Unravelling the Diversity of Grapevine Microbiome

Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.     

Low-level laser therapy attenuates the acute inflammatory response induced by muscle traumatic injury

The purpose of this work was to investigate the effect of early and long-term low-level laser therapy (LLLT) on oxidative stress and inflammatory biomarkers after acute-traumatic muscle injury in Wistar rats. Animals were randomly divided into the following four groups: control group (CG), muscle injury group (IG), CG?+?LLLT, and IG?+?LLLT: laser treatment with doses of 3 and 5 J/cm². Muscle traumatic injury was induced by a single-impact blunt trauma in the rat gastrocnemius. Irradiation for 3 or 5 J/cm² was initiated 2, 12, and 24?h after muscle trauma induction, and the treatment was continued for five consecutive days. All the oxidant markers investigated. namely thiobarbituric acid-reactive substance, carbonyl, superoxide dismutase, glutathione peroxidase, and catalase, were increased as soon as 2?h after muscle injury and remained increased up to 24?h. These alterations were prevented by LLLT at a 3 J/cm² dose given 2?h after the trauma. Similarly, LLLT prevented the trauma-induced proinflammatory state characterized by IL-6 and IL-10. In parallel, trauma-induced reduction in BDNF and VEGF, vascular remodeling and fiber-proliferating markers, was prevented by laser irradiation. In order to test whether the preventive effect of LLLT was also reflected in muscle functionality, we tested the locomotor activity, by measuring distance traveled and the number of rearings in the open field test. LLLT was effective in recovering the normal locomotion, indicating that the irradiation induced biostimulatory effects that accelerated or resolved the acute inflammatory response as well as the oxidant state elicited by the muscle trauma.     

Prediction of maize hybrid performance using similarity in state and similarity by descent information

We evaluated the efficiency of the best linear unbiased predictor (BLUP) and the influence of the use of similarity in state (SIS) and similarity by descent (SBD) in the prediction of untested maize hybrids. Nine inbred lines of maize were crossed using a randomized complete diallel method. These materials were genotyped with 48 microsatellite markers (SSR) associated with the QTL regions for grain yield. Estimates of four coefficients of SIS and four coefficients of SBD were used to construct the additive genetic and dominance matrices, which were later used in combination with the BLUP for predicting genotypic values and specific combining ability (SCA) in unanalyzed hybrids under simulated unbalance. The values of correlations between the genotypic values predicted and the means observed, depending on the degree of unbalance, ranged from 0.48 to 0.99 for SIS and 0.40 to 0.99 using information from SBD. The results obtained for the SCA ranged from 0.26 to 0.98 using the SIS and 0.001 to 0.990 using the SBD information. It was also observed that the predictions using SBD showed less biased than SIS predictions demonstrating that the predictions obtained by these coefficients (SBD) were closer to the observed value, but were less efficient in the ranking of genotypes. Although the SIS showed a bias due to overestimation of relatedness, this type of coefficient may be used where low values are detected in the SBD in the group of parents because of its greater efficiency in ranking the candidates hybrids.     

Clerodanes and other constituents of Cleidion spiciflorum

The polyoxygenated clerodane, spiciflorin (1a), was isolated from Cleidion spiciflorum (Burm. f.) Merr. (Euphorbiaceae). Other constituents were the glucoside of anol (2), columbin, scopoletin, 3,3',4-O-trimethylellagic acid, acetylaleuritolic acid, common triterpenes and phenols.     

Expression of IL-4 receptor on non-bone marrow-derived cells is necessary for the timely elimination of Strongyloides venezuelensis in mice, but not for intestinal IL-4 production

In rodents and in humans, Strongyloides infection induces an immune response which is predominantly Th2 in nature. In an attempt to understand the role of the IL-4R/STAT6 signaling pathway, the pathway activated by the Th2 cytokines IL-4 and IL-13, in the induction of protection during Strongyloides venezuelensis infection, we have carried out experiments in mice lacking the IL-4Ralpha chain. Experiments were also carried out in STAT6 (STAT6(-/-)) and IL-12-deficient (IL-12(-/-)) mice for comparison. There was enhancement of IL-13 and abolition of IFN-gamma production in the small intestine of 7 day-infected IL-12(-/-) animals but worm elimination proceeded with very similar kinetics to those of wild-type mice. In IL-4Ralpha- or STAT6-deficient mice, there was a delay in parasite elimination and a large number of S. venezuelensis adult worms was still present in the small intestine 14 days after infection. Moreover, IgE production was completely abolished in IL-4Ralpha- or STAT6-deficient mice but tissue eosinophilia was normally induced by the parasite infection in deficient mice. Bone marrow transfer experiments showed that worm elimination occurred when a functional IL-4 receptor was present only in non-bone marrow-derived cells but not when IL-4R was only expressed in bone marrow cells. The induction of IL-4, but not IL-13, occurred independently of IL-4R. We believe these results are the first direct evidence that the mechanism responsible for the timely elimination of S. venezuelensis is dependent on the activation of IL-4R and STAT6. Moreover, a functional protective response is dependent on the expression of IL-4Ralpha on non-bone marrow-derived cells.     

Inv21p12q22del21q22 and intellectual disability

Chromosomal rearrangements are common in humans. Pericentric inversions are among the most frequent aberrations (1–2%). Most inversions are balanced and do not cause problems in carriers unless one of the breakpoints disrupts important functional genes, has near submicroscopic copy number variants or hosts “cryptic” complex chromosomal rearrangements. Pericentric inversions can lead to imbalance in offspring. Less than 3% of Down syndrome patients have duplication as a result of parental pericentric inversion of chromosome 21. We report a family with an apparently balanced pericentric inversion of chromosome 21. The proband, a 23-year-old female was referred for prenatal diagnosis at 16 weeks gestation because of increased nuchal translucency. She has a familial history of Down's syndrome and moderate intellectual disability, a personal history of four spontaneous abortions and learning difficulties. Peripheral blood and amniotic fluid samples were collected to perform proband's and fetus' cytogenetic analyses. Additionally, another six family members were evaluated and cytogenetic analysis was performed. Complementary FISH and MLPA studies were carried out. An apparent balanced chromosome 21 pericentric inversion was observed in four family members, two revealed a recombinant chromosome 21 with partial trisomy, and one a full trisomy 21 with an inverted chromosome 21. Array CGH analysis was performed in the mother and the brother's proband. MLPA and aCGH studies identified a deletion of about 1.7 Mb on the long arm of inverted chromosome 21q22.11. We believe the cause of the intellectual disability/learning difficulties observed in the members with the inversion is related to this deletion. The recombinant chromosome 21 has a partial trisomy including the DSCR with no deletion. The risk for carriers of having a child with multiple malformations/intellectual disability is about 30% depending on whether and how this rearrangement interferes with meiosis.     

Corytibacladius Oliveira,Messias & Santos, 1995, a junior synonym of Limnophyes Eaton, 1875 (Diptera: Chironomidae: Orthocladiinae)

Larvae of the blackfly Simulium noelleri Friederichs aggregate at high populatio n densities on dams and spillways at the outlet of ponds. When displaced into the water column from their point of attachment, larvae can secrete silk threads as "life-lines" which enable them to maintain a link to the substratum an d up which they can climb to regain their original position. Experiments were conducted in a laboratory pond outlet to investigate this use of silk threads, larvae being displaced by means of forceps. It was demonstrated that: (i) the length of thread produced , and the speed of climbing the thread are independent of larval size; (ii) within limits, the speed of climbing was independent of both the length of the thread and the time already spent climbing, and (iii) speed of climb became more rapid as larvae neared the point of attachment. The range of locomotion in blackfly larvae is then discussed.     

Identification of Cichlid Fishes from Lake Malawi Using Computer Vision

Background

The explosively radiating evolution of cichlid fishes of Lake Malawi has yielded an amazing number of haplochromine species estimated as many as 500 to 800 with a surprising degree of diversity not only in color and stripe pattern but also in the shape of jaw and body among them. As these morphological diversities have been a central subject of adaptive speciation and taxonomic classification, such high diversity could serve as a foundation for automation of species identification of cichlids.

Methodology/Principal Finding

Here we demonstrate a method for automatic classification of the Lake Malawi cichlids based on computer vision and geometric morphometrics. For this end we developed a pipeline that integrates multiple image processing tools to automatically extract informative features of color and stripe patterns from a large set of photographic images of wild cichlids. The extracted information was evaluated by statistical classifiers Support Vector Machine and Random Forests. Both classifiers performed better when body shape information was added to the feature of color and stripe. Besides the coloration and stripe pattern, body shape variables boosted the accuracy of classification by about 10%. The programs were able to classify 594 live cichlid individuals belonging to 12 different classes (species and sexes) with an average accuracy of 78%, contrasting to a mere 42% success rate by human eyes. The variables that contributed most to the accuracy were body height and the hue of the most frequent color.

Conclusions

Computer vision showed a notable performance in extracting information from the color and stripe patterns of Lake Malawi cichlids although the information was not enough for errorless species identification. Our results indicate that there appears an unavoidable difficulty in automatic species identification of cichlid fishes, which may arise from short divergence times and gene flow between closely related species.