Study on the concordance between different SNP‐genotyping platforms in sheep

.Different SNP genotyping technologies are commonly used in multiple studies to perform QTL detection, genotype imputation, and genomic predictions. Therefore, genotyping errors cannot be ignored, as they can reduce the accuracy of different procedures applied in genomic selection, such as genomic imputation, genomic predictions, and false-positive results in genome-wide association studies. Currently, whole-genome resequencing (WGR) also offers the potential for variant calling analysis and high-throughput genotyping. WGR might overshadow array-based genotyping technologies due to the larger amount and precision of the genomic information provided; however, its comparatively higher price per individual still limits its use in larger populations. Thus, the objective of this work was to evaluate the accuracy of the two most popular SNP-chip technologies, namely, Affymetrix and Illumina, for high-throughput genotyping in sheep considering high-coverage WGR datasets as references. Analyses were performed using two reference sheep genome assemblies, the popular Oar_v3.1 reference genome and the latest available version Oar_rambouillet_v1.0. Our results demonstrate that the genotypes from both platforms are suggested to have high concordance rates with the genotypes determined from reference WGR datasets (96.59% and 99.51% for Affymetrix and Illumina technologies, respectively). The concordance results provided in the current study can pinpoint low reproducible markers across multiple platforms used for sheep genotyping data. Comparing results using two reference genome assemblies also informs how genome assembly quality can influence genotype concordance rates among different genotyping platforms. Moreover, we describe an efficient pipeline to test the reliability of markers included in sheep SNP-chip panels against WGR datasets available on public databases. This pipeline may be helpful for discarding low-reliability markers before exploiting genomic information for gene mapping analyses or genomic predictionS

Transcriptome analysis of perirenal fat from Spanish Assaf suckling lamb carcasses showing different levels of kidney knob and channel fat

[EN] Introduction: Suckling lamb meat is highly appreciated in European Mediterranean countries because of its mild flavor and soft texture. In suckling lamb carcasses, perirenal and pelvic fat depots account for a large fraction of carcass fat accumulation, and their proportions are used as an indicator of carcass quality. Material and Methods: This study aimed to characterize the genetic mechanisms that regulate fat deposition in suckling lambs by evaluating the transcriptomic differences between Spanish Assaf lambs with significantly different proportions of kidney knob and channel fat (KKCF) depots in their carcasses (4 High-KKCF lambs vs. 4 Low-KKCF lambs). Results: The analyzed fat tissue showed overall dominant expression of white adipose tissue gene markers, although due to the young age of the animals (17–36 days), the expression of some brown adipose tissue gene markers (e.g., UCP1, CIDEA) was still identified. The transcriptomic comparison between the High-KKCF and Low-KKCF groups revealed a total of 80 differentially expressed genes (DEGs). The enrichment analysis of the 49 DEGs with increased expression levels in the Low-KKCF lambs identified significant terms linked to the biosynthesis of lipids and thermogenesis, which may be related to the higher expression of the UCP1 gene in this group. In contrast, the enrichment analysis of the 31 DEGs with increased expression in the High-KKCF lambs highlighted angiogenesis as a key biological process supported by the higher expression of some genes, such as VEGF-A and THBS1, which encode a major angiogenic factor and a large adhesive extracellular matrix glycoprotein, respectively. Discussion: The increased expression of sestrins, which are negative regulators of the mTOR complex, suggests that the preadipocyte differentiation stage is being inhibited in the High-KKCF group in favor of adipose tissue expansion, in which vasculogenesis is an essential process. All of these results suggest that the fat depots of the High-KKCF animals are in a later stage of development than those of the Low-KKCF lambs. Further genomic studies based on larger sample sizes and complementary analyses, such as the identification of polymorphisms in the DEGs, should be designed to confirm these results and achieve a deeper understanding of the genetic mechanisms underlying fat deposition in suckling lambsSIThe research described here has been funded by the project EpiMilksheep (RTI2018-093535-B-100) funded by the Spanish Ministry of Science and Innovation. MA-G is funded by a predoctoral fellowship from the Junta de Castilla and León Government and the European Social Fun

Integrated analyses of the methylome and transcriptome to unravel sex differences in the perirenal fat from suckling lambs

[EN] In sheep, differences were observed regarding fat accumulation and fatty acid (FA) composition between males and females, which may impact the quality and organoleptic characteristics of the meat. The integration of different omics technologies is a relevant approach for investigating biological and genetic mechanisms associated with complex traits. Here, the perirenal tissue of six male and six female Assaf suckling lambs was evaluated using RNA sequencing and whole-genome bisulfite sequencing (WGBS). A multiomic discriminant analysis using multiblock (s)PLS-DA allowed the identification of 314 genes and 627 differentially methylated regions (within these genes), which perfectly discriminate between males and females. These candidate genes overlapped with previously reported QTLs for carcass fat volume and percentage of different FAs in milk and meat from sheep. Additionally, differentially coexpressed (DcoExp) modules of genes between males (nine) and females (three) were identified that harbour 22 of these selected genes. Interestingly, these DcoExp were significantly correlated with fat percentage in different deposits (renal, pelvic, subcutaneous and intramuscular) and were associated with relevant biological processes for adipogenesis, adipocyte differentiation, fat volume and FA composition. Consequently, these genes may potentially impact adiposity and meat quality traits in a sex-specific manner, such as juiciness, tenderness and flavourSIThis research work was financially supported by the RTI2018-093535-B-I00 project funded by the “Agencia Estatal de Investigación” of the Spanish Ministry of Science and Innovation (Madrid, Spain). MA-G is funded by the Junta de Castilla y Leon fellowship. This research has used the high- performance computing resources of the Castilla y León Supercomputing Center (SCAYLE, www.scayle.es; León, Spain). PF is the beneficiary of a Maria Zambrano Grant of the University of Leon funding by the Ministry of Universities (Madrid, Spain) and financed by the European Union-Next Generation E

Techno-economic feasibility of selective CO2 capture processes from biogas streams using ionic liquids as physical absorbents

Biogas from anaerobic digestion of sewage sludge is a renewable resource with high energy content, which is composed mainly of CH4 (40-75 vol %) and CO2 (15-60 vol %). Other components, such as water (H2O, 5-10 vol %) and trace amounts of hydrogen sulfide and siloxanes, can also be present. A CH4-rich stream can be produced by removing the CO2 and other impurities so that the upgraded biomethane can be injected into the natural gas grid or used as a vehicle fuel. The main objective of this paper is to assess the technical and economic performance of biogas upgrading processes using ionic liquids that physically absorb CO2. The simulation methodology is based on the COSMO-SAC model as implemented in Aspen Plus. Three different ionic liquids, namely, 1-ethyl-3-methylimidazolium bis(trifluoromethyl)sulfonylimide, 1-hexyl-3-methylimidazoliumbis(trifluoromethyl)sulfonylimide, and trihexyl(tetradecyl)phosphonium bis(trifluoromethyl)sulfonylimide, are considered for CO2 capture in a pressure-swing regenerative absorption process. The simulation software Aspen Plus and Aspen Process Economic Analyzer is used to account for mass and energy balances as well as equipment cost. In all cases, the biogas upgrading plant consists of a multistage compressor for biogas compression, a packed absorption column for CO2 absorption, a flash evaporator for solvent regeneration, a centrifugal pump for solvent recirculation, a preabsorber solvent cooler, and a gas turbine for electricity recovery. The evaluated processes are compared in terms of energy efficiency, capital investment, and biomethane production costs. The overall plant efficiency ranges from 71 to 86%, and the biomethane production cost ranges from 9.18-11.32 per GJ (LHV). A sensitivity analysis is also performed to determine how several technical and economic parameters affect the biomethane production costs. The results of this study show that the simulation methodology developed can predict plant efficiencies and production costs of large scale CO2 capture processes using ionic liquids without having to rely on gas solubility experimental data

Selective miRNA Modulation Fails to Activate HIV Replication in In Vitro Latency Models

HIV remains incurable because of viral persistence in latent reservoirs that are inaccessible to antiretroviral therapy. A potential curative strategy is to reactivate viral gene expression in latently infected cells. However, no drug so far has proven to be successful in vivo in reducing the reservoir, and therefore new anti-latency compounds are needed. We explored the role of microRNAs (miRNAs) in latency maintenance and their modulation as a potential anti-latency strategy. Latency models based on treating resting CD4 T cells with chemokine (C-C motif) ligand 19 (CCL19) or interleukin-7 (IL7) before HIV infection and next-generation sequencing were used to identify the miRNAs involved in HIV latency. We detected four upregulated miRNAs (miRNA-98, miRNA-4516, miRNA-4488, and miRNA-7974). Individual or combined inhibition of these miRNAs was performed by transfection into cells latently infected with HIV. Viral replication, assessed 72 h after transfection, did not increase after miRNA modulation, despite miRNA inhibition and lack of toxicity. Furthermore, the combined modulation of five miRNAs previously associated with HIV latency was not effective in these models. Our results do not support the modulation of miRNAs as a useful strategy for the reversal of HIV latency. As shown with other drugs, the potential of miRNA modulation as an HIV reactivation strategy could be dependent on the latency model usedThis work wasfunded by the Spanish Ministry of Economy and Competitiveness(PIE 13/00040) and the Spanish AIDS Research Network (RIS)(RD16/0025/0001) as part of the Plan Estatal I+D+I and co-financedby Instituto de Salud Carlos III (ISCIII)-Subdirección General deEvaluación y Fomento de la Investigación and Fondo Europeo deDesarrollo Regional (FEDER) (European Regional DevelopmentFund). M.R.L-H. was supported by the Spanish Ministry of Economyand Competitiveness with ISCIII-FEDER funding (PIE 13/00040 and RD12/0017/0017). N.M.E. and C.G. were supported bythe Spanish AIDS Research Network (RD12/0017/0017 and RD16/0025/001

Evaluación preliminar de los entornos interactivos de aprendizaje basados en problemas en la enseñanza universitaria

[ES] Uno de los grandes retos de los cursos de enseñanza universitaria que abordan temas relacionados con la genética y la genómica consiste en mostrar a los estudiantes, de forma simplificada, cómo la genómica puede dar respuesta a determinados problemas mediante la integración de información procedente de distintas fuentes y metodologías. Esto también es necesario para garantizar que los futuros profesionales de la medicina o la veterinaria sean capaces de integrar la genómica en aplicaciones clínicas o de diagnóstico cotidianas. Así, el objetivo principal de este estudio fue evaluar la aceptación por parte del alumnado de enseñanza superior de entornos interactivos de aprendizaje relacionados con la docencia de la genética y la genómica. Así, como grupo de innovación docente de la Universidad de León (ULE) VetGeneULE, hemos desarrollado dos entornos interactivos de aprendizaje basado en problemas, dirigidos a estudiantes de una asignatura de Grado y otra de Máster de titulaciones de la ULE, utilizando la plataforma Genially, uno para facilitar la compresión de las bases de la genética mendeliana y otro poniendo al estudiante al frente de la resolución de un caso de estudio genómico explotando una estrategia de gamificación. En ambos casos, la presentación interactiva ofrece a los estudiantes un entorno teórico-práctico guiado donde el aprendizaje tiene lugar gracias a metodologías pedagógicas alternativas como son la gamificación y el aprendizaje basado en problemas. Tras la realización de la presentación, los estudiantes de forma voluntaria contestaron una encuesta para conocer el grado de interés que les había suscitado este tipo de presentaciones interactivas. Como resultado más importante obtuvimos una muy diferente participación por parte de ambos grupos de alumnos. Sin embargo, todos ellos estaban de acuerdo en que este tipo de presentaciones interactivas eran un complemento muy útil a las clases teóricas para un aprendizaje más profundo y activo

Early Neospora caninum infection dynamics in cattle after inoculation at mid-gestation with high (Nc-Spain7)- or low (Nc-Spain1H)-virulence isolates

© The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.[EN] Early Neospora caninum infection dynamics were investigated in pregnant heifers intravenously inoculated with PBS (G-Control) or 107 tachyzoites of high (G-NcSpain7)- or low (G-NcSpain1H)-virulence isolates at 110 days of gestation. Serial culling at 10 and 20 days post-infection (dpi) was performed. Fever was detected at 1 dpi in both infected groups (P < 0.0001), and a second peak was detected at 3 dpi only in G-NcSpain7 (P < 0.0001). At 10 dpi, Nc-Spain7 was detected in placental samples from one animal related to focal necrosis, and Nc-Spain7 transmission was observed, although no foetal lesions were associated with this finding. The presence of Nc-Spain1H in the placenta or foetuses, as well as lesions, were not detected at 10 dpi. At 20 dpi, G-NcSpain7 animals showed almost 100% positive placental tissues and severe focal necrosis as well as 100% transmission. Remarkably, foetal mortality was detected in two G-NcSpain7 heifers. Only one animal from G-NcSpain1H presented positive placental samples. No foetal mortality was detected, and lesions and parasite transmission to the foetus were not observed in this group. Finally, 100% of G-NcSpain7 heifers at 20 dpi presented specific antibodies, while only 60% of G-NcSpain1H animals presented specific antibodies at 20 dpi. In addition, earlier seroconversion in G-Nc-Spain7 was observed. In conclusion, tachyzoites from Nc-Spain7 reached the placenta earlier and multiplied, leading to lesion development, transmission to the foetus and foetal mortality, whereas Nc-Spain1H showed delayed infection of the placenta and no lesional development or transmission during early infection.SIThis work was supported by the Spanish Ministry of Economy and Competi‑ tiveness (AGL2013-44694-R) and the Community of Madrid (PLATESA2-CM P2018/BAA-4370). Laura Jiménez-Pelayo was fnancially supported by a fellowship from the Complutense University of Madrid and Marta GarcíaSánchez was fnancially supported through a grant from the Spanish Ministry of Economy and Competitiveness (BES-2014-070723). Patricia Vázquez had a Juan de la Cierva-Formación post-doctoral contract (FJCI-2014-20982) from the Spanish Ministry of Economy and Competitiveness (MINECO). Alicia Román-Trufero was supported by a FPI-INIA fellowship from the Spanish National Institute for Agriculture and Food Research and Technology (INIA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Authors gratefully acknowledge to: (1) SERIDA (Regional Service of Agri-food Research and Development of Asturias) Institution and Personal for their facilities and personal support. Special thanks to David Iglesias for their clinical assistance; (2) Mountain Livestock Institute (IGM), University of León CSIC-ULE for their histopathological specialist support, especially to Miguel Fernández for his help during the sampling; (3) Saluvet Group members, especially to Ale‑ jandro Jiménez-Meléndez and Roberto Sánchez-Sánchez; (4) Saluvet-innova members, especially to Paula García-Luna

Crosstalk between Neospora caninum and the bovine host at the maternal-foetal interface determines the outcome of infection

© The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/ zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.[EN]Neospora caninum is an apicomplexan cyst-forming parasite that is considered one of the main causes of abortion. The pathogenic mechanisms associated with parasite virulence at the maternal-foetal interface that are responsible for the outcome of infection are largely unknown. Here, utilizing placentomes from cattle experimentally infected with high-virulence (Nc-Spain7) and low-virulence (Nc-Spain1H) isolates, we studied key elements of the innate and adaptive immune responses, as well as components of the extracellular matrix (ECM), at 10 and 20 days post-infection (dpi). The low-virulence isolate elicited a robust immune response characterized by upregulation of genes involved in pathogen recognition, chemokines and pro-inflammatory cytokines, crucial for its adequate control. In addition, Nc-Spain1H triggered the expression of anti-inflammatory cytokines and other mechanisms implicated in the maintenance of ECM integrity to ensure foetal survival. In contrast, local immune responses were initially (10 dpi) impaired by Nc-Spain7, allowing parasite multiplication. Subsequently (20 dpi), a predominantly pro-inflammatory Th1-based response and an increase in leucocyte infiltration were observed. Moreover, Nc-Spain7-infected placentomes from animals carrying non-viable foetuses exhibited higher expression of the IL-8, TNF-α, iNOS and SERP-1 genes and lower expression of the metalloproteases and their inhibitors than Nc-Spain7-infected placentomes from animals carrying viable foetuses. In addition, profound placental damage characterized by an alteration in the ECM organization in necrotic foci, which could contribute to foetal death, was found. Two different host-parasite interaction patterns were observed at the bovine placenta as representative examples of different evolutionary strategies used by this parasite for transmission to offspring.SIThis work was supported by the Spanish Ministry of Economy and Competitiveness (AGL2013-44694-R and AGL2016-75935-C2-1-R) and the Community of Madrid (PLATESA2-CM P2018/BAA-4370). Laura Jiménez-Pelayo was financially supported by a fellowship from the University Complutense of Madrid (including two research stays in 2017 and 2018) and Marta García-Sánchez was financially supported through a grant from the Spanish Ministry of Economy and Competitiveness (BES-2014-070723). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Selective miRNA inhibition in CD8+ cytotoxic T lymphocytes enhances HIV-1 specific cytotoxic responses

miRNAs dictate relevant virus-host interactions, offering new avenues for interventions to achieve an HIV remission. We aimed to enhance HIV-specific cytotoxic responses—a hallmark of natural HIV control— by miRNA modulation in T cells. We recruited 12 participants six elite controllers and six patients with chronic HIV infection on long-term antiretroviral therapy ("progressors"). Elite controllers exhibited stronger HIV-specific cytotoxic responses than the progressors, and their CD8+T cells showed a miRNA (hsa-miR-10a-5p) significantly downregulated. When we transfected ex vivo CD8(+) T cells from progressors with a synthetic miR-10a-5p inhibitor, miR-10a-5p levels decreased in 4 out of 6 progressors, correlating with an increase in HIV-specific cytotoxic responses. The effects of miR-10a-5p inhibition on HIV-specific CTL responses were modest, short-lived, and occurred before day seven after modulation. IL-4 and TNF-α levels strongly correlated with HIV-specific cytotoxic capacity. Thus, inhibition of miR-10a-5p enhanced HIV-specific CD8(+) T cell capacity in progressors. Our pilot study proves the concept that miRNA modulation is a feasible strategy to combat HIV persistence by enhancing specific cytotoxic immune responses, which will inform new approaches for achieving an antiretroviral therapy-free HIV remission