83 research outputs found
Introduction of exogenous AMF species alters the biological diversity and functionality of AMF communities associated with cowpea
The salinity in arid and semi-arid areas of the world is rapidly expanding due to climate change and anthropogenic activities. The use of inoculants containing beneficial microbes (e.g. arbuscular mycorrhizal fungi (AMF) and rhizobia) is a promising alternative to improve plant production in these regions. Here, we investigated the effect of common agricultural practices such as the use of beneficial microbes as inoculum and crop rotation on cowpea growth and on its association with soil microbes under non- and salt-stressed conditions. Plant experiments were carried out using non-sterilized soil (supplemented or not with NaCl) under greenhouse conditions. Bradyrhizobium yuanmingense BR 3267 strain and a commercial mixture of AMF (Endoplant Riego) were used as inoculants. In parallel, we assessed cowpea growth following succession of buffelgrass (Cenchrus ciliaris) with or without prior soil disturbance. Plant and symbiotic parameters, nutrient content in leaves and AMF and root nodule communities through DNA metabarcoding were evaluated. Under non-stressed conditions, inoculation with AMF and/or BR 3267 strain led to significant increase of cowpea biomass production and higher N or P content in leaves. The imposed saline condition affected the cowpea growth although without significantly affecting the symbiotic parameters. Moreover, the increase of AMF propagules available in the soil at buffelgrass sowing through the inoculation of commercial AMF was a determining factor to mitigate the effects of soil tillage and salinity on cowpea growth. The bacterial communities in the root nodules were affected by AMF communities rather by rhizobia inoculation. Benefits of commercial AMF could be explained by changes in the biological and functionality of the AMF communities associated with cowpea. This study reveals that microbial inoculation and crop rotation are effective practices for improvement of cowpea growth and on mitigating the harmful effects of salt
Dupla inoculação (rizĂłbio e fungos micorrĂzicos arbusculares) mitigam efeitos nocivos da salinidade no crescimento do feijĂŁo-caupi
A salinidade em áreas áridas e semiáridas do mundo está a expandir rapidamente devido Ă s alterações climáticas e atividades humanas. O uso de inĂłculos contendo microrganismos benĂ©ficos, como fungos micorrĂzicos arbusculares (FMA) e bactĂ©rias simbiĂłticas fixadoras de azoto, aliado ao manejo adequado do solo e das culturas, Ă© uma alternativa promissora para melhorar a produção vegetal nessas regiões. Aqui, investigámos o efeito de práticas agrĂcolas comuns, nomeadamente a utilização de microrganismos benĂ©ficos como inĂłculo e a perturbação do solo entre a rotação de culturas, no crescimento do feijĂŁo-caupi e na sua associação com micrĂłbios do solo sob condições salinas e nĂŁo salinas. A estirpe Bradyrhizobium yuanmingense BR 3267, e uma mistura comercial de FMA (Endoplant Riego) foram utilizados como inĂłculos. Paralelamente, avaliámos o crescimento do feijĂŁo-caupi, apĂłs sucessĂŁo ao capim-buffel com ou sem perturbação prĂ©via do solo. Ensaios de plantas em solo nĂŁo-esterilizado (suplementado ou nĂŁo com NaCl) foram realizados em dois ciclos de 75 dias em estufa. Parâmetros vegetais e simbiĂłticos e o teor de nutrientes nas folhas foram determinados, bem como a diversidade bacteriana e de FMA em raĂzes e nĂłdulos de feijĂŁo-caupi por meio de sequenciamento DNA metabarcode.
Os nossos dados revelaram que os parâmetros simbiĂłticos (nĂşmero de nĂłdulos e/ou taxa de colonização) foram melhorados no feijĂŁo-caupi inoculado com Bradyrhizobium e/ou FMA comercial, o que consequentemente resultou em maior teor de N ou P nas folhas. A salinidade imposta afetou negativamente o crescimento do feijĂŁo, porĂ©m sem afetar significativamente os parâmetros simbiĂłticos analisados. O aumento de propágulos de FMA disponĂveis no solo atravĂ©s da inoculação de FMA comercial foi um fator determinante para mitigar os efeitos do manejo do solo no crescimento do feijĂŁo. A perturbação do solo mostrou impacto negativo nos parâmetros vegetais e simbiĂłticos, exceto para o nĂşmero de nĂłdulos. AlĂ©m disso, os efeitos positivos do uso de FMA comercial no crescimento do feijĂŁo-caupi, em condições controlo ou de salinidade podem ser explicados pelas mudanças na funcionalidade das comunidades de FMA associadas ao feijĂŁo-caupi. Por outro lado, as comunidades bacterianas em nĂłdulos ou raĂzes do feijĂŁo nĂŁo foram afetadas pela inoculação de FMA ou de rizĂłbios. Este estudo revela que a dupla inoculação (mistura de rizĂłbio e FMA) e a rotação de culturas, sem a perturbação do solo, sĂŁo práticas eficazes para melhorar o crescimento do feijĂŁo-caupi e mitigar os efeitos nocivos do sal no seu crescimento. Mais, estes resultados tambĂ©m sugerem que os efeitos sinĂ©rgicos entre rizĂłbios e FMA dependem principalmente de um estabelecimento bem-sucedido da simbiose entre FMA e a planta hospedeira e nĂŁo da comunidade de FMA em si
Down-Regulation of Honey Bee IRS Gene Biases Behavior toward Food Rich in Protein
Food choice and eating behavior affect health and longevity. Large-scale research efforts aim to understand the molecular and social/behavioral mechanisms of energy homeostasis, body weight, and food intake. Honey bees (Apis mellifera) could provide a model for these studies since individuals vary in food-related behavior and social factors can be controlled. Here, we examine a potential role of peripheral insulin receptor substrate (IRS) expression in honey bee foraging behavior. IRS is central to cellular nutrient sensing through transduction of insulin/insulin-like signals (IIS). By reducing peripheral IRS gene expression and IRS protein amount with the use of RNA interference (RNAi), we demonstrate that IRS influences foraging choice in two standard strains selected for different food-hoarding behavior. Compared with controls, IRS knockdowns bias their foraging effort toward protein (pollen) rather than toward carbohydrate (nectar) sources. Through control experiments, we establish that IRS does not influence the bees' sucrose sensory response, a modality that is generally associated with food-related behavior and specifically correlated with the foraging preference of honey bees. These results reveal a new affector pathway of honey bee social foraging, and suggest that IRS expressed in peripheral tissue can modulate an insect's foraging choice between protein and carbohydrate sources
Protein Complex Evolution Does Not Involve Extensive Network Rewiring
The formation of proteins into stable protein complexes plays a fundamental role in the operation of the cell. The study of the degree of evolutionary conservation of protein complexes between species and the evolution of protein-protein interactions has been hampered by lack of comprehensive coverage of the high-throughput (HTP) technologies that measure the interactome. We show that new high-throughput datasets on protein co-purification in yeast have a substantially lower false negative rate than previous datasets when compared to known complexes. These datasets are therefore more suitable to estimate the conservation of protein complex membership than hitherto possible. We perform comparative genomics between curated protein complexes from human and the HTP data in Saccharomyces cerevisiae to study the evolution of co-complex memberships. This analysis revealed that out of the 5,960 protein pairs that are part of the same complex in human, 2,216 are absent because both proteins lack an ortholog in S. cerevisiae, while for 1,828 the co-complex membership is disrupted because one of the two proteins lacks an ortholog. For the remaining 1,916 protein pairs, only 10% were never co-purified in the large-scale experiments. This implies a conservation level of co-complex membership of 90% when the genes coding for the protein pairs that participate in the same protein complex are also conserved. We conclude that the evolutionary dynamics of protein complexes are, by and large, not the result of network rewiring (i.e. acquisition or loss of co-complex memberships), but mainly due to genomic acquisition or loss of genes coding for subunits. We thus reveal evidence for the tight interrelation of genomic and network evolution
Use of Robson classification to assess cesarean section rate in Brazil: the role of source of payment for childbirth
Testing for an Unusual Distribution of Rare Variants
Technological advances make it possible to use high-throughput sequencing as a primary discovery tool of medical genetics, specifically for assaying rare variation. Still this approach faces the analytic challenge that the influence of very rare variants can only be evaluated effectively as a group. A further complication is that any given rare variant could have no effect, could increase risk, or could be protective. We propose here the C-alpha test statistic as a novel approach for testing for the presence of this mixture of effects across a set of rare variants. Unlike existing burden tests, C-alpha, by testing the variance rather than the mean, maintains consistent power when the target set contains both risk and protective variants. Through simulations and analysis of case/control data, we demonstrate good power relative to existing methods that assess the burden of rare variants in individuals
Modularity in Protein Complex and Drug Interactions Reveals New Polypharmacological Properties
Recent studies have highlighted the importance of interconnectivity in a large range of molecular and human disease-related systems. Network medicine has emerged as a new paradigm to deal with complex diseases. Connections between protein complexes and key diseases have been suggested for decades. However, it was not until recently that protein complexes were identified and classified in sufficient amounts to carry out a large-scale analysis of the human protein complex system. We here present the first systematic and comprehensive set of relationships between protein complexes and associated drugs and analyzed their topological features. The network structure is characterized by a high modularity, both in the bipartite graph and in its projections, indicating that its topology is highly distinct from a random network and that it contains a rich and heterogeneous internal modular structure. To unravel the relationships between modules of protein complexes, drugs and diseases, we investigated in depth the origins of this modular structure in examples of particular diseases. This analysis unveils new associations between diseases and protein complexes and highlights the potential role of polypharmacological drugs, which target multiple cellular functions to combat complex diseases driven by gain-of-function mutations
A Novel Adaptive Method for the Analysis of Next-Generation Sequencing Data to Detect Complex Trait Associations with Rare Variants Due to Gene Main Effects and Interactions
There is solid evidence that rare variants contribute to complex disease etiology. Next-generation sequencing technologies make it possible to uncover rare variants within candidate genes, exomes, and genomes. Working in a novel framework, the kernel-based adaptive cluster (KBAC) was developed to perform powerful gene/locus based rare variant association testing. The KBAC combines variant classification and association testing in a coherent framework. Covariates can also be incorporated in the analysis to control for potential confounders including age, sex, and population substructure. To evaluate the power of KBAC: 1) variant data was simulated using rigorous population genetic models for both Europeans and Africans, with parameters estimated from sequence data, and 2) phenotypes were generated using models motivated by complex diseases including breast cancer and Hirschsprung's disease. It is demonstrated that the KBAC has superior power compared to other rare variant analysis methods, such as the combined multivariate and collapsing and weight sum statistic. In the presence of variant misclassification and gene interaction, association testing using KBAC is particularly advantageous. The KBAC method was also applied to test for associations, using sequence data from the Dallas Heart Study, between energy metabolism traits and rare variants in ANGPTL 3,4,5 and 6 genes. A number of novel associations were identified, including the associations of high density lipoprotein and very low density lipoprotein with ANGPTL4. The KBAC method is implemented in a user-friendly R package
Genomic expression profiling of human inflammatory cardiomyopathy (DCMi) suggests novel therapeutic targets
The clinical phenotype of human dilated cardiomyopathy (DCM) encompasses a broad spectrum of etiologically distinct disorders. As targeting of etiology-related pathogenic pathways may be more efficient than current standard heart failure treatment, we obtained the genomic expression profile of a DCM subtype characterized by cardiac inflammation to identify possible new therapeutic targets in humans. In this inflammatory cardiomyopathy (DCMi), a distinctive cardiac expression pattern not described in any previous study of cardiac disorders was observed. Two significantly altered gene networks of particular interest and possible interdependence centered around the cysteine-rich angiogenic inducer 61 (CYR61) and adiponectin (APN) gene. CYR61 overexpression, as in human DCMi hearts in situ, was similarly induced by inflammatory cytokines in vascular endothelial cells in vitro. APN was strongly downregulated in DCMi hearts and completely abolished cytokine-dependent CYR61 induction in vitro. Dysbalance between the CYR61 and APN networks may play a pathogenic role in DCMi and contain novel therapeutic targets. Multiple immune cell-associated genes were also deregulated (e.g., chemokine ligand 14, interleukin-17D, nuclear factors of activated T cells). In contrast to previous investigations in patients with advanced or end-stage DCM where etiology-related pathomechanisms are overwhelmed by unspecific processes, the deregulations detected in this study occurred at a far less severe and most probably fully reversible disease stage. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00109-006-0122-9 and is accessible for authorized users
Baseline and Quality Reference Values for Natural Radionuclides in Soils of Rio de Janeiro State, Brazil
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