GWAS identifies an ortholog of the rice D11 gene as a candidate gene for grain size in an international collection of hexaploid wheat.

Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 157 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-derived genotype calls obtained on Chinese Spring proved extremely accurate when compared to the reference (> 99.9%) and showed > 95% agreement with calls made at SNP loci shared with the 90 K SNP array on a subset of 71 Canadian wheat accessions for which both types of data were available. This indicates that GBS can yield a large amount of highly accurate SNP data in hexaploid wheat. The genetic diversity analysis performed using this set of SNP markers revealed the presence of six distinct groups within this collection. A GWAS was conducted to uncover genomic regions controlling variation for grain length and width. In total, seven SNPs were found to be associated with one or both traits, identifying three quantitative trait loci (QTLs) located on chromosomes 1D, 2D and 4A. In the vicinity of the peak SNP on chromosome 2D, we found a promising candidate gene (TraesCS2D01G331100), whose rice ortholog (D11) had previously been reported to be involved in the regulation of grain size. These markers will be useful in breeding for enhanced wheat productivity.

Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils.

Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 177 taxa (2 archaea, 103 bacteria, 41 fungi and 31 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our data set. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.

Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans.

BACKGROUND: Burkholderia cenocepacia is a human opportunistic pathogen causing devastating symptoms in patients suffering from immunodeficiency and cystic fibrosis. Out of the 303 B. cenocepacia strains with available genomes, the large majority were isolated from a clinical context. However, several isolates originate from other environmental sources ranging from aerosols to plant endosphere. Plants can represent reservoirs for human infections as some pathogens can survive and sometimes proliferate in the rhizosphere. We therefore investigated if B. cenocepacia had the same potential. RESULTS: We selected genome sequences from 31 different strains, representative of the diversity of ecological niches of B. cenocepacia, and conducted comparative genomic analyses in the aim of finding specific niche or host-related genetic determinants. Phylogenetic analyses and whole genome average nucleotide identity suggest that strains, registered as B. cenocepacia, belong to at least two different species. Core-genome analyses show that the clade enriched in environmental isolates lacks multiple key virulence factors, which are conserved in the sister clade where most clinical isolates fall, including the highly virulent ET12 lineage. Similarly, several plant associated genes display an opposite distribution between the two clades. Finally, we suggest that B. cenocepacia underwent a host jump from plants/environment to animals, as supported by the phylogenetic analysis. We eventually propose a name for the new species that lacks several genetic traits involved in human virulence. CONCLUSION: Regardless of the method used, our studies resulted in a disunited perspective of the B. cenocepacia species. Strains currently affiliated to this taxon belong to at least two distinct species, one having lost several determining animal virulence factors.

The Genetic Links to Anxiety and Depression (GLAD) Study: Online recruitment into the largest recontactable study of depression and anxiety.

BACKGROUND: Anxiety and depression are common, debilitating and costly. These disorders are influenced by multiple risk factors, from genes to psychological vulnerabilities and environmental stressors, but research is hampered by a lack of sufficiently large comprehensive studies. We are recruiting 40,000 individuals with lifetime depression or anxiety and broad assessment of risks to facilitate future research. METHODS: The Genetic Links to Anxiety and Depression (GLAD) Study (www.gladstudy.org.uk) recruits individuals with depression or anxiety into the NIHR Mental Health BioResource. Participants invited to join the study (via media campaigns) provide demographic, environmental and genetic data, and consent for medical record linkage and recontact. RESULTS: Online recruitment was effective; 42,531 participants consented and 27,776 completed the questionnaire by end of July 2019. Participants' questionnaire data identified very high rates of recurrent depression, severe anxiety, and comorbidity. Participants reported high rates of treatment receipt. The age profile of the sample is biased toward young adults, with higher recruitment of females and the more educated, especially at younger ages. DISCUSSION: This paper describes the study methodology and descriptive data for GLAD, which represents a large, recontactable resource that will enable future research into risks, outcomes, and treatment for anxiety and depression.

Dolphins in a Scaled-Down Mediterranean: The Gulf of Corinth's Odontocetes.

The Gulf of Corinth is a 2400-km2 semi-enclosed inland system (a mediterraneus) in central Greece. Its continental shelf areas, steep bottom relief, and waters up to 500-900m deep offer suitable habitat to neritic and pelagic species. We used photographic capture-recapture, distribution modelling, and direct observations to investigate the abundance, status, habitat preferences, movements, and group size of four odontocete species regularly observed in the Gulf, based on five years (2011-2015) of survey effort from small boats. Striped dolphins (Stenella coeruleoalba) are more abundant (1324 individuals, 95%CI 1158-1515) than was determined from previous estimates. Striped dolphins appear to be confined to the Gulf, where they favour deep and oligotrophic waters, and were encountered in single-species and mixed-species groups. Short-beaked common dolphins (Delphinus delphis) (22 individuals, 95%CI 16-31), individuals with intermediate pigmentation (possibly striped/common dolphin hybrids) (55, 95%CI 36-83), and a single Risso's dolphin (Grampus griseus) were only encountered in mixed-species groups with striped dolphins. Short-beaked common dolphins constitute a discrete conservation unit (subpopulation), and based on the current estimate, would qualify as Critically Endangered according to International Union for the Conservation of Nature (IUCN) Red List criteria. Common bottlenose dolphins (Tursiops truncatus) (39 animals, 95%CI 33-47) occur in single-species groups; they prefer continental shelf waters and areas near fish farms in the northern sector, and several animals appear to move into and out of the Gulf. Additionally, we contribute records of marine fauna and an assessment of the fishing fleet operating in the Gulf. Our study shows that the importance of this vulnerable marine environment has been underestimated, and management action must be taken to mitigate human impact and ensure long-term protection.

Knowledge Translation and Barriers to Imaging Optimization in the Emergency Department: A Research Agenda.

Researchers have attempted to optimize imaging utilization by describing which clinical variables are more predictive of acute disease and, conversely, what combination of variables can obviate the need for imaging. These results are then used to develop evidence-based clinical pathways, clinical decision instruments, and clinical practice guidelines. Despite the validation of these results in subsequent studies, with some demonstrating improved outcomes, their actual use is often limited. This article outlines a research agenda to promote the dissemination and implementation (also known as knowledge translation) of evidence-based interventions for emergency department (ED) imaging, i.e., clinical pathways, clinical decision instruments, and clinical practice guidelines. We convened a multidisciplinary group of stakeholders and held online and telephone discussions over a 6-month period culminating in an in-person meeting at the 2015 Academic Emergency Medicine consensus conference. We identified the following four overarching research questions: 1) what determinants (barriers and facilitators) influence emergency physicians' use of evidence-based interventions when ordering imaging in the ED; 2) what implementation strategies at the institutional level can improve the use of evidence-based interventions for ED imaging; 3) what interventions at the health care policy level can facilitate the adoption of evidence-based interventions for ED imaging; and 4) how can health information technology, including electronic health records, clinical decision support, and health information exchanges, be used to increase awareness, use, and adherence to evidence-based interventions for ED imaging? Advancing research that addresses these questions will provide valuable information as to how we can use evidence-based interventions to optimize imaging utilization and ultimately improve patient care.

Bidirectional microfluidic pumping using an array of magnetic Janus microspheres rotating around magnetic disks.

We demonstrate a novel, flexible and programmable method to pump liquid through microchannels in lab-on-a-chip systems without the use of an external pump. The pumping principle is based on the rotation of ferromagnetic Janus microspheres around permalloy disks, driven by an external rotating magnetic field. By placing the disks close to the edge of the microchannel, a pumping rate of at least 0.3 nL min(-1) was measured using tracking microspheres. Geometric programming of the pumping direction is possible by positioning the magnetic disk close to the side wall. A second degree of freedom in the pumping direction is offered by the rotational direction of the external magnetic field. This method is especially suited for flow-controlled recirculation of chemical and biological species in microchannels - for example, medium recirculation in culture chambers - opening the way towards novel, portable, on-chip applications without the need for external fluidic or electrical connections.

Detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) are important members of the plant microbiome. They are obligate biotrophs that colonize the roots of most land plants and enhance host nutrient acquisition. Many AMF themselves harbor endobacteria in their hyphae and spores. Two types of endobacteria are known in Glomeromycota: rod-shaped Gram-negative Candidatus Glomeribacter gigasporarum, CaGg, limited in distribution to members of the Gigasporaceae family, and coccoid Mollicutes-related endobacteria, Mre, widely distributed across different lineages of AMF. The goal of the present study is to investigate the patterns of distribution and coexistence of the two endosymbionts, CaGg and Mre, in spore samples of several strains of Gigaspora margarita. Based on previous observations, we hypothesized that some AMF could host populations of both endobacteria. To test this hypothesis, we performed an extensive investigation of both endosymbionts in G. margarita spores sampled from Cameroonian soils as well as in the Japanese G. margarita MAFF520054 isolate using different approaches (molecular phylotyping, electron microscopy, fluorescence in situ hybridization and quantitative real-time PCR). We found that a single AMF host can harbour both types of endobacteria, with Mre population being more abundant, variable and prone to recombination than the CaGg one. Both endosymbionts seem to retain their genetic and lifestyle peculiarities regardless of whether they colonize the host alone or together. These findings show for the first time that fungi support an intracellular bacterial microbiome, in which distinct types of endobacteria coexist in a single cell.

Large coronal shear fractures of the capitellum and trochlea treated with headless compression screws.

BACKGROUND: The purpose of this study is to retrospectively evaluate the clinical outcomes of 18 patients with large coronal shear fractures of the capitellum and lateral trochlea that underwent open reduction and internal fixation with headless compression screws. METHODS: Eighteen patients were identified (16 women, 2 men) with an average age of 45 years and an average follow-up of 26 months. Fractures were classified according to the Dubberley classification as 11 type-1A injuries and 7 type-2A injuries. RESULTS: All patients, with the exception of 1, had good to excellent functional results by the Broberg-Morrey scale (mean score, 93.3). Average arc of motion was 128 degrees in flexion/extension and 176 degrees in pronation/supination. Radiographically, 3 patients had subsequent development of avascular necrosis and 5 developed arthrosis. No significant negative correlation was noted between the development of avascular necrosis and clinical outcome. Minor complications occurred in 2 patients, but there were no re-operations. CONCLUSION: Headless compression screw fixation allows for stable fixation in patients with large coronal shear fractures of the distal humerus without posterior comminution. LEVEL OF EVIDENCE: 4.

Development of an on-line SPE-LC-ESI-MS method for urinary nucleosides: hyphenation of aprotic boronic acid chromatography with hydrophilic interaction LC-ESI-MS.

The development of an on-line automated SPE-HPLC--ESI-MS method is described for targeted metabolomic analysis of urinary modified nucleoside levels. The setup comprises a boronate affinity column as a trapping device, a hydrophilic interaction chromatography (HILIC) separation and information-dependent MS detection modes. The system was optimized using standards and tested on biological samples, detecting a number of modified nucleosides. Other urinary biomarkers could also be analyzed by the system developed: for example, the urinary nucleobases were also available for analysis. A simultaneous creatinine-monitoring experiment was also demonstrated to be viable when utilizing the method, which is of benefit as creatinine is a urinary normalizing factor.

Role of nitrogen lewis basicity in boronate affinity chromatography of nucleosides.

Urinary modified nucleosides have a potential role as cancer biomarkers, and most of the methods used in their study have utilized low-pressure phenylboronate affinity chromatography materials for the purification of the cis-diol-containing nucleosides. In this study, a boronate HPLC column was surprisingly shown not to trap the nucleosides as would be expected from experience with the classic Affigel 601 resin but showed only partial selectivity toward cis-diol groups while other groups exhibited better retention. In aprotic conditions, trapping of nucleosides was possible; however, the selectivity toward cis-diol-containing compounds was lost with the Lewis basicity of available nitrogens being the main determinant of retention. The experimental findings are compared to and confirmed by DFT calculations.

Mass spectrometric identification of Rab23 phosphorylation as a response to challenge by cytidine 3',5'-cyclic monophosphate in mouse brain.

While the functions and mechanisms of action of adenosine 3',5'-cyclic monophosphate (cAMP) and guanosine 3',5'-cyclic monophosphate (cGMP) are well established and are the basis of the action of a large number of successful pharmaceuticals, the role of a third naturally occurring cyclic nucleotide, cytidine 3',5'-cyclic monophosphate (cCMP), remains to be elucidated. Immobilized metal affinity chromatography (IMAC) was used to selectively extract proteins phosphorylated in mouse brain in response to challenge by cAMP, cGMP and cCMP, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToFMS) and liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) of tryptic digests to identify Rab23 as the first protein reported to be phosphorylated only in response to cCMP.

El trastorno por déficit de atención e hiperactividad y la Atención Primaria: pasado y perspectivas / Deficit attention hyperactivity disorder and Primary Care: past and future

El trastorno por déficit de atención e hiperactividad (TDAH) es una patología que va adquiriendo progresiva importancia a medida que transcurren los años. La razón principal es la comprobación de que, además de los problemas escolares, familiares y sociales de los niños que lo sufren, muchas alteraciones psiquiátricas y sociales del adolescente y el adulto ocurren en sujetos que han padecido o padecen de este trastorno desde la primera infancia. Dada la magnitud del problema, el TDAH tendría que caracterizarse como un problema de salud pública con implicación de los estamentos sanitarios al igual que ocurre en el campo educativo. El correcto manejo del TDAH supone un diagnóstico temprano y un seguimiento por un equipo multidisciplinar, donde el pediatra de Atención Primaria (PAP) podría ser la piedra angular al menos en los casos no complicados, que representarían más de la mitad de todos ellos. Además de la idoneidad intrínseca del pediatra para el seguimiento del TDAH, se debería tener en cuenta la absoluta escasez de los especialistas de paidoneurología y paidopsiquiatría si todos los afectados acudieran a sus consultas. El pediatra, por otro lado, sigue sin estar familiarizado con el TDAH, remiso a cualquier intervención. El objetivo de este seminario, en el que solamente intervienen PAP, es comenzar un proceso de familiarización con el problema para aquellos que quieran hacerlo y profundizar en él y reafirmarse en aquellos que hayan superado esa primera fase (AU)

The deficit attention hyperactivity disorder (DAHD) is getting more and more important with the coming years. The main reason is that besides school, family and social problems in childhood, many psychiatric and social disorders of adolescents and adults take place in people that have suffered or suffer this disorder since preschool years. DADH should be considered a public health problem involving sanitary instances in the same way as it involves educative instances. The right management of DADH implies an early diagnosis and a follow up by a multidisciplinary team, where the Primary Care paediatrician (PCP) could be the key stone at least in the non complicated cases, which would be more that half of all them. Besides of being the paediatrician intrinsically suitable for the DADH follow up, it should be taken into account the lack of enough specialists in paidoneurology and paidopsichiatry to assist all patients in their settings. The paediatrician, on the other hand, continues without being familiar to this condition and unwilling to any intervention. The objective of this seminar, in witch only PCP are involved, is to begin a proceeding of becoming familiar to the problem for those willing to, and to deepen and reassure their previous information for those who have overcome the first phase yet (AU)

Genotyping of recombinant Pichia pastoris strains.

A simplified amplified-fragment length polymorphism (AFLP) method was used to genotype Pichia pastoris strains obtained by transformation of P. pastoris strain GS115 with a single integration vector. A total of 14 transformants and 3 control strains were analyzed, which generated 16 different band patterns. A clonal variation was obtained after the transformation process due to genetic differences generated during the transformation event of the host strain. Furthermore, the cluster analysis showed that the transformants with lesser genetic differences with respect to the P. pastoris host strain are the recombinant strains with the highest level of recombinant protein production.

In-source CID of guanosine: gas phase ion-molecule reactions.

In-source collision induced dissociation was applied to access second generation ions of protonated guanosine. The in-source gas-phase behavior of [BH2]+-NH3 (m/z 135, C5H3N4O+) was investigated. Adduct formation and reactions with available solvent molecules (H2O and CH3OH) were demonstrated. Several addition/elimination sequences were observed for this particular ion and solvent molecules. Dissociation pathways for the newly formed ions were developed using a QqTOF mass spectrometer, permitting the assignment of elemental compositions of all product ions produced. Reaction schemes were suggested arising from the ring-opened intermediate of the protonated base moiety [BH2]+, obtained from fragmentation of guanosine. The mass spectral data revealed that the in-source CH3OH-reaction product underwent more complex fragmentations than the comparable ion following reaction with H2O. A rearrangement and a parallel radical dissociation pathway were discerned. Apart from the mass spectrometric evidence, the fragmentation schemes are supported by density functional theory calculations, in which the reaction of the ring-opened protonated guanine intermediate with CH3OH and a number of subsequent fragmentations were elaborated. Additionally, an in-source transition from the ring-opened intermediate of protonated guanine to the ring-opened intermediate of protonated xanthine was suggested. For comparison, a low-energy collision induced dissociation study of xanthosine was performed. Its dissociation pathways agreed with our assumption.

Analysis of urinary nucleosides. V. Identification of urinary pyrimidine nucleosides by liquid chromatography/electrospray mass spectrometry.

Modified urinary nucleosides are potentially invaluable in cancer diagnosis, as they reflect altered RNA turnovers. High-performance liquid chromatography (HPLC) was combined with full-scan mass spectrometry, tandem mass spectrometry, MS(n) analysis and accurate mass measurements in order to identify pyrimidine nucleosides purified from urine. Potential nucleosides were assessed by their evident UV absorbance in the HPLC chromatogram and then further examined by the various mass spectrometric techniques. In this manner numerous pyrimidine nucleosides were identified in the urine samples from cancer patients including pseudouridine, cytidine, two methylcytidines and an acetylcytidine. Furthermore, a number of novel modified pyrimidine nucleosides were tentatively identified via critical interpretation of the combined mass spectrometric data.

P2Y12 receptor signalling towards PKB proceeds through IGF-I receptor cross-talk and requires activation of Src, Pyk2 and Rap1.

Previously it was shown that stimulation of the P2Y12 receptor activates PKB signalling in C6 glioma cells [K. Van Kolen and H. Slegers, J. Neurochem. 89, 442.]. In the present study, the mechanisms involved in this response were further elucidated. In cells transfected with the Gbetagamma-scavenger beta-ARK1/GRK2 or Rap1GAPII, stimulation with 2MeSADP failed to enhance PKB phosphorylation demonstrating that the signalling proceeds through Gbetagamma-subunits and Rap1. Moreover, Rap1-GTP pull-down assays revealed that P2Y12 receptor stimulation induced a rapid activation of Rap1. Treatment of cells with the Ca2+ chelator BAPTA-AM and inhibition of Src and PLD2 with PP2 or 1-butanol, respectively, abrogated P2Y12 receptor-mediated activation of Rap1 and PKB. In addition inhibition of PKCzeta decreased basal and 2MeSADP-stimulated phosphorylation of PKB indicating a role for this PKC isoform in PKB signalling. Although the increased PKB phosphorylation was abolished in the presence of the IGF-I receptor tyrosine kinase inhibitor AG 1024, 2MeSADP did not significantly increase receptor phosphorylation. Nevertheless, phosphorylation of a 120 kDa IGF-I receptor-associated protein was observed. The latter protein was identified by MALDI-TOF/TOF-MS as the proline-rich tyrosine kinase 2 (Pyk2) that co-operates with Src in a PLD2-dependent manner. Consistent with the signalling towards Rap1 and PKB, activation of Pyk2 was abrogated by Ca2+ chelation, inhibition of PLD2 and IGF-I receptor tyrosine kinase activity. In conclusion, the data reveal a novel type of cross-talk between P2Y12 and IGF-I receptors that proceeds through Gbetagamma-, Ca2+-and PLD2-dependent activation of the Pyk2/Src pathway resulting in GTP-loading of Rap1 required for an increased PKB phosphorylation.

Study of the mass spectrometric fragmentation of pseudouridine: comparison of fragmentation data obtained by matrix-assisted laser desorption/ionisation post-source decay, electrospray ion trap multistage mass spectrometry, and by a method utilising electrospray quadrupole time-of-flight tandem mass spectrometry and in-source fragmentation.

Many nucleosides and their modified forms have been studied by mass spectrometry elaborating the detailed fragmentation pathways under MS2 and MS(n) conditions. Although the C-nucleoside pseudouridine has been fragmented and studied briefly, usually amongst many other nucleosides, it has not been investigated to the same extent as other nucleosides. In this report a number of different mass spectrometric techniques are applied to obtain a fuller picture of pseudouridine fragmentation. At the same time this study is used to compare different tandem mass spectrometric techniques, including a novel methodology utilising a quadrupole time-of-flight (Q-ToF) instrument for MS(n) analysis comparable with that available with an ion trap mass spectrometer.

First results of a quantitative study of DNA adducts of melphalan in the rat by isotope dilution mass spectrometry using capillary liquid chromatography coupled to electrospray tandem mass spectrometry.

Rats were intravenously injected with a single high dose (10 mg/kg) of the alkylating agent melphalan in order to study DNA-adduct formation. Quantitation of a dGuo-melphalan adduct was done by isotope dilution mass spectrometry using capillary liquid chromatography/mass spectrometry (LC/MS) and [15N5]-labeled dGuo-melphalan as internal standard. DNA-adduct levels were studied in bone marrow, liver and kidney. The instrumental detection limit of the method was determined to be 900 fg (S/N 3, pure standard). These first results clearly show a 10 times higher adduct level in bone marrow compared to kidney and a 6 times higher level compared to liver. More experiments will be necessary to gather more information on the pharmacokinetics of melphalan-DNA adducts under in vivo conditions.