Livestock faecal indicators for animal management, penning, foddering and dung use in early agricultural built environments in the Konya Plain, Central Anatolia

Livestock dung is a valuable material for reconstructing human and animal inter-relations and activity within open areas and built environments. This paper examines the identification and multi-disciplinary analysis of dung remains from three neighbouring sites in the Konya Plain of Central Anatolia, Turkey: Boncuklu (9th-8th millennium cal BC), the Çatalhöyük East Mound (8th-6th millennium cal BC), and the Late Neolithic occupation at the Pınarbaşı rockshelter (7th millennium cal BC). It presents and evaluates data on animal management strategies and husbandry practices through the simultaneous examination of plant and faecal microfossils and biomarkers with thin-section micromorphology and integrated phytolith, dung spherulite, and biomolecular analyses, together with comparative reference geo-ethnoarchaeological assemblages. Herbivore dung and other coprogenic materials have been identified predominantly in open areas, pens and midden deposits through micromorphology and the chemical signatures of their depositional contexts and composition. Accumulations of herbivore faecal material and burnt remains containing calcitic spherulites and phytoliths have provided new information on animal diet, fodder and dung fuel. Evidence from phytoliths from in situ penning deposits at early Neolithic Çatalhöyük have provided new insights into foddering/grazing practices by identifying highly variable herbivorous regimes including both dicotyledonous and grass-based diets. This review illustrates the variability of dung deposits within early agricultural settlements and their potential for tracing continuity and change in ecological diversity, herd management strategies and foddering, health, energy and dung use, as well as the complexity of interactions between people and animals in this key region during the early Holocene

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

Relationships between growth-related traits with carcass and meat quality traits in Spanish Assaf suckling lambs

[EN] Suckling lamb meat is a relevant product in Mediterranean European dairy sheep farms, and the dairy breed Spanish Assaf is widely extended through the Iberian Peninsula. Knowledge of the influence of birth body weight (bBW) and growth rate on suckling lamb carcass and meat quality is scarce, but useful for breeding optimisation and product homogeneity. In turn, these growth-related traits of lambs might be affected by dietary restrictions of their dams. In this study, 34 male Assaf suckling lambs born from two groups of ewes that had been fed diets with different protein levels when they were prepubertal female lambs (17 lambs per group) were analysed. After birth, the suckling lambs were fed ad libitum on milk replacer until their sacrifice (10–12.5 kg live body weight). The quality traits evaluated in carcasses and meat were carcass compactness, fatness and jointing, meat composition, colour, texture and oxidative stability, and fatty acid profile. The dam group did not show significant effects on lamb growth characteristics or carcass and meat quality traits. The bBW factor showed a negative effect on leg subcutaneous fatness and a positive effect on the forequarter and shoulder percentages of the carcass. The bBW also resulted in increased moisture, lipid oxidation stability, and n-3 FA content (lowering the n-6/n-3 ratio) in the meat. Suckling lambs showing very low average daily gain (ADG) tended to present low carcass quality, i.e., higher bone percentage in the loin and low percentages of muscle or fat compared to those showing high ADG. Further studies are needed to confirm and explain the mechanisms of the significant effects reported here for bBW and ADG on the affected quality traits.S

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

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

Role of age and comorbidities in mortality of patients with infective endocarditis

[Purpose]: The aim of this study was to analyse the characteristics of patients with IE in three groups of age and to assess the ability of age and the Charlson Comorbidity Index (CCI) to predict mortality. [Methods]: Prospective cohort study of all patients with IE included in the GAMES Spanish database between 2008 and 2015.Patients were stratified into three age groups:<65 years,65 to 80 years,and ≥ 80 years.The area under the receiver-operating characteristic (AUROC) curve was calculated to quantify the diagnostic accuracy of the CCI to predict mortality risk. [Results]: A total of 3120 patients with IE (1327 < 65 years;1291 65-80 years;502 ≥ 80 years) were enrolled.Fever and heart failure were the most common presentations of IE, with no differences among age groups.Patients ≥80 years who underwent surgery were significantly lower compared with other age groups (14.3%,65 years; 20.5%,65-79 years; 31.3%,≥80 years). In-hospital mortality was lower in the <65-year group (20.3%,<65 years;30.1%,65-79 years;34.7%,≥80 years;p < 0.001) as well as 1-year mortality (3.2%, <65 years; 5.5%, 65-80 years;7.6%,≥80 years; p = 0.003).Independent predictors of mortality were age ≥ 80 years (hazard ratio [HR]:2.78;95% confidence interval [CI]:2.32–3.34), CCI ≥ 3 (HR:1.62; 95% CI:1.39–1.88),and non-performed surgery (HR:1.64;95% CI:11.16–1.58).When the three age groups were compared,the AUROC curve for CCI was significantly larger for patients aged <65 years(p < 0.001) for both in-hospital and 1-year mortality. [Conclusion]: There were no differences in the clinical presentation of IE between the groups. Age ≥ 80 years, high comorbidity (measured by CCI),and non-performance of surgery were independent predictors of mortality in patients with IE.CCI could help to identify those patients with IE and surgical indication who present a lower risk of in-hospital and 1-year mortality after surgery, especially in the <65-year group

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio