Effect of sieving on ex-situ soil respiration of soils from three land use types

This study aims to investigate the effect of sieving on ex situ soil respiration (CO2 flux) measurements from different land use types. We collected soils (0–10 cm) from arable, grassland and woodland sites, allocated them to either sieved (4-mm mesh, freshly sieved) or intact core treatments and incubated them in gas-tight jars for 40 days at 10 °C. Headspace gas was collected on days 1, 3, 17, 24, 31 and 38 and CO2 analysed. Our results showed that sieving (4 mm) did not significantly influence soil respiration measurements, probably because micro aggregates (< 0.25 mm) remain intact after sieving. However, soils collected from grassland soil released more CO2 compared with those collected from woodland and arable soils, irrespective of sieving treatments. The higher CO2 from grassland soil compared with woodland and arable soils was attributed to the differences in the water holding capacity and the quantity and stoichiometry of the organic matter between the three soils. We conclude that soils sieved prior to ex situ respiration experiments provide realistic respiration measurements. This finding lends support to soil scientists planning a sampling strategy that better represents the inhomogeneity of field conditions by pooling, homogenising and sieving samples, without fear of obtaining unrepresentative CO2 flux measurements caused by the disruption of soil architecture

Nanostructured 3D Constructs Based on Chitosan and Chondroitin Sulphate Multilayers for Cartilage Tissue Engineering

Nanostructured three-dimensional constructs combining layer-by-layer technology (LbL) and template leaching were processed and evaluated as possible support structures for cartilage tissue engineering. Multilayered constructs were formed by depositing the polyelectrolytes chitosan (CHT) and chondroitin sulphate (CS) on either bidimensional glass surfaces or 3D packet of paraffin spheres. 2D CHT/CS multi-layered constructs proved to support the attachment and proliferation of bovine chondrocytes (BCH). The technology was transposed to 3D level and CHT/CS multi-layered hierarchical scaffolds were retrieved after paraffin leaching. The obtained nanostructured 3D constructs had a high porosity and water uptake capacity of about 300%. Dynamical mechanical analysis (DMA) showed the viscoelastic nature of the scaffolds. Cellular tests were performed with the culture of BCH and multipotent bone marrow derived stromal cells (hMSCs) up to 21 days in chondrogenic differentiation media. Together with scanning electronic microscopy analysis, viability tests and DNA quantification, our results clearly showed that cells attached, proliferated and were metabolically active over the entire scaffold. Cartilaginous extracellular matrix (ECM) formation was further assessed and results showed that GAG secretion occurred indicating the maintenance of the chondrogenic phenotype and the chondrogenic differentiation of hMSCs

Increased RPA1 gene dosage affects genomic stability potentially contributing to 17p13.3 duplication syndrome

A novel microduplication syndrome involving various-sized contiguous duplications in 17p13.3 has recently been described, suggesting that increased copy number of genes in 17p13.3, particularly PAFAH1B1, is associated with clinical features including facial dysmorphism, developmental delay, and autism spectrum disorder. We have previously shown that patient-derived cell lines from individuals with haploinsufficiency of RPA1, a gene within 17p13.3, exhibit an impaired ATR-dependent DNA damage response (DDR). Here, we show that cell lines from patients with duplications specifically incorporating RPA1 exhibit a different although characteristic spectrum of DDR defects including abnormal S phase distribution, attenuated DNA double strand break (DSB)-induced RAD51 chromatin retention, elevated genomic instability, and increased sensitivity to DNA damaging agents. Using controlled conditional over-expression of RPA1 in a human model cell system, we also see attenuated DSB-induced RAD51 chromatin retention. Furthermore, we find that transient over-expression of RPA1 can impact on homologous recombination (HR) pathways following DSB formation, favouring engagement in aberrant forms of recombination and repair. Our data identifies unanticipated defects in the DDR associated with duplications in 17p13.3 in humans involving modest RPA1 over-expression

Excitations in the field-induced quantum spin liquid state of α-RuCl3

The celebrated Kitaev quantum spin liquid (QSL) is the paradigmatic example of a topological magnet with emergent excitations in the form of Majorana Fermions and gauge fluxes. Upon breaking of time-reversal symmetry, for example in an external magnetic field, these fractionalized quasiparticles acquire non-Abelian exchange statistics, an important ingredient for topologically protected quantum computing. Consequently, there has been enormous interest in exploring possible material realizations of Kitaev physics and several candidate materials have been put forward, recently including α-RuCl3. In the absence of a magnetic field this material orders at a finite temperature and exhibits low-energy spin wave excitations. However, at moderate energies, the spectrum is unconventional and the response shows evidence for fractional excitations. Here we use time-of-flight inelastic neutron scattering to show that the application of a sufficiently large magnetic field in the honeycomb plane suppresses the magnetic order and the spin waves, leaving a gapped continuum spectrum of magnetic excitations. Our comparisons of the scattering to the available calculations for a Kitaev QSL show that they are consistent with the magnetic field induced QSL phase.The work at ORNL’s Spallation Neutron Source and the High Flux Isotope Reactor was supported by the United States Department of Energy (US-DOE), Office of Science - Basic Energy Sciences (BES), Scientific User Facilities Division. Part of the research was supported by the US-DOE, Office of Science - BES, Materials Sciences and Engineering Division (P.K., C.A.B. and J-Q.Y.). D.M. and P.K. acknowledge support from the Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4416. The work at Dresden was in part supported by DFG grant SFB 1143 (J.K. and R.M.). J.K. is supported by the Marie Curie Programme under EC Grant agreements No.703697

A framework for using self-organising maps to analyse spatiotemporal patterns, exemplified by analysis of mobile phone usage

We suggest a visual analytics framework for the exploration and analysis of spatially and temporally referenced values of numeric attributes. The framework supports two complementary perspectives on spatio-temporal data: as a temporal sequence of spatial distributions of attribute values (called spatial situations) and as a set of spatially referenced time series of attribute values representing local temporal variations. To handle a large amount of data, we use the self-organising map (SOM) method, which groups objects and arranges them according to similarity of relevant data features. We apply the SOM approach to spatial situations and to local temporal variations and obtain two types of SOM outcomes, called space-in-time SOM and time-in-space SOM, respectively. The examination and interpretation of both types of SOM outcomes are supported by appropriate visualisation and interaction techniques. This article describes the use of the framework by an example scenario of data analysis. We also discuss how the framework can be extended from supporting explorative analysis to building predictive models of the spatio-temporal variation of attribute values. We apply our approach to phone call data showing its usefulness in real-world analytic scenarios

Correlation of IDH1 Mutation with Clinicopathologic Factors and Prognosis in Primary Glioblastoma: A Report of 118 Patients from China

It has been reported that IDH1 (IDH1R132) mutation was a frequent genomic alteration in grade II and grade III glial tumors but rare in primary glioblastoma (pGBM). To elucidate the frequency of IDH1 mutation and its clinical significance in Chinese patients with pGBM, one hundred eighteen pGBMs were assessed by pyro-sequencing for IDH1 mutation status, and the results were correlated with clinical characteristics and molecular pathological factors. IDH1 mutations were detected in 19/118 pGBM cases (16.1%). Younger age, methylated MGMT promoter, high expression of mutant P53 protein, low expression of Ki-67 or EGFR protein were significantly correlated with IDH1 mutation status. Most notably, we identified pGBM cases with IDH1 mutation were mainly involved in the frontal lobe when compared with those with wild-type IDH1. In addition, Kaplan-Meier survival analysis revealed a highly significant association between IDH1 mutation and a better clinical outcome (p = 0.026 for progression-free survival; p = 0.029 for overall survival). However, in our further multivariable regression analysis, the independent prognostic effect of IDH1 mutation is limited when considering age, preoperative KPS score, extent of resection, TMZ chemotherapy, and Ki-67 protein expression levels, which might narrow its prognostic power in Chinese population in the future

Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat

A novel xylan degrading β-D-xylosidase: purification and biochemical characterization

Aspergillus ochraceus, a thermotolerant fungus isolated in Brazil from decomposing materials, produced an extracellular b-xylosidase that was purified using DEAE-cellulose ion exchange chromatography, Sephadex G-100 and Biogel P-60 gel filtration. b-xylosidase is a glycoprotein (39 % carbohydrate content) and has a molecular mass of 137 kDa by SDS-PAGE, with optimal temperature and pH at 70 C and 3.0–5.5, respectively.b-xylosidase was stable in acidic pH (3.0–6.0) and 70 C for 1 h. The enzyme was activated by 5 mM MnCl2 (28 %)and MgCl2 (20 %) salts. The b-xylosidase produced by A. ochraceus preferentially hydrolyzed p-nitrophenyl-b- D-xylopyranoside, exhibiting apparent Km and Vmax values of 0.66 mM and 39 U (mg protein)-1 respectively, and to a lesser extent p-nitrophenyl-b-D-glucopyranoside. The enzyme was able to hydrolyze xylan from different sources,suggesting a novel b-D-xylosidase that degrades xylan. HPLC analysis revealed xylans of different compositions which allowed explaining the differences in specificity observed by b-xylosidase. TLC confirmed the capacity.This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), and the Conselho de Desenvolvimento Científico e Tecnológico (CNPq). J. A. J. and M. L. T. M. P are Research Fellows of CNPq. M. M. was a recipient of a FAPESP fellowship and this work is part of her Doctoral Thesis. It is also part of the project SISBIOTA CNPq: 563260/2010-6 and FAPESP: 2010/52322-3

Characterisation of a recombinant β-xylosidase (xylA) from Aspergillus oryzae expressed in Pichia pastoris

β-xylosidases catalyse the hydrolysis of short chain xylooligosaccharides from their non-reducing ends into xylose. In this study we report the heterologous expression of Aspergillus oryzae β-xylosidase (XylA) in Pichia pastoris under the control of the glyceraldehyde-3-phosphate dehydrogenase promoter. The recombinant enzyme was optimally active at 55°C and pH 4.5 with Km and Vmax values of 1.0 mM and 250 μmol min−1 mg−1 respectively against 4-nitrophenyl β-xylopyranoside. Xylose was a competitive inhibitor with a Ki of 2.72 mM, whereas fructose was an uncompetitive inhibitor reducing substrate binding affinity (Km) and conversion efficiency (Vmax). The enzyme was characterised to be an exo-cutting enzyme releasing xylose from the non-reducing ends of β-1,4 linked xylooligosaccharides (X2, X3 and X4). Catalytic conversion of X2, X3 and X4 decreased (Vmax and kcat) with increasing chain length