Analysis of both the envelope sequence and the complete genome of a HIV-1 subtype f cluster of rapid expansion in Galicia: coreceptor use prediction and phylogeny

La epidemia por VIH-1 en España, al igual que en el resto de Europa occidental, está dominada por el subtipo B. Sin embargo, recientemente se ha descrito la rápida expansión de un cluster de subsubtipo F1 entre hombres que tienen relaciones sexuales con hombres en Galicia. Los objetivos de este trabajo son analizar la secuencia de la envoltura de los virus del mencionado cluster para predicción de utilización de correceptores y presencia de aminoácidos característicos, así como caracterizar secuencias de genomas completos, determinando las relaciones filogenéticas con virus de subtipo F de otros países. Los análisis filogenéticos permitieron determinar relaciones del cluster F con virus de Brasil, Suiza, Bélgica, Francia y Gran Bretaña. Por otra parte, se han encontrado posiciones características del cluster en la región V3, diferentes de otras cepas F1, así como en otras regiones de la envoltura. Aparte, se han identificado mutaciones características asociadas a tropismo X4. El cluster de VIH-1 de subtipo F recientemente expandido en Galicia procede de una variante ampliamente diseminada en Europa occidental. Los virus de dicho cluster presentan aminoácidos característicos en la envoltura, identificándose en algunos de ellos mutaciones asociadas a tropismo X4, de potencial relevancia biológicaThe HIV-1 epidemic in Spain, as in the rest of Western Europe, is dominated by subtype B. However, it has recently been reported that a subsubtype F1 cluster has rapidly expanded among men who have sex with men in Galicia. The objectives of this work are to analyze the virus envelope sequence of the aforementioned cluster to predict the use of coreceptors and to examine the presence of characteristic amino acids, as well as to characterize full-length genome sequences, determining the phylogenetic relations with subtype F viruses from other countries. The phylogenetic analyses allowed to determine the relation of the Galician F cluster with viruses from Brazil, Switzerland, Belgium, France and Great Britain. On the other hand, characteristic amino acid residues were found in the V3 loop of viruses of the cluster, differing from other F1 strains, as well as in other regions of the envelope. Additionally, characteristic mutations associated with X4 tropism were identified. The HIV-1 subtype F cluster recently expanded in Galicia derives from a variant widely disseminated in Western Europe. The viruses of the mentioned cluster show characteristic amino acids in the envelope, with mutations associated with X4 tropism having been identified in some of them, which are of potential biological relevance

Spatial variation of mammal richness, functional and phylogenetic diversity in the Mexican transition zone

The multi-dimensional analysis of biodiversity addresses several components, including the number of species, as well as their ecological and evolutionary identities. This approach can lead to key biodiversity patterns that remain covered when only species richness is studied. The convergence of the Nearctic and Neotropical biogeographic regions in Mexico suggests spatial variation in biodiversity patterns. In this study we analysed species richness, functional diversity, and phylogenetic diversity of mammal assemblages in relation to abiotic variables and their variation across the biogeographic regions. Our results showed contrasting patterns among biodiversity dimensions: 1) species richness followed the typical global pattern of a gradual increase from the Nearctic towards the Neotropical region, 2) phylogenetic diversity was highest in the Transitional region; and 3) functional diversity was highest in the Neotropical region, but not different between the Nearctic and Transitional regions. Abiotic variables had a significant relation with variation in biodiversity dimensions, but they had a higher contribution to explain functional diversity than species richness and phylogenetic diversity. The decoupled patterns of functional and phylogenetic diversity among the biogeographical regions highlight the complementarity between these dimensions and the importance of transitional regions, and suggest that several historical, environmental and ecological processes may be structuring mammal assemblages. Likewise, different approaches should be followed in accordance to variation of functional and phylogenetic traits among regions

Software-assisted data processing workflow for intact glycoprotein mass spectrometry

Intact protein analysis by mass spectrometry is important for several applications such as assessing post-translational modifications and biotransformation. In particular, intact protein analysis allows the detection of proteoforms that are commonly missed by other approaches such as proteolytic digestion followed by bottom-up analysis. Two quantification methods are mainly used for intact protein data quantification, namely the extracted ion and deconvolution approaches. However, a consensus with regard to a single best practice for intact protein data processing is lacking. Furthermore, many data processing tools are not fit-for-purpose and, as a result, the analysis of intact proteins is laborious and lacks the throughput required to be implemented for the analysis of clinical cohorts. Therefore, in this study, we investigated the application of a software-assisted data analysis and processing workflow in order to streamline intact protein integration, annotation, and quantification via deconvolution. In addition, the assessment of orthogonal data sets generated via middle-up and bottom-up analysis enabled the cross-validation of cleavage proteoform assignments present in seminal prostate-specific antigen (PSA). Furthermore, deconvolution quantification of PSA from patients’ urine revealed results that were comparable with manually performed quantification based on extracted ion electropherograms. Overall, the presented workflow allows fast and efficient processing of intact protein data. The raw data is available on MassIVE using the identifier MSV000086699. Proteomic

Calibration of semi-analytic models of galaxy formation using Particle Swarm Optimization

We present a fast and accurate method to select an optimal set of parameters in semi-analytic models of galaxy formation and evolution (SAMs). Our approach compares the results of a model against a set of observables applying a stochastic technique called Particle Swarm Optimization (PSO), a self-learning algorithm for localizing regions of maximum likelihood in multidimensional spaces that outperforms traditional sampling methods in terms of computational cost. We apply the PSO technique to the SAG semi-analytic model combined with merger trees extracted from a standard $\Lambda$CDM N-body simulation. The calibration is performed using a combination of observed galaxy properties as constraints, including the local stellar mass function and the black hole to bulge mass relation. We test the ability of the PSO algorithm to find the best set of free parameters of the model by comparing the results with those obtained using a MCMC exploration. Both methods find the same maximum likelihood region, however the PSO method requires one order of magnitude less evaluations. This new approach allows a fast estimation of the best-fitting parameter set in multidimensional spaces, providing a practical tool to test the consequences of including other astrophysical processes in SAMs.Comment: 11 pages, 4 figures, 1 table. Accepted for publication in ApJ. Comments are welcom

Severe Deoxygenation Event Caused by the 2011 Eruption of the Submarine Volcano Tagoro (El Hierro, Canary Islands)

The shallow, near-shore submarine volcano Tagoro erupted in October 2011 at the Mar de las Calmas marine reserve, south of El Hierro island. The injection of lava into the ocean had its strongest episode during November 2011 and lasted until March 2012. During this time, in situ measurements of dissolved oxygen were carried out, using a continuous oxygen sensor constantly calibrated with water samples. A severe deoxygenation was observed in the area, particularly during October-November 2011, which was one of the main causes of the high mortality observed among the local marine ecosystem. The measured O2 concentrations were as low as 7.71 µmol kg-1, which represents a -96% decrease with respect to unaffected waters. The oxygen depletion was found in the first 250 m of the water column, with peaks between 70-120 m depth. The deoxygenated plume covered an area of at least 464 km2, distributed particularly south and south-west of the volcano, with occasional patches found north of the island. The oxygen levels were also monitored through the following years, during the degassing stage of the volcano, when oxygen depletion was no longer observed. Additionally, during the eruption, an island-generated anticyclonic eddy interacted with the volcanic plume and transported it for at least 80 km, where the O2 measurements still showed a -8% decrease after mixing and dilution. This feature draws attention to the permanence and transport of volcanic plumes far away from their source and long after the emission.En prens

Acute Impacts of Different Types of Exercise on Circulating α-Klotho Protein Levels

[EN] Elevated plasma α-klotho (αKl) protects against several ageing phenotypes and has been proposed as a biomarker of a good prognosis for different diseases. The beneficial health effects of elevated plasma levels of soluble αKl (SαKl) have been likened to the positive effects of exercise on ageing and chronic disease progression. It has also been established that molecular responses and adaptations differ according to exercise dose. The aim of this study is to compare the acute SαKl response to different exercise interventions, cardiorespiratory, and strength exercise in healthy, physically active men and to examine the behavior of SαKl 72h after acute strength exercise.S