Nota corta. Detección mediante PCR multiplex y caracterización de cepas no toxigénicas de Pseudomonas syringae pv. phaseolicola de distintas zonas de España

The efficient control of halo blight, caused by Pseudomonas syringae pv. phaseolicola, is primarily based on the use of pathogen-free seed. Detection of the pathogen in seeds is currently carried out with high-sensitive methods based on the detection by PCR of genes involved in the biosynthesis of phaseolotoxin, which was believed to be produced by all strains of the pathogen with epidemiological importance. However, field epidemics of halo blight in the county of Castilla y León, Spain, are often associated to nontoxigenic isolates of P. syringae pv. phaseolicola, which cannot be detected using current molecular and serological methods. The results presented in this work show the existence of nontoxigenic isolates of P. syringae pv. phaseolicola in areas other than Castilla y León, indicating the need to establish a reliable methodology for seed certification. A simple two-step methodology is presented with the aim to identify both types of isolates that is based on a multiplex enrichment PCR of seed soakates and on pathogenicity assays.El control eficiente de la grasa de la judía causada por Pseudomonas syringae pv. phaseolicola se basa principalmente en la utilización de semilla libre del patógeno. La detección del patógeno en semilla se efectúa mediante métodos altamente sensibles basados en la detección por PCR de los genes responsables de la biosíntesis de la faseolotoxina, la cual, hasta ahora, se consideraba que era sintetizada por todas las cepas del patógeno con importancia epidemiológica. Sin embargo, en la Comunidad de Castilla y León, España, las epidemias de grasa de la judía en campo se asocian frecuentemente con cepas no toxigénicas de P. syringae pv. phaseolicola, que no pueden ser detectadas con los métodos moleculares y serológicos actuales. Los resultados presentados en este trabajo demuestran la existencia de aislados no toxigénicos de P. syringae pv. phaseolicola en zonas distintas de Castilla y León, lo que implica la necesidad de establecer una metodología fiable para la certificación de semillas de judía. Con este propósito, se presenta un sencillo protocolo en dos fases que permite la identificación de los dos tipos de aislados, y que se basa en una PCR multiplex con enriquecimiento a partir de extractos de semilla y en ensayos de patogenicidad

ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization

BackgroundWhole-exome sequencing (WES) and whole-genome sequencing (WGS) have become indispensable tools to solve rare Mendelian genetic conditions. Nevertheless, there is still an urgent need for sensitive, fast algorithms to maximise WES/WGS diagnostic yield in rare disease patients. Most tools devoted to this aim take advantage of patient phenotype information for prioritization of genomic data, although are often limited by incomplete gene-phenotype knowledge stored in biomedical databases and a lack of proper benchmarking on real-world patient cohorts.MethodsWe developed ClinPrior, a novel method for the analysis of WES/WGS data that ranks candidate causal variants based on the patient's standardized phenotypic features (in Human Phenotype Ontology (HPO) terms). The algorithm propagates the data through an interactome network-based prioritization approach. This algorithm was thoroughly benchmarked using a synthetic patient cohort and was subsequently tested on a heterogeneous prospective, real-world series of 135 families affected by hereditary spastic paraplegia (HSP) and/or cerebellar ataxia (CA).ResultsClinPrior successfully identified causative variants achieving a final positive diagnostic yield of 70% in our real-world cohort. This includes 10 novel candidate genes not previously associated with disease, 7 of which were functionally validated within this project. We used the knowledge generated by ClinPrior to create a specific interactome for HSP/CA disorders thus enabling future diagnoses as well as the discovery of novel disease genes.ConclusionsClinPrior is an algorithm that uses standardized phenotype information and interactome data to improve clinical genomic diagnosis. It helps in identifying atypical cases and efficiently predicts novel disease-causing genes. This leads to increasing diagnostic yield, shortening of the diagnostic Odysseys and advancing our understanding of human illnesses

Fase inicial de selección del pimiento choricero del País Vasco (abstract)

NEI.KER se encuentra realizando una selección de pimiento choricero ante una demanda solicitada por el sector productor. Los resultados presentados en este trabajo corresponden al primer año de los 4 años estimados para un programa de selección genealógica. De un total de 69 entradas evaluadas en el primer año, se han seleccionado 20 como las más aptas para continuar en el segundo año. Con ellas se proseguirá la selección para confirmar resultados, reducir el número de entradas y caracterizar las que mejor comportamiento ofrezcan a escala de cultivo comercialPublishe

Mycotoxins in maize grains grown in organic and conventional agriculture

Maize is traditionally used for bakery in several countries, and autochthonous varieties are increasingly demanded particularly for organic agriculture, but one of the dangers of cereal consumption is mycotoxin contamination. Mycotoxins are dangerous for health and might be present in any grain depending on genotypes and environments. In the present work we assess the natural levels of fumonisin and deoxynivalenol (DON) contaminations in nine diverse open-pollinated maize varieties grown in four different locations, under organic or conventional conditions, in two regions from the humid Spain during two years. Differences were significant among locations and among varieties for fumonisin contamination but not for DON content. Locations were the main environmental source of variation affecting fumonisins while DON was more affected by years. The Basque locations had more fumonisin than the Galician locations, but there were no differences between organic and conventional environments. Fumonisin contamination was more variable than DON among locations and among varieties. Fumonisin and DON were highly correlated on average but correlations were low for each particular environment. Mean fumonisin and DON were below the threshold allowed by the EU, but the white-kernel medium late variety Rebordanes(P)C2 had more than 4.00mg/kg of fumonisin in one location, while the early yellow variety Sarreaus had the lowest contamination. We conclude warning producers of the danger of natural contamination with mycotoxins for some varieties in specific environments.Research was supported by the Spanish Plan for Research and Development (project code AGL2010-22254, AGL2009-12770), the Basque Government, and the Diputación Provincial de Pontevedra.MICINNDiputación de PontevedraPeer Reviewe

Getting Ready for the Next Step: The Eradication of Feral Cats on Large and Highest Priority Mexican Islands

Mexican islands’ biodiversity is very rich and diverse; several reptile, bird, and mammal endemic species live on them. However, ecological and evolutionary processes have been negatively affected by invasive species. To date, more than 20 island endemics, including mammals, birds and reptiles, have gone extinct on Mexican islands. As a very opportunistic predator that adapts easily to different environments, the feral cat is one of the most lethal invasive species. Restoration of island ecosystems can be achieved effectively by the eradication of this noxious species. In Mexico, 18 islands (<400 km2) have been cleared of feral cats using traditional techniques, i.e. trapping and hunting. These techniques are still being implemented on smaller islands or on islands where populations are small. Nevertheless, on big islands with complex terrain and topography, varied habitats and climates, and with non-target species, there are challenges to overcome. This includes Socorro (130 km2), Cerralvo (135 km2), and Guadalupe (240 km2) Islands. To achieve successful cat eradications on these islands, dispersion of toxic baits will be necessary. Currently, bait trials are being developed by Grupo de Ecología y Conservación de Islas, A.C., and supported by Australian and New Zealand institutions, as part of island-specific eradication plans. To date, these studies comprise feral cat and native species ecology for Cerralvo and Socorro Islands. All data gathered is valuable for eradication planning

Short communication. Detection by multiplex PCR and characterization of nontoxigenic strains of "Pseudomonas syringae" pv. phaseolicola from different places in Spain

The efficient control of halo blight, caused by Pseudomonas syringae pv. phaseolicola, is primarily based on the use of pathogen-free seed. Detection of the pathogen in seeds is currently carried out with high-sensitive methods based on the detection by PCR of genes involved in the biosynthesis of phaseolotoxin, which was believed to be produced by all strains of the pathogen with epidemiological importance. However, field epidemics of halo blight in the county of Castilla y León, Spain, are often associated to nontoxigenic isolates of P. syringae pv. phaseolicola, which cannot be detected using current molecular and serological methods. The results presented in this work show the existence of nontoxigenic isolates of P. syringae pv. phaseolicola in areas other than Castilla y León, indicating the need to establish a reliable methodology for seed certification. A simple two-step methodology is presented with the aim to identify both types of isolates that is based on a multiplex enrichment PCR of seed soakates and on pathogenicity assays.El control eficiente de la grasa de la judía causada por Pseudomonas syringae pv. phaseolicola se basa principalmente en la utilización de semilla libre del patógeno. La detección del patógeno en semilla se efectúa mediante métodos altamente sensibles basados en la detección por PCR de los genes responsables de la biosíntesis de la faseolotoxina, la cual, hasta ahora, se consideraba que era sintetizada por todas las cepas del patógeno con importancia epidemiológica. Sin embargo, en la Comunidad de Castilla y León, España, las epidemias de grasa de la judía en campo se asocian frecuentemente con cepas no toxigénicas de P. syringae pv. phaseolicola, que no pueden ser detectadas con los métodos moleculares y serológicos actuales. Los resultados presentados en este trabajo demuestran la existencia de aislados no toxigénicos de P. syringae pv. phaseolicola en zonas distintas de Castilla y León, lo que implica la necesidad de establecer una metodología fiable para la certificación de semillas de judía. Con este propósito, se presenta un sencillo protocolo en dos fases que permite la identificación de los dos tipos de aislados, y que se basa en una PCR multiplex con enriquecimiento a partir de extractos de semilla y en ensayos de patogenicidad

Detección mediante PCR multiplex y caracterización de cepas no toxigénicas de Pseudomonas syringae pv. phaseolicola de distintas zonas de España. Nota corta

El control eficiente de la grasa de la judía causada por Pseudomonas syringae pv. phaseolicola se basa principalmente en la utilización de semilla libre del patógeno. La detección del patógeno en semilla se efectúa mediante métodos altamente sensibles basados en la detección por PCR de los genes responsables de la biosíntesis de la faseolotoxina, la cual, hasta ahora, se consideraba que era sintetizada por todas las cepas del patógeno con importancia epidemiológica. Sin embargo, en la Comunidad de Castilla y León, España, las epidemias de grasa de la judía en campo se asocian frecuentemente con cepas no toxigénicas de P. syringae pv. phaseolicola, que no pueden ser detectadas con los métodos moleculares y serológicos actuales. Los resultados presentados en este trabajo demuestran la existencia de aislados no toxigénicos de P. syringae pv. phaseolicola en zonas distintas de Castilla y León, lo que implica la necesidad de establecer una metodología fiable para la certificación de semillas de judía. Con este propósito, se presenta un sencillo protocolo en dos fases que permite la identificación de los dos tipos de aislados, y que se basa en una PCR multiplex con enriquecimiento a partir de extractos de semilla y en ensayos de patogenicidad.The efficient control of halo blight, caused by Pseudomonas syringae pv. phaseolicola, is primarily based on the use of pathogen-free seed. Detection of the pathogen in seeds is currently carried out with high-sensitive methods based on the detection by PCR of genes involved in the biosynthesis of phaseolotoxin, which was believed to be produced by all strains of the pathogen with epidemiological importance. However, field epidemics of halo blight in the county of Castilla y Leon, Spain, are often associated to nontoxigenic isolates of P syringae pv. phaseolicola, which cannot be detected using current molecular and serological methods. The results presented in this work show the existence of nontoxigenic isolates of P syringae pv. phaseolicola in areas other than Castilla y Leon, indicating the need to establish a reliable methodology for seed certification. A simple two-step methodology is presented with the aim to identify both types of isolates that is based on a multiplex enrichment PCR of seed soakates and on pathogenicity assays.This work was supported with grant AGL2004- 03143, from the Spanish Ministerio de Educación y Ciencia (MEC). A. Rico was funded by a fellowship from the INIA. J. Murillo thanks the MEC for his support (grant PR2005-0299) during a sabbatical leave while this article was written

Changes in environmental CO2 concentration can modify Rhizobium-soybean specificity and condition plant fitness and productivity

Over the past 10 years, it has been demonstrated in the literature that legume responses to elevated [CO2], whether positive, negative, or null, are in part dependent on the Rhizobium species and genotypes that establish symbiosis with the plant. However, all the strains used in these past experiments were isolated in field conditions at ambient [CO2]. We studied for first time the fitness response of soybean inoculated with a Rhizobium strain that has been previously isolated from nodules of plants grown at elevated [CO2] in field conditions at a FACE site. In experiments developed in controlled growth chambers, and in the field under ambient [CO2], the plants inoculated with the strain isolated at elevated [CO2] showed similar response as plants without inoculation. We hypothesize that deficient nodulation may be associated with a change in root exudates caused by the change in [CO2]. This study showed that the strains isolated in nodules at elevated [CO2] are not capable of properly nodulating soybean plants grown at ambient [CO2] and that the origin of strains do not ensure the performance of plants under the same conditions. However, more research is needed in order to understand how changes in environmental conditions can affect the symbiotic relationship and ultimately how we can improve plant fitness in a changeable world.A. Sanz-Sáez was the recipient of a post-doctoral fellowship granted by the Education, Linguistic Policy, and Education Department of the Basque Country, Spain. This research was financially supported by the following grant: GRUPO GobiernoVasco-IT1022-16.Peer reviewe