Integration of host-pathogen functional genomics data into the chromosome-level genome assembly of turbot (Scophthalmus maximus)

Disease resilience is of utmost relevance for turbot aquaculture. Several infective diseases, covering a broad spectrum from viruses, bacteria to different parasites, have been identified by industry. Since they increase mortality rates, reduce feed conversion ratios and slow down growth rate, genetic breeding programs for increasing disease resilience are recognized as a useful alternative for controlling pathologies. For this, knowledge of the genetic basis underlying resilience using genomic tools is essential to develop the best effective breeding strategies. In the present study, we compiled the existing genomic information generated in the last decade to construct an integrated atlas of candidate genes and genomic regions involved in pathogen resistance against the main turbot industrial pathogens (Aeromonas salmonicida, Philasterides dicentrarchi, Enteromyxum scophthalmi and the VHS virus) within the chromosome-level turbot genome assembly recently released. Information comprehends reannotated differentially expressed genes (DEG) in different tissues along temporal series, QTL markers associated with important productive traits (disease resistance and growth) and signatures of domestic or wild selection, represented by runs of homozygosity (ROHi) islands and outlier markers for divergent selection. Most genetic features were successfully relocated in the turbot assembly including 81.1% of the total DEGs, plus all QTL markers, ROHi and outlier markers. The updated annotation of DEGs for resistance to each pathology demonstrated significant changes. While the new annotation of 53–83% of the DEGs was coherent with the original, roughly 10–24% showed imprecise annotations in both assembly versions, ∼5% lost their original annotation and 2–24% were now annotated. Functional enrichment revealed mostly functions related to immune response, such as chemotaxis, apoptosis regulation, leukocyte differentiation, cell adhesion, iron homeostasis and vascular permeability. Some DEGs, such as celsr1a (cadherin EGF LAG seen-pass G-type receptor 1), fgg (fibrinogen gamma chain) and c1qtnf9 (C1q and TNF related 9) were found near pathogen-associated QTL markers. Also, some shared DEGs for resistance to all pathogens were positioned near QTL markers or ROHi, such as hamp (hepcidin-1), plg (plasminogen) and a fibrinogen alpha chain-like gene. Overall, our results provide an integrative insight into the genetic architecture of turbot response to a range of pathogens that could prove useful for future genomic studies to benefit aquaculture breeding programsS

Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus)

Massive genotyping of single nucleotide polymorphisms (SNP) has opened opportunities for analyzing the way in which selection shapes genomes. Artificial or natural selection usually leaves genomic signatures associated with selective sweeps around the responsible locus. Strong selective sweeps are most often identified either by lower genetic diversity than the genomic average and/or islands of runs of homozygosity (ROHi). Here, we conducted an analysis of selective sweeps in turbot (Scophthalmus maximus) using two SNP datasets from a Northeastern Atlantic population (36 individuals) and a domestic broodstock (46 individuals). Twenty-six families (∼ 40 offspring per family) from this broodstock and three SNP datasets applying differing filtering criteria were used to adjust ROH calling parameters. The best-fitted genomic inbreeding estimate (FROH) was obtained by the sum of ROH longer than 1 Mb, called using a 21,615 SNP panel, a sliding window of 37 SNPs and one heterozygous SNP per window allowed. These parameters were used to obtain the ROHi distribution in the domestic and wild populations (49 and 0 ROHi, respectively). Regions with higher and lower genetic diversity within each population were obtained using sliding windows of 37 SNPs. Furthermore, those regions were mapped in the turbot genome against previously reported genetic markers associated with QTL (Quantitative Trait Loci) and outlier loci for domestic or natural selection to identify putative selective sweeps. Out of the 319 and 278 windows surpassing the suggestive pooled heterozygosity thresholds (ZHp) in the wild and domestic population, respectively, 78 and 54 were retained under more restrictive ZHp criteria. A total of 116 suggestive windows (representing 19 genomic regions) were linked to either QTL for production traits, or outliers for divergent or balancing selection. Twenty-four of them (representing 3 genomic regions) were retained under stricter ZHp thresholds. Eleven QTL/outlier markers were exclusively found in suggestive regions of the domestic broodstock, 7 in the wild population and one in both populations; one (broodstock) and two (wild) of those were found in significant regions retained under more restrictive ZHp criteria in the broodstock and the wild population, respectively. Genome mining and functional enrichment within regions associated with selective sweeps disclosed relevant genes and pathways related to aquaculture target traits, including growth and immune-related pathways, metabolism and response to hypoxia, which showcases how this genome atlas of genetic diversity can be a valuable resource to look for candidate genes related to natural or artificial selection in turbot populationsThis study has been supported by the FISHBOOST project (ref. 613611) from the European Community’s Seventh Framework Programme (FP7/2007-2013), European Regional Development Fund (Interreg Va, project “MarGen”), Consellería de Educación, Universidade e Formación Profesional, Xunta de Galicia local government (ref. ED431C 2018/28), and the Strategic Researcher Cluster BioReDes funded by the Regional Government Xunta de Galicia (Spain) (ref. ED431E 2018/09). Computational support for bioinformatic analysis was provided by Centro de Supercomputación de Galicia (CESGA). AC was supported by a predoctoral research fellowship from Xunta de Galicia local government (Spain) (ref. ED481A-2017/091). OA was supported by a predoctoral research fellowship from BioReDes, funded by Xunta de Galicia (Spain) (ref. 2018-PG099)S

The EPICTER score: a bedside and easy tool to predict mortality at 6 months in acute heart failure

Aims: Estimating the prognosis in heart failure (HF) is important to decide when to refer to palliative care (PC). Our objective was to develop a tool to identify the probability of death within 6 months in patients admitted with acute HF. Methods and results: A total of 2848 patients admitted with HF in 74 Spanish hospitals were prospectively included and followed for 6 months. Each factor independently associated with death in the derivation cohort (60% of the sample) was assigned a prognostic weight, and a risk score was calculated. The accuracy of the score was verified in the validation cohort. The characteristics of the population were as follows: advanced age (mean 78 years), equal representation of men and women, significant comorbidity, and predominance of HF with preserved ejection fraction. During follow-up, 753 patients (26%) died. Seven independent predictors of mortality were identified: age, chronic obstructive pulmonary disease, cognitive impairment, New York Heart Association class III-IV, chronic kidney disease, estimated survival of the patient less than 6 months, and acceptance of a palliative approach by the family or the patient. The area under the ROC curve for 6 month death was 0.74 for the derivation and 0.68 for the validation cohort. The model showed good calibration (Hosmer and Lemeshow test, P value 0.11). The 6 month death rates in the score groups ranged from 6% (low risk) to 54% (very high risk). Conclusions: The EPICTER score, developed from a prospective and unselected cohort, is a bedside and easy-to-use tool that could help to identify high-risk patients requiring PC

Estimating the Prevalence of Cardiac Amyloidosis in Old Patients with Heart Failure—Barriers and Opportunities for Improvement: The PREVAMIC Study

Background: Cardiac amyloidosis (CA) could be a common cause of heart failure (HF). The objective of the study was to estimate the prevalence of CA in patients with HF. Methods: Observational, prospective, and multicenter study involving 30 Spanish hospitals. A total of 453 patients >= 65 years with HF and an interventricular septum or posterior wall thickness > 12 mm were included. All patients underwent a Tc-99m-DPD/PYP/HMDP scintigraphy and monoclonal bands were studied, following the current criteria for non-invasive diagnosis. In inconclusive cases, biopsies were performed. Results: The vast majority of CA were diagnosed non-invasively. The prevalence was 20.1%. Most of the CA were transthyretin (ATTR-CM, 84.6%), with a minority of cardiac light-chain amyloidosis (AL-CM, 2.2%). The remaining (13.2%) was untyped. The prevalence was significantly higher in men (60.1% vs 39.9%, p = 0.019). Of the patients with CA, 26.5% had a left ventricular ejection fraction less than 50%. Conclusions: CA was the cause of HF in one out of five patients and should be screened in the elderly with HF and myocardial thickening, regardless of sex and LVEF. Few transthyretin-gene-sequencing studies were performed in older patients. In many patients, it was not possible to determine the amyloid subtype

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

Cultura veterinaria: podcasts históricos ludificados

El origen de este proyecto era la incorporación de Podcast a otros recursos educativos generados en proyectos de innovación previos (píldoras de conocimiento de la Historioteca Veterinaria) para incrementar el conocimiento de la cultura veterinaria histórica y actual. Tras la experiencia sobre creación de un espacio virtual específico denominado Historioteca Veterinaria (Proyecto 341 curso 20-21) en el que se generaron recursos -píldoras de conocimiento- en abierto basados en la ludificación de personajes o hechos históricos, el objetivo de este proyecto es la realización de entrevistas histórico-culturales en formato podcast. El término podcast surge de combinar las palabras de origen inglés POD que significa cápsula (también son las tres letras forman el acrónimo Programming On Demand -programación bajo demanda-) y Broadcast (emisión en directo). El podcast es un programa de audio bajo demanda. O lo que es lo mismo, que se puede escuchar cuándo, dónde y cómo se quiera.Depto. de Sanidad AnimalFac. de VeterinariaFALSEsubmitte

Discovering HIV related information by means of association rules and machine learning

Acquired immunodeficiency syndrome (AIDS) is still one of the main health problems worldwide. It is therefore essential to keep making progress in improving the prognosis and quality of life of affected patients. One way to advance along this pathway is to uncover connections between other disorders associated with HIV/AIDS-so that they can be anticipated and possibly mitigated. We propose to achieve this by using Association Rules (ARs). They allow us to represent the dependencies between a number of diseases and other specific diseases. However, classical techniques systematically generate every AR meeting some minimal conditions on data frequency, hence generating a vast amount of uninteresting ARs, which need to be filtered out. The lack of manually annotated ARs has favored unsupervised filtering, even though they produce limited results. In this paper, we propose a semi-supervised system, able to identify relevant ARs among HIV-related diseases with a minimal amount of annotated training data. Our system has been able to extract a good number of relationships between HIV-related diseases that have been previously detected in the literature but are scattered and are often little known. Furthermore, a number of plausible new relationships have shown up which deserve further investigation by qualified medical experts