Bayesian analysis of the association between casein complex haplotype variants and milk yield, composition, and curve shape parameters in murciano-granadina goats

Considering casein haplotype variants rather than SNPs may maximize the understanding of heritable mechanisms and their implication on the expression of functional traits related to milk production. Effects of casein complex haplotypes on milk yield, milk composition, and curve shape parameters were used using a Bayesian inference for ANOVA. We identified 48 single nucleotide polymorphisms (SNPs) present in the casein complex of 159 unrelated individuals of diverse ancestry, which were organized into 86 haplotypes. The Ali and Schaeffer model was chosen as the best fitting model for milk yield (Kg), protein, fat, dry matter, and lactose (%), while parabolic yield-density was chosen as the best fitting model for somatic cells count (SCC × 103 sc/mL). Peak and persistence for all traits were computed respectively. Statistically significant differences (p < 0.05) were found for milk yield and components. However, no significant difference was found for any curve shape parameter except for protein percentage peak. Those haplotypes for which higher milk yields were reported were the ones that had higher percentages for protein, fat, dry matter, and lactose, while the opposite trend was described by somatic cells counts. Conclusively, casein complex haplotypes can be considered in selection strategies for economically important traits in dairy goats

Software-automatized individual lactation model fitting, peak and persistence and Bayesian criteria comparison for milk yield genetic studies in Murciano-Granadina goats

SPSS model syntax was defined and used to evaluate the individual performance of 49 linear and non-linear models to fit the lactation curve of 159 Murciano-Granadina goats selected for genotyping analyses. Lactation curve shape, peak and persistence were evaluated for each model using 3107 milk yield controls with an average of 3.78 ± 2.05 lactations per goat. Best fit (Adjusted R2) values (0.47) were reached by the five-parameter logarithmic model of Ali and Schaeffer. Three main possibilities were detected: non-fitting (did not converge), standard (Adjusted R2 over 75%) and atypical curves (Adjusted R2 below 75%). All the goats fitted for 38 models. The ability to fit different possible functional forms for each goat, which progressively increased with the number of parameters comprised in each model, translated into a higher sensitivity to explaining curve shape individual variability. However, for models for which all goats fitted, only moderate increases in explanatory and predictive potential (AIC, AICc or BIC) were found. The Ali and Schaeffer model reported the best fitting results to study the genetic variability behind goat milk yield and perhaps enhance the evaluation of curve parameters as trustable future selection criteria to face the future challenges offered by the goat dairy industry

Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK

The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150–154 Mb), Oar6 (4–49 Mb) and Oar13 (68–74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection.Publishe

Revista de Vertebrados de la Estación Biológica de Doñaña

Alimentación de la boga del Guadiana (Chondrostoma polylepis wi/lkommi, Stein. 1866) en la interfase río-embalse de Sierra Boyera (Córdoba. España)Predación del búho real (Bubo bubo) sobre la perdiz roja (Alectoris rufa): selección de edad y sexoAlimentación de la nutria (Lutra lufra L, 1758)en el Nordeste de la Península IbéricaDatos sobre la distribución espacialde micromamíferos en el Parque Nacionalde DoñanaGuía para el reconocimiento microscópico de los pelos de los mamíferos de la Patagonia.Sobre la distribución geográfica de Anaecypris hispanica (STEINDACHNER, 1866) (OSTEICHTHYES, CYPRINIDAE)Cronología del periodo reproductor de Rana temporaria L. en La Coruña (NW de España).Un nuevo caso de melanismo en Natrix natrix (LINNAEUS 1758) procedente de Fuente Dé (Santander)Nuevas citas de anfibios y reptiles para el SE de la Península Ibérica.Datos sobre la dieta invernal del Búho chico (Asia atus) en la provinvia de LeónLa Distribucióndel Mara (Dolichotis patagonum) según criterios ecológicos e históricosSolapamiento entre la dieta de la cabra montés (Capra pyrenaica) y la del muflón (Ovis musimon)Nota sobre dietas de carnívoros e índices de abundancia en una Reserva de caza del norte de España.Discriminación osteométrica en el géneroTalpa (LINNEO, 1758), en el norte IbéricoObservaciones sobre el comportamiento depredativo de algunos colúbridos Ibéricos en estado salvajePeer reviewe

A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds

BACKGROUND: To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. RESULTS: The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. CONCLUSIONS: To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes

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

Anti-tumour necrosis factor discontinuation in inflammatory bowel disease patients in remission: study protocol of a prospective, multicentre, randomized clinical trial

Background: Patients with inflammatory bowel disease who achieve remission with anti-tumour necrosis factor (anti-TNF) drugs may have treatment withdrawn due to safety concerns and cost considerations, but there is a lack of prospective, controlled data investigating this strategy. The primary study aim is to compare the rates of clinical remission at 1?year in patients who discontinue anti-TNF treatment versus those who continue treatment. Methods: This is an ongoing, prospective, double-blind, multicentre, randomized, placebo-controlled study in patients with Crohn?s disease or ulcerative colitis who have achieved clinical remission for ?6?months with an anti-TNF treatment and an immunosuppressant. Patients are being randomized 1:1 to discontinue anti-TNF therapy or continue therapy. Randomization stratifies patients by the type of inflammatory bowel disease and drug (infliximab versus adalimumab) at study inclusion. The primary endpoint of the study is sustained clinical remission at 1?year. Other endpoints include endoscopic and radiological activity, patient-reported outcomes (quality of life, work productivity), safety and predictive factors for relapse. The required sample size is 194 patients. In addition to the main analysis (discontinuation versus continuation), subanalyses will include stratification by type of inflammatory bowel disease, phenotype and previous treatment. Biological samples will be obtained to identify factors predictive of relapse after treatment withdrawal. Results: Enrolment began in 2016, and the study is expected to end in 2020. Conclusions: This study will contribute prospective, controlled data on outcomes and predictors of relapse in patients with inflammatory bowel disease after withdrawal of anti-TNF agents following achievement of clinical remission. Clinical trial reference number: EudraCT 2015-001410-1

Key Factors Associated With Pulmonary Sequelae in the Follow-Up of Critically Ill COVID-19 Patients

Introduction: Critical COVID-19 survivors have a high risk of respiratory sequelae. Therefore, we aimed to identify key factors associated with altered lung function and CT scan abnormalities at a follow-up visit in a cohort of critical COVID-19 survivors. Methods: Multicenter ambispective observational study in 52 Spanish intensive care units. Up to 1327 PCR-confirmed critical COVID-19 patients had sociodemographic, anthropometric, comorbidity and lifestyle characteristics collected at hospital admission; clinical and biological parameters throughout hospital stay; and, lung function and CT scan at a follow-up visit. Results: The median [p25–p75] time from discharge to follow-up was 3.57 [2.77–4.92] months. Median age was 60 [53–67] years, 27.8% women. The mean (SD) percentage of predicted diffusing lung capacity for carbon monoxide (DLCO) at follow-up was 72.02 (18.33)% predicted, with 66% of patients having DLCO < 80% and 24% having DLCO < 60%. CT scan showed persistent pulmonary infiltrates, fibrotic lesions, and emphysema in 33%, 25% and 6% of patients, respectively. Key variables associated with DLCO < 60% were chronic lung disease (CLD) (OR: 1.86 (1.18–2.92)), duration of invasive mechanical ventilation (IMV) (OR: 1.56 (1.37–1.77)), age (OR [per-1-SD] (95%CI): 1.39 (1.18–1.63)), urea (OR: 1.16 (0.97–1.39)) and estimated glomerular filtration rate at ICU admission (OR: 0.88 (0.73–1.06)). Bacterial pneumonia (1.62 (1.11–2.35)) and duration of ventilation (NIMV (1.23 (1.06–1.42), IMV (1.21 (1.01–1.45)) and prone positioning (1.17 (0.98–1.39)) were associated with fibrotic lesions. Conclusion: Age and CLD, reflecting patients’ baseline vulnerability, and markers of COVID-19 severity, such as duration of IMV and renal failure, were key factors associated with impaired DLCO and CT abnormalities