Convergence of miRNA expression profiling, α-synuclein interacton and GWAS in Parkinson's disease

miRNAs were recently implicated in the pathogenesis of numerous diseases, including neurological disorders such as Parkinson''s disease (PD). miRNAs are abundant in the nervous system, essential for efficient brain function and play important roles in neuronal patterning and cell specification. To further investigate their involvement in the etiology of PD, we conducted miRNA expression profiling in peripheral blood mononuclear cells (PBMCs) of 19 patients and 13 controls using microarrays. We found 18 miRNAs differentially expressed, and pathway analysis of 662 predicted target genes of 11 of these miRNAs revealed an over-representation in pathways previously linked to PD as well as novel pathways. To narrow down the genes for further investigations, we undertook a parallel approach using chromatin immunoprecipitation-sequencing (ChIP-seq) analysis to uncover genome-wide interactions of α-synuclein, a molecule with a central role in both monogenic and idiopathic PD. Convergence of ChIP-seq and miRNomics data highlighted the glycosphingolipid biosynthesis and the ubiquitin proteasome system as key players in PD. We then tested the association of target genes belonging to these pathways with PD risk, and identified nine SNPs in USP37 consistently associated with PD susceptibility in three genome-wide association studies (GWAS) datasets (0.46≤OR≤0.63) and highly significant in the meta-dataset (3.36×10⁻⁴−3). A SNP in ST8SIA4 was also highly associated with PD (p = 6.15×10⁻³) in the meta-dataset. These findings suggest that several miRNAs may act as regulators of both known and novel biological processes leading to idiopathic PD.     

Revealing the structural origin of the redox-Bohr effect: the first solution structure of a cytochrome from Geobacter sulfurreducens

Gs (Geobacter sulfurreducens) can transfer electrons to the exterior of its cells, a property that makes it a preferential candidate for the development of biotechnological applications. Its genome encodes over 100 cytochromes and, despite their abundance and key functional roles, to date there is no structural information for these proteins in solution. The trihaem cytochrome PpcA might have a crucial role in the conversion of electronic energy into protonmotive force, a fundamental step for ATP synthesis in the presence of extracellular electron acceptors. In the present study, 15N-labelled PpcA was produced and NMR spectroscopy was used to determine its solution structure in the fully reduced state, its backbone dynamics and the pH-dependent conformational changes. The structure obtained is well defined, with an average pairwise rmsd (root mean square deviation) of 0.25?? (1??=0.1?nm) for the backbone atoms and 0.99?? for all heavy atoms, and constitutes the first solution structure of a Gs cytochrome. The redox-Bohr centre responsible for controlling the electron/proton transfer was identified, as well as the putative interacting regions between PpcA and its redox partners. The solution structure of PpcA will constitute the foundation for studies aimed at mapping out in detail these interacting regions.     

The role of individual variation in flowering and pollination in the reproductive success of a crepuscular buzz-pollinated plant

Background and AimsPlant individuals within a population differ in their phenology and interactions with pollinators. However, it is still unknown how individual differences affect the reproductive success of plants that have functionally specialized pollination systems. Here, we evaluated whether plant individual specialization in phenology (temporal specialization) and in pollination (pollinator specialization) affect the reproductive success of the crepuscular-bee-pollinated plant Trembleya laniflora (Melastomataceae).MethodsWe quantified flowering activity (amplitude, duration and overlap), plant–pollinator interactions (number of flowers visited by pollinators) and reproductive success (fruit set) of T. laniflora individuals from three distinct locations in rupestrian grasslands of southeastern Brazil. We estimated the degree of individual temporal specialization in flowering phenology and of individual specialization in plant–pollinator interactions, and tested their relationship with plant reproductive success.Key Results Trembleya laniflora presented overlapping flowering, a temporal generalization and specialized pollinator interactions. Flowering overlap among individuals and populations was higher than expected by chance but did not affect the individual interactions with pollinators and nor their reproductive success. In contrast, higher individual generalization in the interactions with pollinators was related to higher individual reproductive success.ConclusionsOur findings suggest that individual generalization in plant–pollinator interaction reduces the potential costs of specialization at the species level, ensuring reproductive success. Altogether, our results highlight the complexity of specialization/generalization of plant–pollinator interactions at distinct levels of organization, from individuals to populations, to species.     

Differences in Al tolerance between Plantago algarbiensis and P. almogravensis reflect their ability to respond to oxidative stress

We evaluated the impact of low pH and aluminum (Al) on the leaves and roots of Plantago almogravensis Franco and Plantago algarbiensis Samp., focusing on energy partitioning in photosystem II, H₂O₂ levels, lipid peroxidation, electrolyte leakage (EL), protein oxidation, total soluble protein content and antioxidant enzyme activities. In both species, Al triggered more changes in oxidative metabolism than low pH alone, particularly in the roots. We found that Al increased the levels of H₂O₂ in P. algarbiensis roots, but reduced the levels of H₂O₂ in P. almogravensis leaves and roots. Neither low pH nor Al affected the spatial heterogeneity of chlorophyll fluorescence, the maximum photochemical efficiency of PSII (F_v/F_m), the actual quantum efficiency of PSII (?_PSII) or the quantum yields of regulated (?_NPQ) and nonregulated (?_NO) energy dissipation, and there was no significant change in total soluble protein content and EL. In P. algarbiensis, Al increased the carbonyl content and the activities of superoxide dismutase (SOD) and catalase (CAT) in the roots, and also CAT, ascorbate peroxidase and guaiacol peroxidase activities in the leaves. In P. almogravensis, Al reduced the level of malondialdehyde in the roots as well as SOD activity in the leaves and roots. We found that P. almogravensis plantlets could manage the oxidative stress caused by low pH and Al, whereas the P. algarbiensis antioxidant system was unable to suppress Al toxicity completely, leading to the accumulation of H₂O₂ and consequential protein oxidation in the roots.     

The virtues and limitations of exploring the eco‐evolutionary dynamics of sexually selected traits

Most studies on eco‐evolutionary feedbacks concern the influence of abiotic factors, or predator–prey and host–parasite interactions, while studies involving sexual interactions are lagging behind. This is at odds with the potential of these interactions to engage in such processes. Indeed, there is now ample evidence that sexual selection is affected by ecological change and that sexually selected traits can evolve rapidly, which may modify the ecological context of populations, and thus the selection pressures they will be exposed to. Here we review evidence for such eco‐evolutionary processes. We discuss examples of eco‐evolutionary change in an attempt to understand the challenges related with identifying and characterizing such processes. In particular, we focus on the challenges associated with accurately identifying the components of the feedback as well as their causal relation. Finally, we evaluate scenarios where understanding eco‐evolutionary feedbacks of sexual selection may help us appreciate the effects of sexual selection in shaping evolutionary processes.     

Identification of species by multiplex analysis of variable-length sequences

The quest for a universal and efficient method of identifying species has been a longstanding challenge in biology. Here, we show that accurate identification of species in all domains of life can be accomplished by multiplex analysis of variable-length sequences containing multiple insertion/deletion variants. The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups. We also demonstrate that the identification of prokaryotic and viral species with numeric profiles of fragment lengths is generally straightforward. A computational platform is presented to facilitate the planning of projects and includes a large data set with nearly 1800 numeric profiles for species in all domains of life (1556 for eukaryotes, 105 for prokaryotes and 130 for viruses). Finally, a SPInDel profiling kit for discrimination of 10 mammalian species was successfully validated on highly processed food products with species mixtures and proved to be easily adaptable to multiple screening procedures routinely used in molecular biology laboratories. These results suggest that SPInDel is a reliable and cost-effective method for broad-spectrum species identification that is appropriate for use in suboptimal samples and is amenable to different high-throughput genotyping platforms without the need for DNA sequencing.     

A single-point mutation in FGFR2 affects cell cycle and Tgfβ signalling in osteoblasts

Fgf and Tgfβ are key regulators of bone development. It is not known, however, whether there is a relationship between defective Fgf signalling, resulting in a premature cranial suture fusion, and Tgfβ signalling. We used mouse calvaria osteoblasts carrying a mutation (hFGFR2-C278F) associated with Crouzon and Pfeiffer syndromes to investigate effects of this mutation on cell growth and possible mechanisms underlying it. Mutated osteoblasts displayed reduced S-phase, increased apoptosis and increased differentiation. As Tgfβ signalling appeared to be required in an autocrine/paracrine manner for osteoblast proliferation, we tested the hypothesis that reduced growth might be due, at least in part, to an altered balance between FGF and Tgfβ signalling. Tgfβ expression was indeed decreased in mutated osteoblasts, as compared to osteoblasts carrying the wild type hFGFR2. Treatment with Tgfβ, however, neither increased proliferation in mutated osteoblasts, unlike in controls, nor rescued proliferation in control osteoblasts treated with an Erk1/2 inhibitor. Significantly, Erk2, that is important for proliferation, was reduced relatively to Erk1 in mutated cells. Altogether this study suggests that the hFGFR2-C278F mutation affects the osteoblast ability to respond to Tgfβ stimulation via the Erk pathway and that the overall effect of the mutation is a loss of function.     

Genomic analysis of Grapevine Retrotransposon 1 (Gret1) in Vitis vinifera

The complete sequence of the first retrotransposon isolated in Vitis vinifera, Gret1, was used to design primers that permitted its analysis in the genome of grapevine cultivars. This retroelement was found to be dispersed throughout the genome with sites of repeated insertions. Fluorescent in situ hybridization indicated multiple Gret1 loci distributed throughout euchromatic portions of chromosomes. REMAP and IRAP proved to be useful as molecular markers in grapevine. Both of these techniques showed polymorphisms between cultivars but not between clones of the same cultivar, indicating differences in Gret1 distribution between cultivars. The combined cytological and molecular results suggest that Gret1 may have a role in gene regulation and in explaining the enormous phenotypic variability that exists between cultivars.     

Circadian rhythm in locomotor activity in the burrower crayfish Procambarus acanthophorus (Villalobos 1948)

Crayfish Procambarus acanthophorus is a burrower that spends long periods building deep tunnels to reach the water table during the dry season; thus, its survival entertains a close ecological relationship with the sediment. The aim of this work was to determine whether the properties of the circadian rhythm of locomotor activity could be modified by the sediment availability. Experiments were conducted in both aquaria filled with sediment or filled with water, under cycles of Bright and Dim Illumination (BI:DI, 12:12 h) or under continuous DI:DI. The rhythm of locomotor activity was entrained with the photoperiod in aquaria with sediment or water; however, statistical differences between conditions were obtained comparing the period and the level of activity under free-running. These data suggest that the substrate’s sensorial perception could be encoded as a significant ecological parameter that exerts influence in the physiological mechanisms that control the temporal order in P. acanthophorus.