Vitamins K interact with N-terminus α-synuclein and modulate the protein fibrillization in vitro. Exploring the interaction between quinones and α-synuclein

In the last decades, a series of compounds, including quinones and polyphenols, has been described as having anti-fibrillogenic action on α-synuclein (α-syn) whose aggregation is associated to the pathogenesis of Parkinson’s disease (PD). Most of these molecules act as promiscuous anti-amyloidogenic agents, interacting with the diverse amyloidogenic proteins (mostly unfolded) through non-specific hydrophobic interactions. Herein we investigated the effect of the vitamins K (phylloquinone, menaquinone and menadione), which are 1,4-naphthoquinone (1,4-NQ) derivatives, on α-syn aggregation, comparing them with other anti-fibrillogenic molecules such as quinones, polyphenols and lipophilic vitamins. Vitamins K delayed α-syn fibrillization in substoichiometric concentrations, leading to the formation of short, sheared fibrils and amorphous aggregates, which are less prone to produce leakage of synthetic vesicles. In seeding conditions, menadione and 1,4-NQ significantly inhibited fibrils elongation, which could be explained by their ability to destabilize preformed fibrils of α-syn. Bidimensional NMR experiments indicate that a specific site at the N-terminal α-syn (Gly31/Lys32) is involved in the interaction with vitamins K, which is corroborated by previous studies suggesting that Lys is a key residue in the interaction with quinones. Together, our data suggest that 1,4-NQ, recently showed up by our group as a potential scaffold for designing new monoamine oxidase inhibitors, is also capable to modulate α-syn fibrillization in vitro.     

Identification of the rhizobial symbiont of Astragalus glombiformis in Eastern Morocco as Mesorhizobium camelthorni

Astragalus gombiformis is a desert symbiotic nitrogen-fixing legume of great nutritional value as fodder for camels and goats. However, there are no data published on the rhizobial bacteria that nodulate this wild legume in northern Africa. Thirty-four rhizobial bacteria were isolated from root nodules of A. gombifomis grown in sandy soils of the South-Eastern of Morocco. Twenty-five isolates were able to renodulate their original host and possessed a nodC gene copy. The phenotypic and genotypic characterizations carried out illustrated the diversity of the isolates. Phenotypic analysis showed that isolates used a great number of carbohydrates as sole carbon source. However, although they were isolated from arid sandy soils, the isolates do not tolerate drought stress applied in vitro. The phenotypic diversity corresponded mainly to the diversity in the use of some carbohydrates. The genetic analysis as assessed by repetitive extragenic palindromic (REP)-polymerase chain reaction (PCR) showed that the isolates clustered into 3 groups at a similarity coefficient of 81 %. The nearly-complete 16S rRNA gene sequence from a representative strain of each PCR-group showed they were closely related to members of the genus Mesorhizobium of the family Phyllobactericeae within the Alphaproteobacteria. Sequencing of the housekeeping genes atpD, glnII and recA, and their concatenated phylogenetic analysis, showed they are closely related to Mesorhizobium camelthorni. Sequencing of the symbiotic nodC gene from each strain revealed they had 83.53 % identity with the nodC sequence of the type strain M. camelthorni CCNWXJ 40-4^T.     

White rot Basidiomycetes isolated from Chiloé National Park in Los Lagos region, Chile

Wood decomposition is an important component in forest ecosystems but information about the diversity of fungi causing decay is lacking. This is especially true for the temperate rain forests in Chile. These investigations show results of a biodiversity study of white-rot fungi in wood obtained from Chiloé National Park in Los Lagos region, Chile. Culturing from white-rotted wood followed by sequencing of the complete internal transcribed spacer region of the ribosomal DNA (rDNA) or partial large subunit region of the rDNA, identified 12 different species in the Basidiomycota. All of these fungi were characterized as white rot fungi and were identified with a BLAST match of 97 % or greater to sequences in the GenBank database. Fungi obtained were species of Phlebia, Mycoacia, Hyphodontia, Bjerkandera, Phanerochaete, Stereum, Trametes, and Ceriporiopsis. This report identifies for the first time in Chile the species Ceriporiopsis subvermispora, Hyphodontia radula, Phlebia radiata, Phanerochaete affinis, Peniophora cinerea, Stereum gausapatum, Phlebia setulosa and Phanerochaete sordida. Scanning electron microscopy was used to characterize the type of decay caused by the fungi that were isolated and a combination of selective lignin degraders and simultaneous white rot fungi were found. Fungi that cause a selective degradation of lignin are of interest for bioprocessing technologies that require modification or degradation of lignin without cellulose removal.     

Enlarging a training set for genomic selection by imputation of un-genotyped animals in populations of varying genetic architecture

Background

The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped.

Methods

Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets.

Results

Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams.

Conclusions

Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.     

Driving vascular endothelial cell fate of human multipotent Isl1+ heart progenitors with VEGF modified mRNA

Distinct families of multipotent heart progenitors play a central role in the generation of diverse cardiac, smooth muscle and endothelial cell lineages during mammalian cardiogenesis. The identification of precise paracrine signals that drive the cell-fate decision of these multipotent progenitors, and the development of novel approaches to deliver these signals in vivo, are critical steps towards unlocking their regenerative therapeutic potential. Herein, we have identified a family of human cardiac endothelial intermediates located in outflow tract of the early human fetal hearts (OFT-ECs), characterized by coexpression of Isl1 and CD144/vWF. By comparing angiocrine factors expressed by the human OFT-ECs and non-cardiac ECs, vascular endothelial growth factor (VEGF)-A was identified as the most abundantly expressed factor, and clonal assays documented its ability to drive endothelial specification of human embryonic stem cell (ESC)-derived Isl1⁺ progenitors in a VEGF receptor-dependent manner. Human Isl1-ECs (endothelial cells differentiated from hESC-derived ISL1⁺ progenitors) resemble OFT-ECs in terms of expression of the cardiac endothelial progenitor- and endocardial cell-specific genes, confirming their organ specificity. To determine whether VEGF-A might serve as an in vivo cell-fate switch for human ESC-derived Isl1-ECs, we established a novel approach using chemically modified mRNA as a platform for transient, yet highly efficient expression of paracrine factors in cardiovascular progenitors. Overexpression of VEGF-A promotes not only the endothelial specification but also engraftment, proliferation and survival (reduced apoptosis) of the human Isl1⁺ progenitors in vivo. The large-scale derivation of cardiac-specific human Isl1-ECs from human pluripotent stem cells, coupled with the ability to drive endothelial specification, engraftment, and survival following transplantation, suggest a novel strategy for vascular regeneration in the heart.     

Disturbances, elevation, topography and spatial proximity drive vegetation patterns along an altitudinal gradient of a top biodiversity hotspot

The correlation between vegetation patterns (species distribution and richness) and altitudinal variation has been widely reported for tropical forests, thereby providing theoretical basis for biodiversity conservation. However, this relationship may have been oversimplified, as many other factors may influence vegetation patterns, such as disturbances, topography and geographic distance. Considering these other factors, our primary question was: is there a vegetation pattern associated with substantial altitudinal variation (10–1,093 m a.s.l.) in the Atlantic Rainforest—a top hotspot for biodiversity conservation—and, if so, what are the main factors driving this pattern? We addressed this question by sampling 11 1-ha plots, applying multivariate methods, correlations and variance partitioning. The Restinga (forest on sandbanks along the coastal plains of Brazil) and a lowland area that was selectively logged 40 years ago were floristically isolated from the other plots. The maximum species richness (>200 spp. per hectare) occurred at approximately 350 m a.s.l. (submontane forest). Gaps, multiple stemmed trees, average elevation and the standard deviation of the slope significantly affected the vegetation pattern. Spatial proximity also influenced the vegetation pattern as a structuring environmental variable or via dispersal constraints. Our results clarify, for the first time, the key variables that drive species distribution and richness across a large altitudinal range within the Atlantic Rainforest.     

Endophytic bacteria isolated from orchid and their potential to promote plant growth

Twelve endophytic bacteria were isolated from the meristem of in vitro Cymbidium eburneum orchid, and screened according to indole yield quantified by colorimetric assay, in vitro phosphate solubilization, and potential for plant growth promotion under greenhouse conditions. Eight strains with positive results were classified into the genus Paenibacillus by FAME profile, and evaluated for their ability to increase survival and promote the growth of in vitro germinated Cattleya loddigesii seedlings during the acclimatization process. The obtained results showed that all strains produced detectable indole levels and did not exhibit potential for solubilizing inorganic phosphate. Particularly, an increase of the total biomass and number of leaves was observed. Two strains of Paenibacillus macerans promoted plant growth under greenhouse conditions. None of the treatments had a deleterious effect on growth of inoculated plants. These results suggest that these bacterial effects could be potentially useful to promote plant growth during seedling acclimatization in orchid species other than the species of origin.     

Forest cover, extinction thresholds and time lags in woody plants (Myrtaceae) in the Brazilian Atlantic Forest: resources for conservation

Efforts to conserve tropical forests could be strengthened based on ecological knowledge, such as extinction thresholds in ecological processes. Many studies of extinction thresholds associated with habitat reduction have focused on animals, generally at the patch scale. However, certain plant groups are very interesting models with which to study this type of relationship, such as Myrtaceae in Neotropical forests. Because trees are long-lived organisms, local extinctions in response to habitat loss may occur in different ways due to a time lag. In this study, our objective was to assess the occurrence of extinction thresholds at the landscape scale for Myrtaceae in a large biome and the pattern of species reduction in different tree size classes. We studied nine landscapes with different amounts of available habitat (between 5 and 55 % forest cover) in different parts of the Atlantic Forest in Bahia, Brazil, and in each landscape, we evaluated four plant classes based on tree circumference: saplings (CBH between 8 and 15 cm), young (CBH between 15 and 30 cm) adults (CBH ≥30 cm) and total (all individuals with CBH ≥8 cm). Landscapes with forest cover less than 25 % presented an approximately sixfold reduction in Myrtaceae total species richness compared with landscapes with forest cover greater than 40 %. We identified a relationship with a threshold between the amount of available habitat at the landscape level and Myrtaceae richness, with a reduction in total, sapling and young species below a threshold of 40 % forest cover, whereas adults had an extinction threshold at 30 % forest cover. We discuss the differences among the categories of plants associated with a time lag and the possibilities and limitations in applying these results in environmental management.     

Diversity and abundance of climbers from the Atlantic Forest, southeastern Brazil

Climbing plant community composition and abundance was compared between the Alto da Serra de Paranapiacaba Biological Reserve (ASPRB) and the Nascentes de Paranapiacaba Municipal Natural Park (NPMNP), two protected areas in the largest Atlantic Forest remnant, southeastern Brazil. Climbing plants ≥1 cm in diameter were sampled in 52 quadrats of 10 × 20 m (1.04 ha). From these data we calculated the Shannon–Wiener diversity index, calculated abundance and importance values for families, performed a principal coordinate analysis, and created a similarity dendrogram (TWINSPAN). The composition and abundance of species between ASPRB and NPMNP differed significantly due to the successional state of the ASPRB forest, which was affected by more recent disturbance. There we found 34 species, while in the NPMNP, species richness was 72, with only 24 species in common. The two areas formed two groups corresponding to two distinct floristic subsets. These montane forests were characterized by a predominance of species of the Asteraceae. The high species richness, floristic composition, and community composition reflect the greater degree of conservation in the area of NPMNP. The high density and community composition of climbers in the more conserved area of rainforest may be due to the low intensity of disturbance.