Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids

The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical Bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species

Ranking factors affecting emissions of GHG from incubated agricultural soils

Agriculture significantly contributes to global greenhouse gas (GHG) missions and there is a need to develop effective mitigation strategies. The efficacy of methods to reduce GHG fluxes from agricultural soils can be affected by a range of interacting management and environmental factors. Uniquely, we used the Taguchi experimental design methodology to rank the relative importance of six factors known to affect the emission of GHG from soil: nitrate (NO3?) addition, carbon quality (labile and non-labile C), soil temperature, water-filled pore space (WFPS) and extent of soil compaction. Grassland soil was incubated in jars where selected factors, considered at two or three amounts within the experimental range, were combined in an orthogonal array to determine the importance and interactions between factors with a L16 design, comprising 16 experimental units. Within this L16 design, 216 combinations of the full factorial experimental design were represented. Headspace nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) concentrations were measured and used to calculate fluxes. Results found for the relative influence of factors (WFPS and NO3? addition were the main factors affecting N2O fluxes, whilst glucose, NO3? and soil temperature were the main factors affecting CO2 and CH4 fluxes) were consistent with those already well documented. Interactions between factors were also studied and results showed that factors with Little individual influence became more influential in combination. The proposed methodology offers new possibilities for GHG researchers to study interactions between influential factors and address the optimized sets of conditions to reduce GHG emissions in agro-ecosystems, while reducing the number of experimental units required compared with conventional experimental procedures that adjust one variable at a time

Influence of Tillage and Liming on N2O emission from a rainfed crop

Nitrous oxide (N2O) is the main greenhouse gas (GHG) produced by agricultural soils due to microbial processes. The application of N fertilizers is associated with an increase of N2O losses. However, it is possible to mitigate these emissions by the introduction of adequate management practices (Snyder et al., 2009). Soil conservation practices (i.e.no tillage, NT) have recently become widespread because they promote several positive effects (increases in soil organic carbonand soil fertility, reduction of soil erosion, etc). In terms of GHG emissions, there is no consensus in the literature on the effects of tillage on N2O. Several studies found that NT can produce greater (Baggs et al., 2003), lower (Malhi et al., 2006) or similar (Grandey et al., 2006) N2O emissions compared to traditional tillage (TT). This large uncertainty is associated with the duration of tillage practices and climatic variability. Liming is widely use to solve problems of soil acidity (Al toxicity, yield penalties, etc). Several studies show a decrease in N2O emissions with liming (Barton et al., 2013) whereas no significant effects or increases were observed in others (Galbally et al., 2010). The aim of this work was to evaluate the effects of tillage (NT vs TT) and liming application or not of Ca-amendment) on N2O emissions from an acid soil during a rainfed crop

El perfil emergente del directivo de RSC

La RSC (responsabilidad social corporativa) constituye un criterio transversal que define una nueva forma de gestionar las organizaciones, mirando más hacia la necesaria implicación de los grupos de interés y abierta al diálogo y a la sostenibilidad a largo plazo, sin renunciar por ello al beneficio. El responsable de RSC, sea cual sea la denominación que se le dé en cada empresa, se enfrenta a la tarea de introducir este criterio en la gestión diaria de la empresa. ¿Quiénes son estos profesionales de la RSC? ¿Cuál es su background profesional? ¿Cuáles son sus capacidades y competencias para hacer frente a semejante reto? Según los propios responsables de RSC, quien sea designado para desempeñar esta función en una empresa debe ser una persona con visión estratégica y capacidad de innovación y creatividad, orientada al diálogo y al consenso, y con una gran capacidad para motivar y convencer al resto de la organización acerca de la necesidad de sacrificar eficacia presente a favor de beneficios futuros a largo plazo. ¿Son -o deberían ser- los responsables de RSC agentes de cambio en sus empresas?Responsabilidad Social Corporativa; Agente de cambio;

Antiagregación y anticoagulación en síndromes coronarios agudos: niveles de evidencia

Management of acute coronary syndromes (ACS) has moved rapidly in parallel with our understanding of the pathophysiological basis of the disease. In the eighties, the demonstration of the pivotal role of coronary thrombosis in the etiology of a ACS led to administration of aspirin and unfractionated heparin. In recent years, new medical and invasive therapies have been developed: anti-platelets (thienopyridines and glycoprotein Ilb/IlIa inhibitors), antithrombins (low molecularweight heparins) and most recently, factor Xa inhibitors (pentasaccharides). As new treatments are rapidly added, clinicians are constantly challenged to incorporate new information and guidelines into their practices in a timely fashion

NRF2 and primary cilia: An emerging partnership

When not dividing, many cell types target their centrosome to the plasma membrane, where it nucleates assembly of a primary cilium, an antenna-like signaling structure consisting of nine concentric microtubule pairs surrounded by membrane. Primary cilia play important pathophysiological roles in many tissues, their dysfunction being associated with cancer and ciliopathies, a diverse group of congenital human diseases. Several recent studies have unveiled functional connections between primary cilia and NRF2 (nuclear factor erythroid 2-related factor 2), the master transcription factor orchestrating cytoprotective responses to oxidative and other cellular stresses. These NRF2-cilia relationships are reciprocal: primary cilia, by promoting autophagy, downregulate NRF2 activity. In turn, NRF2 transcriptionally regulates genes involved in ciliogenesis and Hedgehog (Hh) signaling, a cilia-dependent pathway with major roles in embryogenesis, stem cell function and tumorigenesis. Nevertheless, while we found that NRF2 stimulates ciliogenesis and Hh signaling, a more recent study reported that NRF2 negatively affects these processes. Herein, we review the available evidence linking NRF2 to primary cilia, suggest possible explanations to reconcile seemingly contradictory data, and discuss what the emerging interplay between primary cilia and NRF2 may mean for human health and disease.This work was funded by European Regional Development Fund (ERDF/FEDER)-cofunded grants from the Spanish Ministry of Economy and Competitiveness (MINECO) to F.R.G.G. (SAF2015-66568-R and RYC2013-14887). A.M.H. was supported by a FEDER-cofunded predoctoral contract from the Community of Madrid governmen

Pathophysiology of migraines

Migraines are one of the most disabling neurovascular disorders of which there is still no exact etiology. Most of the studies concerning the pathophysiology of migraines revolve around the notion that the key players are meningeal vascular mechanisms working in conjunction with local trigeminal afferents. Cortical spreading depression, the Trigeminovascular system, and the Blood-Brain-Barrier are other potential contributors but need further investigation. This literature thesis will explore the relationship between the vasculature and neurological mechanisms in the initiation of migraine episodes and provide a plausible mechanism that combines current evidence provided by the literature