Global phylogeny of Hadrosauridae (Dinosauria: Ornithopoda) using parsimony and Bayesian methods

The late Cretaceous hadrosaurids were the most specialized and diverse clade of ornithopod dinosaurs. Parsimony and Bayesian methods were implemented to elucidate the phylogenetic relationships of all hadrosaurid species. Traditional and geometric morphometrics were applied to discover patterns of variation containing phylogenetic information. In total, 286 phylogenetically informative characters (196 cranial and 90 postcranial) were defined and documented: the most extensive character data set ever constructed for hadrosaurid dinosaurs. Of these, 136 characters were used for the first time in phylogenetic analysis of these ornithopods, and 93 were modified from those of other authors. Parsimony and the Bayesian analysis (using the Mk model without the gamma parameter) confirmed the split of hadrosaurids into Saurolophinae and Lambeosaurinae. Saurolophines included a major clade composed of the Prosaurolophus–Saurolophus and the Kritosaurus–Gryposaurus–Secernosaurus subclades. Edmontosaurus and Shantungosaurus were recovered outside the major clade of saurolophines. The Brachylophosaurus clade was recovered as the most basal clade of saurolophines in the parsimony analysis, whereas following the Bayesian analysis it was recovered as the sister clade to the Kritosaurus–Gryposaurus–Secernosaurus clade. These two analyses resulted in a Lambeosaurinae composed of a succession of Eurasian sister taxa to two major clades: the Parasaurolophus clade and the Hypacrosaurs altispinus–Corythosaurus clade. In contrast, the Bayesian analysis using the Mk model with the gamma parameter included, resulted in an unbalanced hadrosauroid tree, with a paraphyletic Saurolophinae, and with the Prosaurolophus clade, Edmontosaurus, and Shantungosaurus as successively closer sister taxa to Lambeosaurinae. Based on the strict reduced consensus tree derived from the parsimony analysis, Hadrosauridae was redefined as the clade stemming from the most recent common ancestor of Hadrosaurus foulkii and Parasaurolophus walkeri. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 435–502.     

Circular RNA AFF4 modulates osteogenic differentiation in BM-MSCs by activating SMAD1/5 pathway through miR-135a-5p/FNDC5/Irisin axis

Bone marrow-derived mesenchymal stem cells (BM-MSCs), the common progenitor cells of adipocytes and osteoblasts, have been recognized as the key mediator during bone formation. Herein, our study aim to investigate molecular mechanisms underlying circular RNA (circRNA) AFF4 (circ_AFF4)-regulated BM-MSCs osteogenesis. BM-MSCs were characterized by FACS, ARS, and ALP staining. Expression patterns of circ_AFF4, miR-135a-5p, FNDC5/Irisin, SMAD1/5, and osteogenesis markers, including ALP, BMP4, RUNX2, Spp1, and Colla1 were detected by qRT-PCR, western blot, or immunofluorescence staining, respectively. Interactions between circ_AFF4 and miR-135a-5p, FNDC5, and miR-135a-5p were analyzed using web tools including TargetScan, miRanda, and miRDB, and further confirmed by luciferase reporter assay and RNA pull-down. Complex formation between Irisin and Integrin αV was verified by Co-immunoprecipitation. To further verify the functional role of circ_AFF4 in vivo during bone formation, we conducted animal experiments harboring circ_AFF4 knockdown, and born samples were evaluated by immunohistochemistry, hematoxylin and eosin, and Masson staining. Circ_AFF4 was upregulated upon osteogenic differentiation induction in BM-MSCs, and miR-135a-5p expression declined as differentiation proceeds. Circ_AFF4 knockdown significantly inhibited osteogenesis potential in BM-MSCs. Circ_AFF4 stimulated FNDC5/Irisin expression through complementary binding to its downstream target molecule miR-135a-5p. Irisin formed an intermolecular complex with Integrin αV and activated the SMAD1/5 pathway during osteogenic differentiation. Our work revealed that circ_AFF4, acting as a sponge of miR-135a-5p, triggers the promotion of FNDC5/Irisin via activating the SMAD1/5 pathway to induce osteogenic differentiation in BM-MSCs. These findings gained a deeper insight into the circRNA-miRNA regulatory system in the bone marrow microenvironment and may improve our understanding of bone formation-related diseases at physiological and pathological levels.Subject terms: Stem cells, Diseases     

MicroRNAs transcriptionally regulate promoter activity in Arabidopsis thaliana

Micro RNAs(mi RNAs) are vital regulators that repress gene expression in the cytoplasm in two main ways: m RNA degradation and translational inhibition. Several animal studies have shown that mi RNAs also target promoters, thereby activating expression.Whether this mi RNA action also occurs in plants is unknown. In this study, we demonstrated that several mi RNAs regulate target promoters in Arabidopsis thaliana. For example, mi R5658 was predominantly present in the nucleus and activated the expression of AT3 G25290 directly by binding to its promoter. Our observations suggest that this mode of action may be a general feature of plant mi RNAs, and thus provide insight into the vital roles of plant mi RNAs in the nucleus.     

Hydrogen sulfide:A novel component in Arabidopsis peroxisomes which triggers catalase inhibition

Plant peroxisomes have the capacity to generate different reactive oxygen and nitrogen species(ROS and RNS),such as H_2O_2,superoxide radical(O_2~-),nitric oxide and peroxynitrite(ONOO~-).These organelles have an active nitrooxidative metabolism which can be exacerbated by adverse stress conditions.Hydrogen sulfide(H_2S)is a new signaling gasotransmitter which can mediate the posttranslational modification(PTM)persulfidation.We used Arabidopsis thaliana transgenic seedlings expressing cyan fluorescent protein(CFP)fused to a canonical peroxisome targeting signal 1(PTS1)to visualize peroxisomes in living cells,as well as a specific fluorescent probe which showed that peroxisomes contain H_2S.H_2S was also detected in chloroplasts under glyphosate-induced oxidative stress conditions.Peroxisomal enzyme activities,including catalase,photorespiratory H_2O_2-generating glycolate oxidase(GOX)and hydroxypyruvate reductase(HPR),were assayed in vitro with a H_2S donor.In line with the persulfidation of this enzyme,catalase activity declined significantly in the presence of the H_2S donor.To corroborate the inhibitory effect of H_2S on catalase activity,we also assayed pure catalase from bovine liver and pepper fruit-enriched samples,in which catalase activity was inhibited.Taken together,these data provide evidence of the presence of H_2S in plant peroxisomes which appears to regulate catalase activity and,consequently,the peroxisomal H_2O_2 metabolism.     

Choice of hydrogen uptake (Hup) status in legume‐rhizobia symbioses

The H₂ is an obligate by-product of N-fixation. Recycling of H₂ through uptake hydrogenase (Hup) inside the root nodules of leguminous plants is often considered an advantage for plants. However, many of the rhizobium-legume symbioses found in nature, especially those used in agriculture are shown to be Hup⁻, with the plants releasing H₂ produced by nitrogenase activity from root nodules into the surrounding rhizosphere. Recent studies have suggested that, H₂ induces plant-growth-promoting rhizobacteria, which may explain the widespread of Hup⁻ symbioses in spite of the low energy efficiency of such associations. Wild legumes grown in Nova Scotia, Canada, were surveyed to determine if any plant-growth characteristics could give an indication of Hup choice in leguminous plants. Out of the plants sampled, two legumes, Securigera varia and Vicia cracca, showed Hup⁺ associations. Securigera varia exhibited robust root structure as compared with the other plants surveyed. Data from the literature and the results from this study suggested that plants with established root systems are more likely to form the energy-efficient Hup⁺ symbiotic relationships with rhizobia. Conversely, Hup⁻ associations could be beneficial to leguminous plants due to H₂-oxidizing plant-growth-promoting rhizobacteria that allow plants to compete successfully, early in the growing season. However, some nodules from V. cracca tested Hup⁺, while others were Hup⁻. This was similar to that observed in Glycine max and Pisum sativum, giving reason to believe that Hup choice might be affected by various internal and environmental factors.     

Editorial: Twin peaks mission

The Y human chromosome has many ancient genes whose fidelity seems to have been preserved by tandem sequences and palindromic ‘hairpins’, compared/repaired by ‘gene conversion’. That a primary function of recombination machinery is DNA repair has been suggested, and rejected, several times; this new evidence is very persuasive. The process, better called gene conservation than gene conversion, could operate in all diploid organisms, accounting for the retention of long gene sequences without ‘informational meltdown’ ('concerted evolution'). It resembles rocket‐science computer‐redundancy error‐checking, comparison of three or four sequences, not just two. If recognition of errors in ‘converted’ sequences can be followed by either repair or rejection, the rejection option can account for the vast wastage of meiotic products. The repair option might be used in Drosophila oocytes and even zygotic nuclei, possibly other oocytes, ancient asexual lineages such as mycorrhizal fungi, perhaps the Y itself. Both evolutionary stasis (conservatism) and development and deployment of complex developmental modules can be understood in these terms so both the evolution of biodiversity and the practice of systematics may have these mechanisms as their bases. The main individual‐fitness and evolutionary advantages of diploidy were not primarily cloaking of recessive al‐leles, or allelic recombination and Mendelism, but conserving long DNA sequences.     

Spectrum structures and biological functions of 8-mers in the human genome

The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.