644 research outputs found

    The influence of alfalfa-switchgrass intercropping on microbial community structure and function

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    The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N2O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia-oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia-oxidizing bacteria abundance in fertilized plots significantly correlated to N2O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization

    Chemosensory properties of murine nasal and cutaneous trigeminal neurons identified by viral tracing

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    BACKGROUND: Somatosensation of the mammalian head is mainly mediated by the trigeminal nerve that provides innervation of diverse tissues like the face skin, the conjunctiva of the eyes, blood vessels and the mucouse membranes of the oral and nasal cavities. Trigeminal perception encompasses thermosensation, touch, and pain. Trigeminal chemosensation from the nasal epithelia mainly evokes stinging, burning, or pungent sensations. In vitro characterization of trigeminal primary sensory neurons derives largely from analysis of complete neuronal populations prepared from sensory ganglia. Thus, functional properties of primary trigeminal afferents depending on the area of innervation remain largely unclear. RESULTS: We established a PrV based tracing technique to identify nasal and cutaneous trigeminal neurons in vitro. This approach allowed analysis and comparison of identified primary afferents by means of electrophysiological and imaging measurement techniques. Neurons were challenged with several agonists that were reported to exhibit specificity for known receptors, including TRP channels and purinergic receptors. In addition, TTX sensitivity of sodium currents and IB4 binding was investigated. Compared with cutaneous neurons, a larger fraction of nasal trigeminal neurons showed sensitivity for menthol and capsaicin. These findings pointed to TRPM8 and TRPV1 receptor protein expression largely in nasal neurons whereas for cutaneous neurons these receptors are present only in a smaller fraction. The majority of nasal neurons lacked P2X(3 )receptor-mediated currents but showed P2X(2)-mediated responses when stimulated with ATP. Interestingly, cutaneous neurons revealed largely TTX resistant sodium currents. A significantly higher fraction of nasal and cutaneous afferents showed IB4 binding when compared to randomly chosen trigeminal neurons. CONCLUSION: In conclusion, the usability of PrV mediated tracing of primary afferents was demonstrated. Using this technique it could be shown that compared with neurons innervating the skin nasal trigeminal neurons reveal pronounced chemosensitivity for TRPM8 and TRPV1 channel agonists and only partially meet properties typical for nociceptors. In contrast to P2X(3 )receptors, TRPM8 and TRPV1 receptors seem to be of pronounced physiological relevance for intranasal trigeminal sensation

    Analysis of water vapor adsorption in soils by means of a lysimeter and numerical modeling

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    Daily temperature oscillations can cause adsorption (and desorption) of atmospheric water vapor by soils. The resulting daily fluctuations in the amount of liquid water in the soil can be measured by high-precision weighing lysimeters. We analyzed the data of a lysimeter in a sandy dune sediment in southern Spain using Codebright, a thermohydraulic numerical model for unsaturated flow that takes into account water, vapor, and heat transport in the soil, as well as soil–atmosphere interactions such as precipitation, evaporation, and solar radiation. The analysis shows that daily temperature oscillations, psychrometrics, and soil water retention can explain the fluctuations of the amount of liquid water in the soil. The retention curve, especially its driest part, is essential for the existence of these fluctuations. The fluctuations could not be reproduced by a model using the van Genuchten retention curve with a constant residual saturation. On the other hand, satisfactory results could be obtained by models using retention curves that at their driest part still show a change of saturation with suction. Moreover, the models suggest within the top few decimeters of the soil a pattern of alternating bands of condensation and evaporation, which follows the daily temperature oscillations that fade out deeper in the soil.We are very grateful to André Peters for providing the AWAT filter and give special thanks to Daniel Jesus Martínez, Fernando Ruiz Bermudo, and Antonio Nicolas Martínez for their excellent technical assistance and support.We are grateful for the support and collaboration of the Biological Station of Doñana, the Biological Reserve of Doñana, and the administration of the Doñana National Park. The contract of Lidia Molano Leno (PEJ-2014-A-68763) was financed by the Ministry of Economy, Industry and Competitiveness of Spain (MINECO) and co-financed by the European Investment Bank (EIB) and the European Social Fund (ESF). Likewise, this work has been financed by the CLIGRO Project (MICINN, CGL2016-77473-C3-1-R) of the Spanish National Plan for Scientific and Technical Research and Innovation. The infrastructure has been co-financed by European Research Funds (SE Scientific Infrastructures and Techniques and Equipment 2013, IGME13-1E-2113).Peer ReviewedPostprint (published version

    Simplifying asteroseismic analysis of solar-like oscillators: An application of principal component analysis for dimensionality reduction

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    The asteroseismic analysis of stellar power density spectra is often computationally expensive. The models used in the analysis may use several dozen parameters to accurately describe features in the spectra caused by oscillation modes and surface granulation. Many parameters are often highly correlated, making the parameter space difficult to quickly and accurately sample. They are, however, all dependent on a smaller set of parameters, namely the fundamental stellar properties. We aim to leverage this to simplify the process of sampling the model parameter space for the asteroseismic analysis of solar-like oscillators, with an emphasis on mode identification. Using a large set of previous observations, we applied principal component analysis to the sample covariance matrix to select a new basis on which to sample the model parameters. Selecting the subset of basis vectors that explains the majority of the sample variance, we redefine the model parameter prior probability density distributions in terms of a smaller set of latent parameters. We are able to reduce the dimensionality of the sampled parameter space by a factor of two to three. The number of latent parameters needed to accurately model the stellar oscillation spectra cannot be determined exactly but is likely only between four and six. Using two latent parameters, the method is able to describe the bulk features of the oscillation spectrum, while including more latent parameters allows for a frequency precision better than 10%\approx10\% of the small frequency separation for a given target. We find that sampling a lower-rank latent parameter space still allows for accurate mode identification and parameter estimation on solar-like oscillators over a wide range of evolutionary stages. This allows for the potential to increase the complexity of spectrum models without a corresponding increase in computational expense.Comment: Accepted for publication in Astronomy & Astrophysics. 11 pages. 10 figure

    The trans-activation domain of the sporulation response regulator Spo0A revealed by X-ray crystallography

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    Sporulation in Bacillus involves the induction of scores of genes in a temporally and spatially co-ordinated programme of cell development. Its initiation is under the control of an expanded two-component signal transduction system termed a phosphorelay. The master control element in the decision to sporulate is the response regulator, Spo0A, which comprises a receiver or phosphoacceptor domain and an effector or transcription activation domain. The receiver domain of Spo0A shares sequence similarity with numerous response regulators, and its structure has been determined in phosphorylated and unphosphorylated forms. However, the effector domain (C-Spo0A) has no detectable sequence similarity to any other protein, and this lack of structural information is an obstacle to understanding how DNA binding and transcription activation are controlled by phosphorylation in Spo0A. Here, we report the crystal structure of C-Spo0A from Bacillus stearothermophilus revealing a single alpha -helical domain comprising six alpha -helices in an unprecedented fold. The structure contains a helix-turn-helix as part of a three alpha -helical bundle reminiscent of the catabolite gene activator protein (CAP), suggesting a mechanism for DNA binding. The residues implicated in forming the sigma (A)-activating region clearly cluster in a flexible segment of the polypeptide on the opposite side of the structure from that predicted to interact with DNA. The structural results are discussed in the context of the rich array of existing mutational data
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