Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): insights from broad geographic sampling

Dendrocincla woodcreepers are ant-following birds widespread throughout tropical America. Species in the genus are widely distributed and show little phenotypic variation. Notwithstanding, several subspecies have been described, but the validity of some of these taxa and the boundaries among them have been discussed for decades. Recent genetic evidence based on limited sampling has pointed to the paraphyly of D. fuliginosa, showing that its subspecies constitute a complex that also includes D. anabatina and D. turdina. In this study we sequenced nuclear and mitochondrial markers for over two hundred individuals belonging to the D. fuliginosa complex to recover phylogenetic relationships, describe intraspecific genetic diversity and provide historical biogeographic scenarios of diversification. Our results corroborate the paraphyly of D. fuliginosa, with D. turdina and D. anabatina nested within its recognized subspecies. Recovered genetic lineages roughly match the distributions of described subspecies and congruence among phylogenetic structure, phenotypic diagnosis and distribution limits were used to discuss current systematics and taxonomy within the complex, with special attention to Northern South America. Our data suggest the origin of the complex in western Amazonia, associated with the establishment of upland forests in the area during the early Pliocene. Paleoclimatic cycles and river rearrangements during the Pleistocene could have, at different times, both facilitated dispersal across large Amazonian rivers and the Andes and isolated populations, likely playing an important role in differentiation of extant species. Previously described hybridization in the headwaters of the Tapajós river represents a secondary contact of non-sister lineages that cannot be used to test the role of the river as primary source of diversification. Based on comparisons of D. fuliginosa with closely related understory upland forest taxa, we suggest that differential habitat use could influence diversification processes in a historically changing landscape, and should be considered for proposing general mechanisms of diversification.Peer reviewe

Optimization of bioactive compound’s extraction conditions from beetroot by means of artificial neural networks (ANN)

The present work used an artificial neural network (ANN) model to correlate beetroot extraction conditions with total phenolic compounds (TPC), anthocyanins (ANT) and antioxidant activity (AOA). The input variables were extraction time, type of solvent, solvent volume/sample mass (VMR = volume to mass ratio) and order of extraction. The ANN models produced showed very good accuracy (R>94%), being suitable for data mining using weight analysis techniques. The experiments involved variable conditions: solvents (methanol, ethanol: water and acetone: water), extraction times (15 and 60 min), VMR (5, 10 and 20), order of extract (3 sequential extractions). The TPC were evaluated by the Folin-Ciocalteu method, ANT by the SO 2 bleaching method and AOA following the ABTS method. The experimental results showed that the extracting solutions used in this study exhibited similar extraction efficiency for TPC, but not for AOA. Also, the results allowed concluding that a higher VMR originated extracts with higher amounts of TPC and AOA.info:eu-repo/semantics/publishedVersio

Serum microRNA array analysis identifies miR-140-3p, miR-33b-3p and miR-671-3p as potential osteoarthritis biomarkers involved in metabolic processes.

Background: MicroRNAs (miRNAs) in circulation have emerged as promising biomarkers. In this study, we aimed to identify a circulating miRNA signature for osteoarthritis (OA) patients and in combination with bioinformatics analysis to evaluate the utility of selected differentially expressed miRNAs in the serum as potential OA biomarkers. Methods: Serum samples were collected from 12 primary OA patients, and 12 healthy individuals were screened using the Agilent Human miRNA Microarray platform interrogating 2549 miRNAs. Receiver Operating Characteristic (ROC) curves were constructed to evaluate the diagnostic performance of the deregulated miRNAs. Expression levels of selected miRNAs were validated by quantitative real-time PCR (qRT-PCR) in all serum and in articular cartilage samples from OA patients (n = 12) and healthy individuals (n = 7). Bioinformatics analysis was used to investigate the involved pathways and target genes for the above miRNAs. Results: We identified 279 differentially expressed miRNAs in the serum of OA patients compared to controls. Two hundred and five miRNAs (73.5%) were upregulated and 74 (26.5%) downregulated. ROC analysis revealed that 77 miRNAs had area under the curve (AUC) > 0.8 and p < 0.05. Bioinformatics analysis in the 77 miRNAs revealed that their target genes were involved in multiple signaling pathways associated with OA, among which FoxO, mTOR, Wnt, pI3K/akt, TGF-β signaling pathways, ECM-receptor interaction, and fatty acid biosynthesis. qRT-PCR validation in seven selected out of the 77 miRNAs revealed 3 significantly downregulated miRNAs (hsa-miR-33b-3p, hsa-miR-671-3p, and hsa-miR-140-3p) in the serum of OA patients, which were in silico predicted to be enriched in pathways involved in metabolic processes. Target-gene analysis of hsa-miR-140-3p, hsa-miR-33b-3p, and hsa-miR-671-3p revealed that InsR and IGFR1 were common targets of all three miRNAs, highlighting their involvement in regulation of metabolic processes that contribute to OA pathology. Hsa-miR-140-3p and hsa-miR-671-3p expression levels were consistently downregulated in articular cartilage of OA patients compared to healthy individuals. Conclusions: A serum miRNA signature was established for the first time using high density resolution miR-arrays in OA patients. We identified a three-miRNA signature, hsa-miR-140-3p, hsa-miR-671-3p, and hsa-miR-33b-3p, in the serum of OA patients, predicted to regulate metabolic processes, which could serve as a potential biomarker for the evaluation of OA risk and progression.Peer reviewedFinal Published versio

DNA Methylation Status of the Methylenetetrahydrofolate Reductase Gene is associated with Depressive Symptoms in Japanese Workers: A Cross-Sectional Study

Abstract Background: Polymorphisms in methylenetetrahydrofolate reductase (MTHFR) gene, that is considered to be the most important genetic determinant of blood homocysteine concentration, are associated with various diseases, including psychiatric disorders. However, the epigenetic factors influencing on the transcription and expression of this gene are unclear. The current study aims to detect the relationship between epigenetic factor-DNA methylation status, on the human MTHFR gene and depressive symptoms in Japanese workers. Methods: 774 DNA samples were extracted from saliva samples collected from subjects recruited for a mental health study, and an Illumina Human Methylation 450K Microarray Assay was used to examine DNA methylation profile across the human MTHFR gene. Depressive symptoms were determined by K6 questionnaire. Four independent DNA pools were created based on K6 scores, and the methylation levels were compared among the pools. Results: The DNA methylation level was lower in subjects with higher degrees of depression for both the entire gene (p=2.10×1

Critical Exponents, Hyperscaling and Universal Amplitude Ratios for Two- and Three-Dimensional Self-Avoiding Walks

We make a high-precision Monte Carlo study of two- and three-dimensional self-avoiding walks (SAWs) of length up to 80000 steps, using the pivot algorithm and the Karp-Luby algorithm. We study the critical exponents $\nu$ and $2\Delta_4 -\gamma$ as well as several universal amplitude ratios; in particular, we make an extremely sensitive test of the hyperscaling relation $d\nu = 2\Delta_4 -\gamma$. In two dimensions, we confirm the predicted exponent $\nu = 3/4$ and the hyperscaling relation; we estimate the universal ratios $\ / \ = 0.14026 \pm 0.00007$, $\ / \ = 0.43961 \pm 0.00034$ and $\Psi^* = 0.66296 \pm 0.00043$ (68\% confidence limits). In three dimensions, we estimate $\nu = 0.5877 \pm 0.0006$ with a correction-to-scaling exponent $\Delta_1 = 0.56 \pm 0.03$ (subjective 68\% confidence limits). This value for $\nu$ agrees excellently with the field-theoretic renormalization-group prediction, but there is some discrepancy for $\Delta_1$. Earlier Monte Carlo estimates of $\nu$, which were $\approx\! 0.592$, are now seen to be biased by corrections to scaling. We estimate the universal ratios $\ / \ = 0.1599 \pm 0.0002$ and $\Psi^* = 0.2471 \pm 0.0003$; since $\Psi^* > 0$, hyperscaling holds. The approach to $\Psi^*$ is from above, contrary to the prediction of the two-parameter renormalization-group theory. We critically reexamine this theory, and explain where the error lies.Comment: 87 pages including 12 figures, 1029558 bytes Postscript (NYU-TH-94/09/01

Spiral and Interlocking Grain in Eucalyptus Dunnii

Spiral grain in 181 trees from a 9-year-old plantation-grown Eucalyptus dunnii was normally distributed with mean 0.33 degrees (to the left) and standard deviation 1.7 degrees, and was affected by family and by crown asymmetry. Interlocking grain was common, exhibiting a mean amplitude of 3.4 degrees (standard deviation 1.5 degrees) and a mean wavelength of 39 mm (standard deviation 12 mm). The relatively large amplitude of interlocking grain means that most trees will have spiral grain that alternates between left and right during each year. The wavelength of interlocking grain is influenced by tree size, but amplitude of interlocking is under genetic control. Both spiral grain and the amplitude of any interlocking were heritable (h2 = 0.99 and 0.63 respectively)

The microRNA-29 family in cartilage homeostasis and osteoarthritis

MicroRNAs have been shown to function in cartilage development and homeostasis, as well as in progression of osteoarthritis. The objective of the current study was to identify microRNAs involved in the onset or early progression of osteoarthritis and characterise their function in chondrocytes. MicroRNA expression in mouse knee joints post-DMM surgery was measured over 7 days. Expression of miR-29b-3p was increased at day 1 and regulated in the opposite direction to its potential targets. In a mouse model of cartilage injury and in end-stage human OA cartilage, the miR-29 family were also regulated. SOX9 repressed expression of miR-29a-3p and miR-29b-3p via the 29a/b1 promoter. TGFβ1 decreased expression of miR-29a, b and c (3p) in primary chondrocytes, whilst IL-1β increased (but LPS decreased) their expression. The miR-29 family negatively regulated Smad, NFκB and canonical WNT signalling pathways. Expression profiles revealed regulation of new WNT-related genes. Amongst these, FZD3, FZD5, DVL3, FRAT2, CK2A2 were validated as direct targets of the miR-29 family. These data identify the miR-29 family as microRNAs acting across development and progression of OA. They are regulated by factors which are important in OA and impact on relevant signalling pathways

Equilibrium swelling and universal ratios in dilute polymer solutions: Exact Brownian dynamics simulations for a delta function excluded volume potential

A narrow Gaussian excluded volume potential, which tends to a delta-function repulsive potential in the limit of a width parameter d* going to zero, has been used to examine the universal consequences of excluded volume interactions on the equilibrium and linear viscoelastic properties of dilute polymer solutions. Brownian dynamics simulations data, acquired for chains of finite length, has been extrapolated to the limit of infinite chain length to obtain model independent predictions. The success of the method in predicting well known aspects of static solution properties suggests that it can be used as a systematic means by which the influence of solvent quality on both equilibrium and non-equilibrium properties can be studied.Comment: Revised version submitted to Physical Review Letters. 4 pages, 2 figures (revised with additional data