Porcine reproductive and respiratory syndrome virus impacts on gut microbiome in a strain virulence‐dependent fashion

[EN] Porcine reproductive and respiratory syndrome (PRRS) is a viral disease defined by reproductive problems, respiratory distress and a negative impact on growth rate and general condition. Virulent PRRS virus (PRRSV) strains have emerged in the last years with evident knowledge gaps in their impact on the host immune response. Thus, the present study examines the impact of acute PRRS virus (PRRSV) infection, with two strains of different virulence, on selected immune parameters and on the gut microbiota composition of infected pigs using 16S rRNA compositional sequencing. Pigs were infected with a low virulent (PRRS_3249) or a virulent (Lena) PRRSV-1 strain and euthanized at 1, 3, 6, 8 or 13 days post-inoculation (dpi). Faeces were collected from each animal at the necropsy time-point. Alpha and beta diversity analyses demonstrated that infection, particularly with the Lena strain, impacted the microbiome composition from 6 dpi onwards. Taxonomic differences revealed that infected pigs had higher abundance of Treponema and Methanobrevibacter (FDR < 0.05). Differences were more considerable for Lena- than for PRRS_3249-infected pigs, showing the impact of strain virulence in the intestinal changes. Lena-infected pigs had reduced abundancies of anaerobic commensals such as Roseburia, Anaerostipes, Butyricicoccus and Prevotella (P < 0.05). The depletion of these desirable commensals was significantly correlated to infection severity measured by viraemia, clinical signs, lung lesions and immune parameters (IL-6, IFN-γ and Hp serum levels). Altogether, the results from this study demonstrate the indirect impact of PRRSV infection on gut microbiome composition in a strain virulence-dependent fashion and its association with selected immune markersSIJ. G omez-Laguna is supported by a ‘Ram on y Cajal’ contract of the Spanish Ministry of Economy and Competitiveness (RYC-2014-16735). Hector Arg€uello is supported by the ‘Beatriz Galindo’ Programme from the Spanish Ministry of Education (BEAGAL-18-106). This work was partially supported by the Spanish Ministry of Education and Science (AGL2016-76111-R). Research in the Cotter laboratory is funded by Science Foundation Ireland in the form of a centre grants (APC Microbiome Ireland, Grant Number SFI/12/RC/2273, and Vistamilk, Grant Number SFI/16/RC/3835) and by the European Commission under the Horizon 2020 programme under grant number 818368 (MASTER

Porcine reproductive and respiratory syndrome virus impacts on gut microbiome in a strain virulence‐dependent fashion

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease defined by reproductive problems, respiratory distress and a negative impact on growth rate and general condition. Virulent PRRS virus (PRRSV) strains have emerged in the last years with evident knowledge gaps in their impact on the host immune response. Thus, the present study examines the impact of acute PRRS virus (PRRSV) infection, with two strains of different virulence, on selected immune parameters and on the gut microbiota composition of infected pigs using 16S rRNA compositional sequencing. Pigs were infected with a low virulent (PRRS_3249) or a virulent (Lena) PRRSV‐1 strain and euthanized at 1, 3, 6, 8 or 13 days post‐inoculation (dpi). Faeces were collected from each animal at the necropsy time‐point. Alpha and beta diversity analyses demonstrated that infection, particularly with the Lena strain, impacted the microbiome composition from 6 dpi onwards. Taxonomic differences revealed that infected pigs had higher abundance of Treponema and Methanobrevibacter (FDR < 0.05). Differences were more considerable for Lena‐ than for PRRS_3249‐infected pigs, showing the impact of strain virulence in the intestinal changes. Lena‐infected pigs had reduced abundancies of anaerobic commensals such as Roseburia, Anaerostipes, Butyricicoccus and Prevotella (P < 0.05). The depletion of these desirable commensals was significantly correlated to infection severity measured by viraemia, clinical signs, lung lesions and immune parameters (IL‐6, IFN‐γ and Hp serum levels). Altogether, the results from this study demonstrate the indirect impact of PRRSV infection on gut microbiome composition in a strain virulence‐dependent fashion and its association with selected immune markers.info:eu-repo/semantics/publishedVersio

Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms

P. 1-17Background: The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms. Results: Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms. Conclusions: Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production.S

Porcine reproductive and respiratory syndrome virus impacts on gut microbiome in a strain virulence-dependent fashion

Altres ajuts: Science Foundation Ireland SFI/12/RC/2273 i Vistamilk SFI/16/RC/3835Porcine reproductive and respiratory syndrome (PRRS) is a viral disease defined by reproductive problems, respiratory distress and a negative impact on growth rate and general condition. Virulent PRRS virus (PRRSV) strains have emerged in the last years with evident knowledge gaps in their impact on the host immune response. Thus, the present study examines the impact of acute PRRS virus (PRRSV) infection, with two strains of different virulence, on selected immune parameters and on the gut microbiota composition of infected pigs using 16S rRNA compositional sequencing. Pigs were infected with a low virulent (PRRS_3249) or a virulent (Lena) PRRSV-1 strain and euthanized at 1, 3, 6, 8 or 13 days post-inoculation (dpi). Faeces were collected from each animal at the necropsy time-point. Alpha and beta diversity analyses demonstrated that infection, particularly with the Lena strain, impacted the microbiome composition from 6 dpi onwards. Taxonomic differences revealed that infected pigs had higher abundance of Treponema and Methanobrevibacter (FDR < 0.05). Differences were more considerable for Lena- than for PRRS_3249-infected pigs, showing the impact of strain virulence in the intestinal changes. Lena-infected pigs had reduced abundancies of anaerobic commensals such as Roseburia, Anaerostipes, Butyricicoccus and Prevotella (P < 0.05). The depletion of these desirable commensals was significantly correlated to infection severity measured by viraemia, clinical signs, lung lesions and immune parameters (IL-6, IFN-γ and Hp serum levels). Altogether, the results from this study demonstrate the indirect impact of PRRSV infection on gut microbiome composition in a strain virulence-dependent fashion and its association with selected immune markers. PRRSV, a porcine respiratory pathogen, indirectly impacts on gut microbiome composition in a strain virulence dependent fashion in association with selected immune markers

Alert classification for the ALeRCE broker system: The real-time stamp classifier

We present a real-time stamp classifier of astronomical events for the Automatic Learning for the Rapid Classification of Events broker, ALeRCE. The classifier is based on a convolutional neural network, trained on alerts ingested from the Zwicky Transient Facility (ZTF). Using only the science, reference, and difference images of the first detection as inputs, along with the metadata of the alert as features, the classifier is able to correctly classify alerts from active galactic nuclei, supernovae (SNe), variable stars, asteroids, and bogus classes, with high accuracy (~94%) in a balanced test set. In order to find and analyze SN candidates selected by our classifier from the ZTF alert stream, we designed and deployed a visualization tool called SN Hunter, where relevant information about each possible SN is displayed for the experts to choose among candidates to report to the Transient Name Server database. From 2019 June 26 to 2021 February 28, we have reported 6846 SN candidates to date (11.8 candidates per day on average), of which 971 have been confirmed spectroscopically. Our ability to report objects using only a single detection means that 70% of the reported SNe occurred within one day after the first detection. ALeRCE has only reported candidates not otherwise detected or selected by other groups, therefore adding new early transients to the bulk of objects available for early follow-up. Our work represents an important milestone toward rapid alert classifications with the next generation of large etendue telescopes, such as the Vera C. Rubin Observatory.The authors acknowledge support from the National Agency of Research and Development’s Millennium Science Initiative through grant IC12009, awarded to the Millennium Institute of Astrophysics (RC, ER, CV, FF, PE, GP, FEB, IR, PSS, GC, SE, Ja, EC, DR, DRM, MC) and from the National Agency for Research and Development (ANID) grants: BASAL Center of Mathematical Modelling AFB-170001 (CV, FF, IR, ECN, CS, ECI) and Centro de Astrofísica y Tecnologías Afines AFB170002 (FEB, PSS, MC); FONDECYT Regular #1171678 (PE), #1200710 (FF), #1190818(FEB), #1200495 (FEB), #1171273 (MC), #1201793(GP); FONDECYT Postdoctorado #3200250 (PSS); FONDECYT Iniciación #11191130 (CV); Magíster Nacional 2019 #22190947 (ER). This work was funded in part by project CORFO 10CEII-9157 Inria Chile (PS). The authors acknowledge financial support from the Spanish Ministry of Science, Innovation, and Universities (MICIU) under the 2019 Ramón y Cajal program RYC2019- 027683 (LG)

Structural and vibrational study of pseudocubic CdIn2Se4 under compression

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp5077565We report a comprehensive experimental and theoretical study of the structural and vibrational properties of a-CdIn2Se4 under compression. Angle-dispersive synchrotron X-ray diffraction and Raman spectroscopy evidence that this ordered-vacancy compound with pseudocubic structure undergoes a phase transition (7 GPa) toward a disordered rocksalt structure as observed in many other ordered-vacancy compounds. The equation of state and the pressure dependence of the Raman-active modes of this semiconductor have been determined and compared both to ab initio total energy and lattice dynamics calculations and to related compounds. Interestingly, on decreasing pressure, at similar to 2 GPa, CdIn2Se4 transforms into a spinel structure which, according to calculations, is energetically competitive with the initial pseudocubic phase. The phase behavior of this compound under compression and the structural and compressibility trends in AB(2)Se(4) selenides are discussed.This study was supported by the Spanish government MEC under Grant Nos: MAT2013-46649-C4-3-P, MAT2013-46649-C4-2-P, MAT2010-21270-C04-03/04, and CTQ2009-14596-C02-01, by MALTA Consolider Ingenio 2010 Project (CSD2007-00045) and by Generalitat Valenciana (GVA-ACOMP-2013-1012). A.M. and P.R-H. acknowledge computing time provided by Red Espanola de Supercomputacion (RES) and MALTA-Cluster, and also to S. Munoz-Rodriguez for providing a data-parsing application. J.A.S. acknowledges Juan de la Cierva fellowship program for financial support.Santamaría Pérez, D.; Gomis, O.; Pereira, ALJ.; Vilaplana Cerda, RI.; Popescu, C.; Sans Tresserras, JÁ.; Manjón Herrera, FJ.... (2014). Structural and vibrational study of pseudocubic CdIn2Se4 under compression. Journal of Physical Chemistry C. 118(46):26987-26999. https://doi.org/10.1021/jp5077565S26987269991184

Structural and vibrational properties of CdAl2S4 under high pressure: Experimental and theoretical approach

"This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp5037926.”The behavior of defect chalcopyrite CdAl2S4 at high pressures and ambient temperature has been investigated in a joint experimental and theoretical study. High-pressure X-ray diffraction and Raman scattering measurements were complemented with theoretical ab initio calculations. The equation of state and pressure dependences of the structural parameters of CdAl2S4 were determined and compared to those of other AB(2)X(4) ordered-vacancy compounds. The pressure dependence of the Raman-active mode frequencies is reported, as well as the theoretical phonon dispersion curves and phonon density of states at 1 atm. Our measurements suggest that defect chalcopyrite CdAl2S4 undergoes a phase transition above 15 GPa to a disordered-rocksalt structure, whose equation of state was also obtained up to 25 GPa. In a downstroke from 25 GPa to 1 atm, our measurements indicate that CdAl2S4 does not return to the defect chalcopyrite phase; it partially retains the disordered-rocksalt phase and partially transforms into the spinel structure. The nature of the spinel structure was confirmed by the good agreement of our experimental results with our theoretical calculations. All in all, our experimental and theoretical results provide evidence that the spinel and defect chalcopyrite phases of CdAl2S4 are competitive at 1 atm. This result opens the way to the synthesis of spinel-type CdAl2S4 at near-ambient conditions.Financial support from the Spanish Consolider Ingenio 2010 Program (Project CSD2007-00045) is acknowledged. This work was also supported by Spanish MICCIN under Project MAT2010-21270-C04-03/04 and by Vicerrectorado de Investigacion de la Universitat Politecnica de Valencia under Projects UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11. Supercomputer time was provided by the Red Espanola de Supercomputacion (RES) and the MALTA cluster. J.A.S. acknowledges the Juan de la Cierva fellowship program for financial support. AM. and P.R.-H. acknowledge S. Munoz Rodriguez for providing a data-parsing application.Sans Tresserras, JÁ.; Santamaría Pérez, D.; Popescu, C.; Gomis, O.; Manjón Herrera, FJ.; Vilaplana Cerda, RI.; Muñoz, A.... (2014). Structural and vibrational properties of CdAl2S4 under high pressure: Experimental and theoretical approach. Journal of Physical Chemistry C. 118(28):15363-15374. https://doi.org/10.1021/jp5037926S15363153741182

NEXTGENDEM: información genética, geoespacial y supercomputación para mejorar la gestión de especies y espacios en Macaronesia

Project NEXTGENDEM (MAC2/4.6d/236, https://lupus.itccanarias.org/nextgendem/es/) complements multiple research disciplines to provide verified and validated scientific data that help managers make more informed conservation decisions. As a result of the mobilization and enrichment of the sample and data banks of the Jardín Botánico Canario “Viera y Clavijo” -UA CSIC and the Instituto Nacional de Investigação e Desenvolvimento Agrário de Cabo Verde, tools will be developed for the estimation of phylogenetic diversity of the terrestrial endemic flora of these islands, the approximation to the molecular taxonomic identification of samples, phylogenetic reconstruction, and territorial analysis merging biotic and abiotic variables. Our main objective is to organise, analyse and apply the most relevant scientific knowledge to guide in situ and ex situ actions to improve the conservation status of the flora of Gran Canaria (Canary Islands) and Santiago (Cape Verde), although we plan to incorporate other Macaronesian territories in future projectsEl proyecto NEXTGENDEM (MAC2/4.6d/236, https://lupus.itccanarias.org/nextgendem/es/) complementa múltiples disciplinas de investigación para proporcionar datos científicos contrastados y validados que faciliten a los gestores la toma de decisiones de conservación más informadas. A consecuencia de la movilización y el enriquecimiento de los bancos de muestras y datos del Jardín Botánico Canario ¿Viera y Clavijo¿ ¿ UA CSIC y del Instituto Nacional de Investigação e Desenvolvimento Agrário de Cabo Verde, se pondrán a punto herramientas para la estimación de la diversidad filogenética de la flora terrestre insular, la aproximación a la identificación taxonómica molecular de muestras, la reconstrucción de filogenias, y el análisis territorial integrado con variables bióticas y abióticas. Nuestro objetivo principal es organizar, analizar y aplicar el conocimiento científico más relevante para guiar actuaciones in situ y ex situ que mejoren el estado de conservación de las floras de Gran Canaria (Islas Canarias) y Santiago (Cabo Verde), aunque prevemos incorporar otros territorios macaronésicos en futuros proyecto

National trends in total cholesterol obscure heterogeneous changes in HDL and non-HDL cholesterol and total-to-HDL cholesterol ratio : a pooled analysis of 458 population-based studies in Asian and Western countries

Background: Although high-density lipoprotein (HDL) and non-HDL cholesterol have opposite associations with coronary heart disease, multi-country reports of lipid trends only use total cholesterol (TC). Our aim was to compare trends in total, HDL and nonHDL cholesterol and the total-to-HDL cholesterol ratio in Asian and Western countries. Methods: We pooled 458 population-based studies with 82.1 million participants in 23 Asian and Western countries. We estimated changes in mean total, HDL and non-HDL cholesterol and mean total-to-HDL cholesterol ratio by country, sex and age group. Results: Since similar to 1980, mean TC increased in Asian countries. In Japan and South Korea, the TC rise was due to rising HDL cholesterol, which increased by up to 0.17 mmol/L per decade in Japanese women; in China, it was due to rising non-HDL cholesterol. TC declined in Western countries, except in Polish men. The decline was largest in Finland and Norway, at similar to 0.4 mmol/L per decade. The decline in TC in most Western countries was the net effect of an increase in HDL cholesterol and a decline in non-HDL cholesterol, with the HDL cholesterol increase largest in New Zealand and Switzerland. Mean total-to-HDL cholesterol ratio declined in Japan, South Korea and most Western countries, by as much as similar to 0.7 per decade in Swiss men (equivalent to similar to 26% decline in coronary heart disease risk per decade). The ratio increased in China. Conclusions: HDL cholesterol has risen and the total-to-HDL cholesterol ratio has declined in many Western countries, Japan and South Korea, with only a weak correlation with changes in TC or non-HDL cholesterol.Peer reviewe

Contributions of mean and shape of blood pressure distribution to worldwide trends and variations in raised blood pressure: A pooled analysis of 1018 population-based measurement studies with 88.6 million participants

© The Author(s) 2018. Background: Change in the prevalence of raised blood pressure could be due to both shifts in the entire distribution of blood pressure (representing the combined effects of public health interventions and secular trends) and changes in its high-blood-pressure tail (representing successful clinical interventions to control blood pressure in the hypertensive population). Our aim was to quantify the contributions of these two phenomena to the worldwide trends in the prevalence of raised blood pressure. Methods: We pooled 1018 population-based studies with blood pressure measurements on 88.6 million participants from 1985 to 2016. We first calculated mean systolic blood pressure (SBP), mean diastolic blood pressure (DBP) and prevalence of raised blood pressure by sex and 10-year age group from 20-29 years to 70-79 years in each study, taking into account complex survey design and survey sample weights, where relevant. We used a linear mixed effect model to quantify the association between (probittransformed) prevalence of raised blood pressure and age-group- and sex-specific mean blood pressure. We calculated the contributions of change in mean SBP and DBP, and of change in the prevalence-mean association, to the change in prevalence of raised blood pressure. Results: In 2005-16, at the same level of population mean SBP and DBP, men and women in South Asia and in Central Asia, the Middle East and North Africa would have the highest prevalence of raised blood pressure, and men and women in the highincome Asia Pacific and high-income Western regions would have the lowest. In most region-sex-age groups where the prevalence of raised blood pressure declined, one half or more of the decline was due to the decline in mean blood pressure. Where prevalence of raised blood pressure has increased, the change was entirely driven by increasing mean blood pressure, offset partly by the change in the prevalence-mean association. Conclusions: Change in mean blood pressure is the main driver of the worldwide change in the prevalence of raised blood pressure, but change in the high-blood-pressure tail of the distribution has also contributed to the change in prevalence, especially in older age groups