we provide a foretaste of this exciting new era by conducting a genome scan in the mosquito <it>Aedes aegypti </it>with the aim to look for candidate genes involved in resistance to <it>Bacillus thuringiensis </it>subsp. <it>israelensis </it>(<it>Bti</it>) insecticidal toxins.</p> <p>Results</p> <p>The genome of a <it>Bti</it>-resistant and a <it>Bti</it>-susceptible strains was surveyed using about 500 MITE-based molecular markers, and the loci showing the highest inter-strain genetic differentiation were sequenced and mapped on the <it>Aedes aegypti </it>genome sequence. Several good candidate genes for <it>Bti</it>-resistance were identified in the vicinity of these highly differentiated markers. Two of them, coding for a cadherin and a leucine aminopeptidase, were further examined at the sequence and gene expression levels. In the resistant strain, the cadherin gene displayed patterns of nucleotide polymorphisms consistent with the action of positive selection (e.g. an excess of high compared to intermediate frequency mutations), as well as a significant under-expression compared to the susceptible strain.</p> <p>Conclusion</p> <p>Both sequence and gene expression analyses agree to suggest a role for positive selection in the evolution of this cadherin gene in the resistant strain. However, it is unlikely that resistance to <it>Bti </it>is conferred by this gene alone, and further investigation will be needed to characterize other genes significantly associated with <it>Bti </it>resistance in <it>Ae. aegypti</it>. Beyond these results, this article illustrates how genome scans can build on the body of new genomic information (here, full genome sequence and MITE characterization) to finally hold their promises and help pinpoint candidate genes for adaptation and speciation.</p

Homodyne estimation of Gaussian quantum discord

We address the experimental estimation of Gaussian quantum discord for two-mode squeezed thermal state, and demonstrate a measurement scheme based on a pair of homodyne detectors assisted by Bayesian analysis which provides nearly optimal estimation for small value of discord. Besides, though homodyne detection is not optimal for Gaussian discord, the noise ratio to the ultimate quantum limit, as dictacted by the quantum Cramer-Rao bound, is limited to about 10 dB.Comment: 5+3 pages, 3 figures, published versio

A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection

<p>Abstract</p> <p>Background</p> <p>For most organisms, developing hundreds of genetic markers spanning the whole genome still requires excessive if not unrealistic efforts. In this context, there is an obvious need for methodologies allowing the low-cost, fast and high-throughput genotyping of virtually any species, such as the Diversity Arrays Technology (DArT). One of the crucial steps of the DArT technique is the genome complexity reduction, which allows obtaining a genomic representation characteristic of the studied DNA sample and necessary for subsequent genotyping. In this article, using the mosquito <it>Aedes aegypti </it>as a study model, we describe a new genome complexity reduction method taking advantage of the abundance of miniature inverted repeat transposable elements (MITEs) in the genome of this species.</p> <p>Results</p> <p><it>Ae. aegypti </it>genomic representations were produced following a two-step procedure: (1) restriction digestion of the genomic DNA and simultaneous ligation of a specific adaptor to compatible ends, and (2) amplification of restriction fragments containing a particular MITE element called <it>Pony </it>using two primers, one annealing to the adaptor sequence and one annealing to a conserved sequence motif of the <it>Pony </it>element. Using this protocol, we constructed a library comprising more than 6,000 DArT clones, of which at least 5.70% were highly reliable polymorphic markers for two closely related mosquito strains separated by only a few generations of artificial selection. Within this dataset, linkage disequilibrium was low, and marker redundancy was evaluated at 2.86% only. Most of the detected genetic variability was observed between the two studied mosquito strains, but individuals of the same strain could still be clearly distinguished.</p> <p>Conclusion</p> <p>The new complexity reduction method was particularly efficient to reveal genetic polymorphisms in <it>Ae. egypti</it>. Overall, our results testify of the flexibility of the DArT genotyping technique and open new prospects as regards its application to a wider range of species, including animals which have been refractory to it so far. DArT has also a role to play in the current burst of whole-genome scans carried out in various organisms, which track signatures of selection in order to unravel the basis of genetic adaptation.</p

Analysis of the potential of near-ground measurements of CO2 and CH4 in London, UK, for the monitoring of city-scale emissions using an atmospheric transport model

Carbon dioxide (CO2) and methane (CH4) mole fractions were measured at four near-ground sites located in and around London during the summer of 2012 with a view to investigating the potential of assimilating such measurements in an atmospheric inversion system for the monitoring of the CO2 and CH4 emissions in the London area. These data were analysed and compared with simulations using a modelling framework suited to building an inversion system: a 2 km horizontal resolution south of England configuration of the transport model CHIMERE driven by European Centre for Medium-Range Weather Forecasts (ECMWF) meteorological forcing, coupled to a 1 km horizontal resolution emission inventory (the UK National Atmospheric Emission Inventory). First comparisons reveal that local sources, which cannot be represented in the model at a 2 km resolution, have a large impact on measurements. We evaluate methods to filter out the impact of some of the other critical sources of discrepancies between the measurements and the model simulation except that of the errors in the emission inventory, which we attempt to isolate. Such a separation of the impact of errors in the emission inventory should make it easier to identify the corrections that should be applied to the inventory. Analysis is supported by observations from meteorological sites around the city and a 3-week period of atmospheric mixing layer height estimations from lidar measurements. The difficulties of modelling the mixing layer depth and thus CO2 and CH4 concentrations during the night, morning and late afternoon lead to focusing on the afternoon period for all further analyses. The discrepancies between observations and model simulations are high for both CO2 and CH4 (i.e. their root mean square (RMS) is between 8 and 12 parts per million (ppm) for CO2 and between 30 and 55 parts per billion (ppb) for CH4 at a given site). By analysing the gradients between the urban sites and a suburban or rural reference site, we are able to decrease the impact of uncertainties in the fluxes and transport outside the London area and in the model domain boundary conditions. We are thus able to better focus attention on the signature of London urban CO2 and CH4 emissions in the atmospheric CO2 and CH4 concentrations. This considerably improves the statistical agreement between the model and observations for CO2 (with model–data RMS discrepancies that are between 3 and 7 ppm) and to a lesser degree for CH4 (with model–data RMS discrepancies that are between 29 and 38 ppb). Between one of the urban sites and either the rural or suburban reference site, selecting the gradients during periods wherein the reference site is upwind of the urban site further decreases the statistics of the discrepancies in general, though not systematically. In a further attempt to focus on the signature of the city anthropogenic emission in the mole fraction measurements, we use a theoretical ratio of gradients of carbon monoxide (CO) to gradients of CO2 from fossil fuel emissions in the London area to diagnose observation-based fossil fuel CO2 gradients, and compare them with the fossil fuel CO2 gradients simulated with CHIMERE. This estimate increases the consistency between the model and the measurements when considering only one of the two urban sites, even though the two sites are relatively close to each other within the city. While this study evaluates and highlights the merit of different approaches for increasing the consistency between the mesoscale model and the near-ground data, and while it manages to decrease the random component of the analysed model–data discrepancies to an extent that should not be prohibitive to extracting the signal from the London urban emissions, large biases, the sign of which depends on the measurement sites, remain in the final model–data discrepancies. Such biases are likely related to local emissions to which the urban near-ground sites are highly sensitive. This questions our current ability to exploit urban near-ground data for the atmospheric inversion of city emissions based on models at spatial resolution coarser than 2 km. Several measurement and modelling concepts are discussed to overcome this challenge

Comparaison des propriétés en frottement d’un revêtement d’anodisation dure avec une oxydation micro-arcs formée sur aluminium.

Une étude menée dans le cadre du projet ROMA (Reprise mécanique de l’oxydation micro-arcs) pour lequel collabore la société Galvanoplastie Industrielle Toulousaine (GIT) et le Laboratoire Génie de Production (LGP) de Tarbes a permis de mettre en place un essai reproductible pour comparer les propriétés tribologiques de revêtements d’OAD et d’OMA. Explications

Disentangling methane and carbon dioxide sources and transport across the Russian Arctic from aircraft measurements

A more accurate characterization of the sources and sinks of methane (CH4) and carbon dioxide (CO2) in the vulnerable Arctic environment is required to better predict climate change. A large-scale aircraft campaign took place in September 2020 focusing on the Siberian Arctic coast. CH4 and CO2 were measured in situ during the campaign and form the core of this study. Measured ozone (O3) and carbon monoxide (CO) are used here as tracers. Median CH4 mixing ratios are fairly higher than the monthly mean hemispheric reference (Mauna Loa, Hawaii, US) with 1890&ndash;1969 ppb vs 1887 ppb respectively, while CO2 mixing ratios from all flights are lower (408.09&ndash;411.50 ppm vs 411.52 ppm). We also report on three case studies. Our analysis suggests that during the campaign the European part of Russia&rsquo;s Arctic and Western Siberia were subject to long-range transport of polluted air masses, while the East was mainly under the influence of local emissions of greenhouse gases. The relative contributions of the main anthropogenic and natural sources of CH4 are simulated using the Lagrangian model FLEXPART in order to identify dominant sources in the boundary layer and in the free troposphere. In western terrestrial flights, air masses composition is influenced by emissions from wetlands and anthropogenic activities (waste management, fossil fuel industry and to a lesser extent the agricultural sector), while in the East, emissions are dominated by freshwaters, wetlands, and the oceans, with a likely contribution from anthropogenic sources related to fossil fuels. Our results highlight the importance of the contributions from freshwater and oceans emissions. Considering the large uncertainties associated to them, our study suggests that the emissions from these aquatic sources should receive more attention in Siberia.</p

Association of Plasma Aß Peptides with Blood Pressure in the Elderly

Background Aß peptides are often considered as catabolic by-products of the amyloid ß protein precursor (APP), with unknown physiological functions. However, several biological properties have been tentatively attributed to these peptides, including a role in vasomotion. We assess whether plasma Aß peptide levels might be associated with systolic and diastolic blood pressure values (SBP and DBP, respectively). Methodology/Principal Findings Plasma Aß1-40 and Aß1-42 levels were measured using an xMAP-based assay in 1,972 individuals (none of whom were taking antihypertensive drugs) from 3 independent studies: the French population-based 3C and MONA-LISA (Lille) studies (n = 627 and n = 769, respectively) and the Australian, longitudinal AIBL study (n = 576). In the combined sample, the Aß1-42/ Aß1-40 ratio was significantly and inversely associated with SBP (p = 0.03) and a similar trend was observed for DBP (p = 0.06). Using the median age (69) as a cut-off, the Aß1-42/Aß1-40 ratio was strongly associated with both SBP and DBP in elderly individuals (p = 0.002 and p = 0.03, respectively). Consistently, a high Aß1-42/ Aß1-40 ratio was associated with a lower risk of hypertension in both the combined whole sample (odds ratio [OR], 0.71; 95% confidence interval [CI], 0.56-0.90) and (to an even greater extent) in the elderly subjects (OR, 0.53; 95% CI, 0.37–0.75). Lastly, all these associations appeared to be primarily driven by the level of plasma Aß1-40. Conclusion The plasma Aß1-42/Aß1-40 ratio is inversely associated with SBP, DBP and the risk of hypertension in elderly subjects, suggesting that Aß peptides affect blood pressure in vivo. These results may be particularly relevant in Alzheimer\u27s disease, in which a high Aß1-42/Aß1-40 plasma ratio is reportedly associated with a decreased risk of incident disease