Genetic regulation of compost and plant degradation mechanisms in Agaricus bisporus

posterAgaricus bisporus (common button mushroom) is an economically significant mushroom with an annual global value in excess of $4.7 billion (Eastwood et al, 2015). When commercially grown, A. bisporus mushrooms are mostly picked from the first and second flush. This is due to the third flush resulting in reduced yields (Royse and Sanchez, 2008), which are also often more prone to disease. This occurs despite significant nutrients and nitrogen being available in the compost for A. bisporus to utilise. To further understand why this is occurring, microarray analysis was carried out on compost samples throughout a full commercial growth cycle, with the aim of identifying genes that may be responsible for this reduction in yield

Birch bark tar in early Medieval England:continuity of tradition or technological revival?

International audienc

The PneuCarriage Project : A multi-centre comparative study to identify the best serotyping methods for examining pneumococcal carriage in vaccine evaluation studies

Background: The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies. Methods and Findings: Reference sample sets were distributed to 15 research groups for blinded testing. Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples. The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries. Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample). For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples. Fifteen methods had ≥70% sensitivity to detect the dominant (major) serotype, whilst only eight methods had ≥70% sensitivity to detect minor serotypes. For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%). The microarray had the highest sensitivity (95.8%) and high PPV (93.7%). The major limitation of this study is that not all of the available alternative serotyping methods were included. Conclusions: Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations. Microarray with a culture amplification step was the top-performing method. Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high. © 2015 Satzke et al. *For a complete list of authors, please see acknowledgments in the published article

How well do global ocean biogeochemistry models simulate dissolved iron distributions?

Numerical models of ocean biogeochemistry are relied upon to make projections about the impact of climate change on marine resources and test hypotheses regarding the drivers of past changes in climate and ecosystems. In large areas of the ocean, iron availability regulates the functioning of marine ecosystems and hence the ocean carbon cycle. Accordingly, our ability to quantify the drivers and impacts of fluctuations in ocean ecosystems and carbon cycling in space and time relies on first achieving an appropriate representation of the modern marine iron cycle in models. When the iron distributions from 13 global ocean biogeochemistry models are compared against the latest oceanic sections from the GEOTRACES program, we find that all models struggle to reproduce many aspects of the observed spatial patterns. Models that reflect the emerging evidence for multiple iron sources or subtleties of its internal cycling perform much better in capturing observed features than their simpler contemporaries, particularly in the ocean interior. We show that the substantial uncertainty in the input fluxes of iron results in a very wide range of residence times across models, which has implications for the response of ecosystems and global carbon cycling to perturbations. Given this large uncertainty, iron fertilization experiments based on any single current generation model should be interpreted with caution. Improvements to how such models represent iron scavenging and also biological cycling are needed to raise confidence in their projections of global biogeochemical change in the ocean

What are the implications of climate change for trans-Atlantic aircraft routing and flight time?

The effect of wind changes on aircraft routing has been identified as a potential impact of climate change on aviation. This is of particular interest for trans-Atlantic flights, where the pattern of upper-level winds over the north Atlantic, in particular the location and strength of the jet stream, strongly influences both the optimal flight route and the resulting flight time. Eastbound trans-Atlantic flights can often be routed to take advantage of the strong tailwinds in the jet stream, shortening the flight time and reducing fuel consumption. Here we investigate the impact of climate change on upper-level winds over the north Atlantic, using five climate model simulations from the Fifth Coupled Model Intercomparison Project, considering a high greenhouse-gas emissions scenario. The impact on aircraft routing and flight time are quantified using flight routing software. The climate models agree that the jet stream will be on average located 1 degree further north, with a small increase in mean strength, by 2100. However daily variations in both its location and speed are significantly larger than the magnitude of any changes due to climate change. The net effect of climate change on trans-Atlantic aircraft routes is small; in the annual-mean eastbound routes are 1 min shorter and located further north and westbound routes are 1 min longer and more spread out around the great circle. There are, however, seasonal variations; route time changes are larger in winter, while in summer both eastbound and westbound route times increase

Theoretical studies of 31P NMR spectral properties of phosphanes and related compounds in solution

Selected theoretical methods, basis sets and solvation models have been tested in their ability to predict 31P NMR chemical shifts of large phosphorous-containing molecular systems in solution. The most efficient strategy was found to involve NMR shift calculations at the GIAO-MPW1K/6-311++G(2d,2p)//MPW1K/6-31G(d) level in combination with a dual solvation model including the explicit consideration of single solvent molecules and a continuum (PCM) solvation model. For larger systems it has also been established that reliable 31P shift predictions require Boltzmann averaging over all accessible conformations in solution

Inconsistent strategies to spin up models in CMIP5: implications for ocean biogeochemical model performance assessment

International audienceDuring the fifth phase of the Coupled Model Inter-comparison Project (CMIP5) substantial efforts were made to systematically assess the skill of Earth system models. One goal was to check how realistically representative marine biogeochemical tracer distributions could be reproduced by models. In routine assessments model historical hind-casts were compared with available modern biogeochemi-cal observations. However, these assessments considered neither how close modeled biogeochemical reservoirs were to equilibrium nor the sensitivity of model performance to initial conditions or to the spin-up protocols. Here, we explore how the large diversity in spin-up protocols used for marine biogeochemistry in CMIP5 Earth system models (ESMs) contributes to model-to-model differences in the simulated fields. We take advantage of a 500-year spin-up simulation of IPSL-CM5A-LR to quantify the influence of the spin-up protocol on model ability to reproduce relevant data fields. Amplification of biases in selected biogeochemical fields (O2, NO3, Alk-DIC) is assessed as a function of spin-up duration. We demonstrate that a relationship between spin-up duration and assessment metrics emerges from our model results and holds when confronted with a larger ensemble of CMIP5 models. This shows that drift has implications for performance assessment in addition to possibly aliasing estimates of climate change impact. Our study suggests that differences in spin-up protocols could explain a substantial part of model disparities, constituting a source of model-to-model uncertainty

Probing Quark-Gluon Interactions with Transverse Polarized Scattering

We have extracted QCD matrix elements from our data on double polarized inelastic scattering of electrons on nuclei. We find the higher twist matrix element \tilde{d_2}, which arises strictly from quark- gluon interactions, to be unambiguously non zero. The data also reveal an isospin dependence of higher twist effects if we assume that the Burkhardt-Cottingham Sum rule is valid. The fundamental Bjorken sum rule obtained from the a0 matrix element is satisfied at our low momentum transfer.Comment: formerly "Nachtmann Moments of the Proton and Deuteron Spin Structure Functions

Proton Spin Structure in the Resonance Region

We have examined the spin structure of the proton in the region of the nucleon resonances (1.085 GeV < W < 1.910 GeV) at an average four momentum transfer of Q^2 = 1.3 GeV^2. Using the Jefferson Lab polarized electron beam, a spectrometer, and a polarized solid target, we measured the asymmetries A_parallel and A_perp to high precision, and extracted the asymmetries A_1 and A_2, and the spin structure functions g_1 and g_2. We found a notably non-zero A_perp, significant contributions from higher-twist effects, and only weak support for polarized quark--hadron duality.Comment: 6 pages, 4 figures, REVTeX4, similar to PRL submission, plots colorized and appenix added, v3: minor edit, matches PR

Proton G_E/G_M from beam-target asymmetry

The ratio of the proton's electric to magnetic form factor, G_E/G_M, can be extracted in elastic electron-proton scattering by measuring either cross sections, beam-target asymmetry or recoil polarization. Separate determinations of G_E/G_M by cross sections and recoil polarization observables disagree for Q^2 > 1 (GeV/c)^2. Measurement by a third technique might uncover an unknown systematic error in either of the previous measurements. The beam-target asymmetry has been measured for elastic electron-proton scattering at Q^2 = 1.51 (GeV/c)^2 for target spin orientation aligned perpendicular to the beam momentum direction. This is the largest Q^2 at which G_E/G_M has been determined by a beam-target asymmetry experiment. The result, \muG_E/G_M = 0.884 +/- 0.027 +/- 0.029, is compared to previous world data.Comment: 8 pages, 6 figures, Updated to be version published in Physical Review