Nitrogen-fixing bacteria communities occurring in soils under different uses in the Western Amazon Region as indicated by nodulation of siratro (Macroptilium atropurpureum)

Understanding native communities is a crucial step for the management of biological nitrogen fixation, since they may be either a source of efficient strains or a limiting factor when efficient strains need to be introduced. This work aimed to evaluate the density, diversity and efficiency of Leguminosae nodulating bacterial (LNB) communities and their component strains in soils under various land use systems (LUSs): pristine forest, agriculture, pasture, agroforestry, young secondary forest, and old secondary forest,. The LNB communities were trapped from these soils by using the promiscuous host siratro under controlled conditions. We also studied their relationships with physical and chemical attributes of the soil. Agroforestry and agriculture soil samples induced the highest number of nodules in siratro, while forest soil samples induced the lowest number of nodules. No relationship was found between LNB and Leguminosae species diversity in the LUSs. The soil chemical variables that were most related to differences in nodule number and shoot dry matter weight of plants inoculated with soil suspensions of the LUSs were, respectively: Ca²⁺, Mg²⁺, base saturation, exchangeable bases and Cu²⁺; and pH, cation exchange capacity, B, Cu²⁺ and clay. Although, LNB communities from all LUSs were efficient under controlled and similar conditions, they were found to be composed of strains with variable efficiency: inefficient, efficient, highly efficient and superior efficiency. Efficient strains occurred at the highest frequency in all LUSs. The isolated strains presented similar and new sequences that were phylogenetically related to well known LNB genera in α-and β-Proteobacteria. Unusual genera in these branches, as well as in other branches, which are probably endophytic bacteria, were also isolated from nodules. These data support siratro as a useful trap species to study the LNB biodiversity of diverse ecosystems in tropical soils. The fact that the highest diversity and nodulation were seen in managed systems such as agriculture and agroforestry suggests a high resilience of LNB communities to changes in land use after deforestation in a region where large forest areas are still preserved and can be a source of propagules.     

A bacterial ortholog of class II lysyl-tRNA synthetase activates lysine

Aminoacyl-tRNA synthetases produce aminoacyl-tRNAs, essential substrates for accurate protein synthesis. Beyond their central role in translation some of these enzymes or their orthologs are recruited for alternative functions, not always related to their primary cellular role. We investigate here the enzymatic properties of GenX (also called PoxA and YjeA), an ortholog of bacterial class II lysyl-tRNA synthetase. GenX is present in most Gram-negative bacteria and is homologous to the catalytic core of lysyl-tRNA synthetase, but it lacks the amino terminal anticodon binding domain of the latter enzyme. We show that, in agreement with its well-conserved lysine binding site, GenX can activate in vitro l-lysine and lysine analogs, but does not acylate tRNA^Lys or other cellular RNAs.     

A Novel MicroRNA-132-Surtuin-1 Axis Underlies Aberrant B-cell Cytokine Regulation in Patients with Relapsing-Remitting Multiple Sclerosis

Clinical trial results demonstrating that B-cell depletion substantially reduces new relapses in patients with multiple sclerosis (MS) have established that B cells play a role in the pathophysiology of MS relapses. The same treatment appears not to impact antibodies directed against the central nervous system, which underscores the contribution of antibody-independent functions of B cells to disease activity. One mechanism by which B cells are now thought to contribute to MS activity is by over-activating T cells, including through aberrant expression of B cell pro-inflammatory cytokines. However, the mechanisms underlying the observed B cell cytokine dysregulation in MS remain unknown. We hypothesized that aberrant expression of particular microRNAs might be involved in the dysregulated pro-inflammatory cytokine responses of B cells of patients with MS. Through screening candidate microRNAs in activated B cells of MS patients and matched healthy subjects, we discovered that abnormally increased secretion of lymphotoxin and tumor necrosis factor α by MS B cells is associated with abnormally increased expression of miR-132. Over-expression of miR-132 in normal B cells significantly enhanced their production of lymphotoxin and tumor necrosis factor α. The over-expression of miR-132 also suppressed the miR-132 target, sirtuin-1. We confirmed that pharmacological inhibition of sirtuin-1 in normal B cells induces exaggerated lymphotoxin and tumor necrosis factor α production, while the abnormal production of these cytokines by MS B cells can be normalized by resveratrol, a sirtuin-1 activator. These results define a novel miR-132-sirtuin-1 axis that controls pro-inflammatory cytokine secretion by human B cells, and demonstrate that a dysregulation of this axis underlies abnormal pro-inflammatory B cell cytokine responses in patients with MS.     

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data

The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data.     

Circadian Clock Genes Modulate Human Bone Marrow Mesenchymal Stem Cell Differentiation,Migration and Cell Cycle

Many of the components that regulate the circadian clock have been identified in organisms and humans. The influence of circadian rhythm (CR) on the regulation of stem cells biology began to be evaluated. However, little is known on the role of CR on human mesenchymal stem cell (hMSCs) properties. The objective of this study was to investigate the influence of CR on the differentiation capacities of bone marrow hMSCs, as well as the regulation of cell cycle and migration capabilities. To that, we used both a chemical approach with a GSK-3β specific inhibitor (2’E,3’Z-6-bromoindirubin-3’-oxime, BIO) and a knockdown of CLOCK and PER2, two of the main genes involved in CR regulation. In these experimental conditions, a dramatic inhibition of adipocyte differentiation was observed, while osteoblastic differentiation capacities were not modified. In addition, cell migration was decreased in PER2^-/- cells. Lastly, downregulation of circadian clock genes induced a modification of the hMSCs cell cycle phase distribution, which was shown to be related to a change of the cyclin expression profile. Taken together, these data showed that CR plays a role in the regulation of hMSCs differentiation and division, and likely represent key factor in maintaining hMSCs properties.     

The role of diet and temperature in shaping cranial diversification of South American human populations: an approach based on spatial regression and divergence rate tests

Aim Understanding the importance of ecological factors in the origin and maintenance of patterns of phenotypic variation among populations, in an explicit geographical context, is one of the main goals of human biology, ecology and evolutionary biology. Here we study the ecological factors responsible for craniofacial variation among human populations from South America. Location South America. Methods We studied a dataset of 718 males from 40 South American populations, coming from groups that inhabited different geographical and ecological regions. Cranial size and shape variation were studied using 30 cranial measurements. We first used spatial correlograms and interpolated maps to address spatial patterns. We then regressed the shape (principal component scores) and size variables against ecology (mean annual temperature and diet) using multiple and multivariate spatial regression. Finally, the expected magnitudes of shape and size divergence under the influence of genetic drift and mutations alone were evaluated using neutral expectation for the divergence rate. Results The spatial correlograms showed a cline affecting the entire South American distribution. Interpolated maps showed that size and allometric shape vary from south‐east to north‐west. Multiple and multivariate regression analyses suggested that diet has the largest and most significant effect on this pattern of size and allometric shape variation. Finally, the results of the divergence rate test suggested that random processes alone cannot account for the morphological divergence exhibited by cranial size and allometric shape scores among southernmost populations. Main conclusions Correlograms, spatial regression and divergence rate analyses showed that although local factors (neutral processes or local environmental conditions) are important to explain spatial interpopulation differentiation in cranial characteristics among these populations, there is significant correlation of cranial size and allometric shape variation with diet. Gene flow among human populations, or local environmental conditions, could explain spatial variation mainly at smaller spatial scales, whereas the large‐scale pattern of the South American dataset is mainly related to the high proportion of carbohydrates and low proportion of proteins consumed.