Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important ...component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor . A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.
Earth system processes exhibit complex patterns across time, as do the models that seek to replicate these processes. Model output may or may not be significantly related to observations at different ...times and on different frequencies. Conventional model diagnostics provide an aggregate view of model-data agreement, but usually do not identify the time and frequency patterns of model-data disagreement, leaving unclear the steps required to improve model response to environmental drivers that vary on characteristic frequencies. Wavelet coherence can quantify the times and timescales at which two time series, for example time series of models and measurements, are significantly different. We applied wavelet coherence to interpret the predictions of 20 ecosystem models from the North American Carbon Program (NACP) Site-Level Interim Synthesis when confronted with eddy-covariance-measured net ecosystem exchange (NEE) from 10 ecosystems with multiple years of available data. Models were grouped into classes with similar approaches for incorporating phenology, the calculation of NEE, the inclusion of foliar nitrogen (N), and the use of model-data fusion. Models with prescribed, rather than prognostic, phenology often fit NEE observations better on annual to interannual timescales in grassland, wetland and agricultural ecosystems. Models that calculated NEE as net primary productivity (NPP) minus heterotrophic respiration (HR) rather than gross ecosystem productivity (GPP) minus ecosystem respiration (ER) fit better on annual timescales in grassland and wetland ecosystems, but models that calculated NEE as GPP minus ER were superior on monthly to seasonal timescales in two coniferous forests. Models that incorporated foliar nitrogen (N) data were successful at capturing NEE variability on interannual (multiple year) timescales at Howland Forest, Maine. The model that employed a model-data fusion approach often, but not always, resulted in improved fit to data, suggesting that improving model parameterization is important but not the only step for improving model performance. Combined with previous findings, our results suggest that the mechanisms driving daily and annual NEE variability tend to be correctly simulated, but the magnitude of these fluxes is often erroneous, suggesting that model parameterization must be improved. Few NACP models correctly predicted fluxes on seasonal and interannual timescales where spectral energy in NEE observations tends to be low, but where phenological events, multi-year oscillations in climatological drivers, and ecosystem succession are known to be important for determining ecosystem function. Mechanistic improvements to models must be made to replicate observed NEE variability on seasonal and interannual timescales.
Gene fusions are known to drive many human cancers. Therefore, the functional characterization of newly discovered fusions is critical to understanding the oncobiology of these tumors and to enable ...therapeutic development. NPM1-TYK2 is a novel fusion identified in CD30 + lymphoproliferative disorders, and here we present the functional evaluation of this fusion gene as an oncogene. The chimeric protein consists of the amino-terminus of nucleophosmin 1 (NPM1) and the carboxyl-terminus of tyrosine kinase 2 (TYK2), including the kinase domain. Using in vitro lymphoid cell transformation assays and in vivo tumorigenic xenograft models we present direct evidence that the fusion gene is an oncogene. NPM1 fusion partner provides the critical homodimerization needed for the fusion kinase constitutive activation and downstream signaling that are responsible for cell transformation. As a result, our studies identify NPM1-TYK2 as a novel fusion oncogene and suggest that inhibition of fusion homodimerization could be a precision therapeutic approach in cutaneous T-cell lymphoma patients expressing this chimera.
In this study, we present two approaches to developing composite electrolytes exploiting the self-assembling nature of colloidal fillers. The first system comprises of oligomers of poly(ethylene ...glycol) dimethyl ether, branched fumed silica particulates and lithium salt. The fumed silica forms a three-dimensional, self-supporting network that provides mechanical stability. The large pores of the network has little effect on diffusivity of ions and oligomers, lithium transference number and ionic conductivity, with the latter showing values >10
−3 S/cm at ambient conditions. The second system consists of Li exchanged hectorite clay in a mixture of low molar mass carbonates. Similar to the fumed silica, the clay provides mechanical stability through formation of a three-dimensional network. In addition, the immobile clay platelets also serve as the anion rendering the system to be a single ion conductor. Near-unity transference number is observed in this case. However, the room temperature conductivity of the clay composite is lower than the fumed silica, revealing a value of about 10
−4 S/cm. The lower conductivity can be attributed to the clay not being in a fully exfoliated form as evident from morphological analysis.
Traditional preparation of rigid material for compositional analysis has involved time-consuming and physically demanding grinding processes, such as the use of mortar and pestle. This paper ...describes a simple and relatively inexpensive new device capable of quickly, safely, and efficiently pulverizing rigid and brittle biomass material, or geologic materials, such as rock and sediment. The high sample recovery obtained with this device is comparable to that achieved by much more expensive analytical equipment.
Bivalves are good candidates for tag and recapture studies because the accrual of shell material provides a stable record of growth. Obtaining measurements for tagged individuals over time relies on ...the resilience of markings or tagging devices to environmental stress as well as the readability of identifying markings upon capture. Tagging devices should also be easy and quick to apply in order to minimize potential stress to the animal during extirpation from the water. A variety of methods to attach devices to the inside and outside of bivalve shells have been used in tagging studies. This paper describes a low cost, commercially available, self-adhesive numbered tag for application to clams and other bivalves. Tests of the tag demonstrate its resilience to severe conditions over a short time scale with a ninety-five percent recovery of individuals with tags remaining intact. Ninety-four percent recovery of individuals with tags intact was also achieved in long-term studies. No problems with legibility of tags recovered occurred in any of the tests.
ENVIRONMENTAL SCIENCES Correction for “Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche,” by Emmanuelle Morin, ...Annegret Kohler, Adam R. Baker, Marie Foulongne-Oriol, Vincent Lombard, Laszlo G. Nagy, Robin A. Ohm, Aleksandrina Patyshakuliyeva, Annick Brun, Andrea L. Aerts, Andrew M. Bailey, Christophe Billette, Pedro M. Coutinho, Greg Deakin, Harshavardhan Doddapaneni, Dimitrios Floudas, Jane Grimwood, Kristiina Hildén, Ursula Kües, Kurt M. LaButti, Alla Lapidus, Erika A. Lindquist, Susan M. Lucas, Claude Murat, Robert W. Riley, Asaf A. Salamov, Jeremy Schmutz, Venkataramanan Subramanian, Han A. B. Wösten, Jianping Xu, Daniel C. Eastwood, Gary D. Foster, Anton S. M. Sonnenberg, Dan Cullen, Ronald P. de Vries, Taina Lundell, David S. Hibbett, Bernard Henrissat, Kerry S. Burton, Richard W. Kerrigan, Michael P. Challen, Igor V. Grigoriev, and Francis Martin, which appeared in issue 43, October 23, 2012, of Proc Natl Acad Sci USA (109:17501–17506; first published October 8, 2012; 10.1073/pnas.1206847109). The authors note that the following statement should be added to the Acknowledgments: “G.D. is a PhD student funded by the Teagasc Walsh Fellowship scheme and jointly supervised by K.S.B., and HM Grogan, Teagasc, Ireland.”
Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important ...component of the human diet for over 200 y and worldwide cultivation of the button mushroom forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.
We report on Bayesian parameter estimation of the mass and equatorial radius of the millisecond pulsar PSR J0030+0451, conditional on pulse-profile modeling of Neutron Star Interior Composition ...Explorer X-ray spectral-timing event data. We perform relativistic ray-tracing of thermal emission from hot regions of the pulsar's surface. We assume two distinct hot regions based on two clear pulsed components in the phase-folded pulse-profile data; we explore a number of forms (morphologies and topologies) for each hot region, inferring their parameters in addition to the stellar mass and radius. For the family of models considered, the evidence (prior predictive probability of the data) strongly favors a model that permits both hot regions to be located in the same rotational hemisphere. Models wherein both hot regions are assumed to be simply connected circular single-temperature spots, in particular those where the spots are assumed to be reflection-symmetric with respect to the stellar origin, are strongly disfavored. For the inferred configuration, one hot region subtends an angular extent of only a few degrees (in spherical coordinates with origin at the stellar center) and we are insensitive to other structural details; the second hot region is far more azimuthally extended in the form of a narrow arc, thus requiring a larger number of parameters to describe. The inferred mass M and equatorial radius Req are, respectively, 1.34 − 0.16 + 0.15 M and 12.71 − 1.19 + 1.14 km , while the compactness GM R eq c 2 = 0.156 − 0.010 + 0.008 is more tightly constrained; the credible interval bounds reported here are approximately the 16% and 84% quantiles in marginal posterior mass.
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