Elucidating the mystery of the tripartite symbiosis plant – mycorrhizal fungi – dark septate endophytes

Non-Peer ReviewedThis study provides information on the tripartite symbiotic relationships formed by arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) in crops growing in the semiarid region of the Canadian Prairie. We found the symbiotic root systems of wheat, pea, chickpea and lentil to be morphologically distinct. The relationship between DSE and AMF abundance in roots ranged from negative in lentil to positive in wheat

Structural implications of the DFD-in domain in computer-aided molecular design of MAP kinase interacting kinase 2 inhibitors.

Protein translation is a key process on cell development and proliferation that is often deregulated in cancer. MAP kinase interacting kinases 1 and 2(Mnk1/2) play a pivotal role in regulating the capdependent translation through phosphorylation ofeIF4E transcription factor. Thus, Mnk1/2 targeting have been proposed as a novel therapeutic strategy that would minimize side-effects in contrast to other therapies. For this reason, there is a growing interestin designing in silico new Mnk1/2 inhibitors which demands from reliable structural models. Interestingly,the catalytic domain of Mnk proteins are characterized by a DFD motif instead of the characteristicDFG motif of other kinases. However, Mnk2 structural models described in literature are DFG mutated and do not contain the activation loop. Molecular design techniques have been applied to obtain a structural model of the full wild type Mnk2 protein including the activation loop. The effect of the loop on the interaction mechanism of well-known ligands has been evaluated. Obtained results suggest that the presence of the activation loop is determinant for the correct prediction of the active site and it is essential for the design of new inhibitors

Pulse-wheat rotations influence the potential of nitrous oxide (N2O) production in the Canadian prairie

Non-Peer Reviewe

Bases for the management of the AM symbiosis in cropping systems of the prairie

Non-Peer Reviewe

LES-based Study of the Roughness Effects on the Wake of a Circular Cylinder from Subcritical to Transcritical Reynolds Numbers

This paper investigates the effects of surface roughness on the flow past a circular cylinder at subcritical to transcritical Reynolds numbers. Large eddy simulations of the flow for sand grain roughness of size k/D = 0.02 are performed (D is the cylinder diameter). Results show that surface roughness triggers the transition to turbulence in the boundary layer at all Reynolds numbers, thus leading to an early separation caused by the increased momentum deficit, especially at transcritical Reynolds numbers. Even at subcritical Reynolds numbers, boundary layer instabilities are triggered in the roughness sublayer and eventually lead to the transition to turbulence. The early separation at transcritical Reynolds numbers leads to a wake topology similar to that of the subcritical regime, resulting in an increased drag coefficient and lower Strouhal number. Turbulent statistics in the wake are also affected by roughness; the Reynolds stresses are larger due to the increased turbulent kinetic energy production in the boundary layer and separated shear layers close to the cylinder shoulders.We acknowledge “Red Española de Surpercomputación” (RES) for awarding us access to the MareNostrum III machine based in Barcelona, Spain (Ref. FI-2015-2-0026 and FI-2015-3-0011). We also acknowledge PRACE for awarding us access to Fermi and Marconi Supercomputers at Cineca, Italy (Ref. 2015133120). Oriol Lehmkuhl acknowledges a PDJ 2014 Grant by AGAUR (Generalitat de Catalunya). Ugo Piomelli acknowledges the support of the Natural Sciences and Engineering Research Council (NSERC) of Canada under the Discovery Grant Programme (Grant No. RGPIN-2016-04391). Ricard Borrell acknowledges a Juan de la Cierva postdoctoral grant (IJCI-2014-21034). Ivette Rodriguez, Oriol Lehmkuhl, Ricard Borrell and Assensi Oliva acknowledge Ministerio de Economía y Competitividad, Secretaría de Estado de Investigación, Desarrollo e Innovación, Spain (ref. ENE2014-60577-R).Peer ReviewedPostprint (author's final draft

First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Nepal

BACKGROUND: Tuberculosis (TB) is a major public health problem in Nepal. Strain variation in Mycobacterium tuberculosis may influence the outcome of TB infection and disease. To date, the phylogenetic diversity of M. tuberculosis in Nepal is unknown. METHODS AND FINDINGS: We analyzed 261 M. tuberculosis isolates recovered from pulmonary TB patients recruited between August 2009 and August 2010 in Nepal. M. tuberculosis lineages were determined by single nucleotide polymorphisms (SNP) typing and spoligotyping. Drug resistance was determined by sequencing the hot spot regions of the relevant target genes. Overall, 164 (62.8%) TB patients were new, and 97 (37.2%) were previously treated. Any drug resistance was detected in 50 (19.2%) isolates, and 16 (6.1%) were multidrug-resistant. The most frequent M. tuberculosis lineage was Lineage 3 (CAS/Delhi) with 106 isolates (40.6%), followed by Lineage 2 (East-Asian lineage, includes Beijing genotype) with 84 isolates (32.2%), Lineage 4 (Euro-American lineage) with 41 (15.7%) isolates, and Lineage 1 (Indo-Oceanic lineage) with 30 isolates (11.5%). Based on spoligotyping, we found 45 different spoligotyping patterns that were previously described. The Beijing (83 isolates, 31.8%) and CAS spoligotype (52, 19.9%) were the dominant spoligotypes. A total of 36 (13.8%) isolates could not be assigned to any known spoligotyping pattern. Lineage 2 was associated with female sex (adjusted odds ratio [aOR] 2.58, 95% confidence interval [95% CI] 1.42-4.67, p = 0.002), and any drug resistance (aOR 2.79; 95% CI 1.43-5.45; p = 0.002). We found no evidence for an association of Lineage 2 with age or BCG vaccination status. CONCLUSIONS: We found a large genetic diversity of M. tuberculosis in Nepal with representation of all four major lineages. Lineages 3 and 2 were dominating. Lineage 2 was associated with clinical characteristics. This study fills an important gap on the map of the M. tuberculosis genetic diversity in the Asian reg

Parentage studies in Salmo salar L., 1758 using microsatellites

Seven microsatellite loci were examined to assess their usefulness in parentage studies of Salmo salar L.,1758, using 105 offspring from 21 families of salmon proceeding from the Cares, Sella and Narcea Rivers in Asturias (northwestern Spain). Although we found that only the SSOSL311 and SSOSL417 loci had high levels of variability (He 0.7), the entire set of loci enabled us to correctly assign both parents for at least 80 % of all samples. Full siblings and non-related individuals presented means of relatedness coefficients close to those theoretically expected for each group of individuals (R = 0.5, and R = 0, respectively), and pairs of full sibling individuals with R values of less than zero were only 4% (Narcea), 6% (Sella) and 12.5% (Cares) of the samples.En este trabajo se analiza la capacidad de siete loci microsatélites para establecer relaciones de parentesco entre individuos en muestras de salmón atlántico Salmo salar L., 1758. Para ello, se han utilizado 105 individuos procedentes de 21 familias creadas por cruzamientos individuales entre reproductores pertenecientes a los ríos asturianos Narcea, Cares y Sella. Aunque sólo dos de los loci analizados (SSOSL311 y SSOSL417) presentan altos niveles de variabilidad en estas muestras (He 0,7), en conjunto permiten asignar correctamente a ambos parentales al menos al 80 % de los descendientes. Las distribuciones de los coeficientes de relación genética (R) entre hermanos completos y no relacionados exhiben medias cercanas a las esperadas teóricamente (R = 0,5 y R = 0, respectivamente) y solamente el 4% (en el río Narcea), el 6% (en el Sella) y el 12,5 % (en el Cares) de las comparaciones entre hermanos completos muestran valores de R menores que cero.Instituto Español de Oceanografí

Abundant Occurrence of Basal Radial Glia in the Subventricular Zone of Embryonic Neocortex of a Lissencephalic Primate, the Common Marmoset Callithrix jacchus

Subventricular zone (SVZ) progenitors are a hallmark of the developing neocortex. Recent studies described a novel type of SVZ progenitor that retains a basal process at mitosis, sustains expression of radial glial markers, and is capable of self-renewal. These progenitors, referred to here as basal radial glia (bRG), occur at high relative abundance in the SVZ of gyrencephalic primates (human) and nonprimates (ferret) but not lissencephalic rodents (mouse). Here, we analyzed the occurrence of bRG cells in the embryonic neocortex of the common marmoset Callithrix jacchus, a near-lissencephalic primate. bRG cells, expressing Pax6, Sox2 (but not Tbr2), glutamate aspartate transporter, and glial fibrillary acidic protein and retaining a basal process at mitosis, occur at similar relative abundance in the marmoset SVZ as in human and ferret. The proportion of progenitors in M-phase was lower in embryonic marmoset than developing ferret neocortex, raising the possibility of a longer cell cycle. Fitting the gyrification indices of 26 anthropoid species to an evolutionary model suggested that the marmoset evolved from a gyrencephalic ancestor. Our results suggest that a high relative abundance of bRG cells may be necessary, but is not sufficient, for gyrencephaly and that the marmoset's lissencephaly evolved secondarily by changing progenitor parameters other than progenitor typ

Application of microsatellite markers to the management of farmed stocks of turbot Scophthalmus maximus (L., 1758)

In the present study, eight microsatellite loci were used to estimate genetic relatedness and pedigree determination in turbot Scophthalmus maximus (L., 1758). Through genotypic analysis of broodstocks and their progenies, from two different turbot hatcheries, the capacity of these loci to correctly classify individuals as related or non-related was examined. Relatedness coefficients among related and non-related individuals presented means close to those theoretically expected, and the percentages of related individuals included in all relatedness coefficients found to be below the R = 0 value ranged from 0% (hatchery A) to 29 % (hatchery B). The identification of both parents for each individual was possible in more than 80 % of the cases from hatchery A, but only 41% of those from hatchery B.Se utilizaron ocho loci microsatélites en la estimación de relaciones genéticas y determinación de pedigríes en rodaballo Scophthalmus maximus (L., 1758). Mediante el análisis de los genotipos de reproductores y descendientes de dos piscifactorías se investigó la capacidad de los loci para clasificar correctamente a los individuos como emparentados o no. Las distribuciones de los coeficientes de relación genética (R) entre individuos emparentados y no relacionados exhiben medias cercanas a las esperadas teóricamente y el porcentaje de individuos emparentados que forman el total de coeficientes de relación genética que se encuentran por debajo del valor R = 0 oscilan entre el 0 % (estación A) y el 29 % (estación B). Así mismo, la identificación correcta de ambos parentales para cada descendiente fue posible en más del 80 % de los casos en la estación A y en sólo el 41 % en la estación B.Instituto Español de Oceanografí