Project description:In our target article, we tested the replicability of 4 popular psychopathology network estimation methods that aim to reveal causal relationships among symptoms of mental illness. We started with the focal data set from the 2 foundational psychopathology network papers (i.e., the National Comorbidity Survey-Replication) and identified the National Survey of Mental Health and Wellbeing as a close methodological match for comparison. We compared the psychopathology networks estimated in each data set-as well as in 10 sets of random split-halves within each data set-with the goal of quantifying the replicability of the network parameters as they are interpreted in the extant psychopathology network literature. We concluded that current psychopathology network methods have limited replicability both within and between samples and thus have limited utility. Here we respond to the 2 commentaries on our target article, concluding that the findings of Steinley, Hoffman, Brusco, and Sher (2017)-along with other recent developments in the literature-provide further conclusive evidence that psychopathology networks have poor replicability and utility. (PsycINFO Database Record
Project description:Agaricomycetes produce the most efficient enzyme systems to degrade wood and the most complex morphological structures in the fungal kingdom. Despite decades-long interest in their genetic bases, the evolution and functional diversity of both wood-decay and fruiting body formation are incompletely known.Here, we perform comparative genomic and transcriptomic analyses of wood-decay and fruiting body development in Auriculariopsis ampla and Schizophyllum commune (Schizophyllaceae), species with secondarily simplified morphologies and enigmatic wood-decay strategy and weak pathogenicity to woody plants. The plant cell wall degrading enzyme repertoires of Schizophyllaceae are transitional between those of white rot species and less efficient wood-degraders such as brown rot or mycorrhizal fungi. Rich repertoires of suberinase and tannase genes were found in both species, with tannases restricted to Agaricomycetes that preferentially colonize bark-covered wood, suggesting potential complementation of their weaker wood-decaying abilities and adaptations to wood colonization through the bark. Fruiting body transcriptomes of A. ampla and S. commune revealed a high rate of divergence in developmental gene expression, but also several genes with conserved developmental expression, including novel transcription factors and small-secreted proteins, some of the latter might represent fruiting body effectors. Taken together, our analyses highlighted novel aspects of wood-decay and fruiting body development in a widely distributed family of mushroom-forming fungi.
Project description:AIM: By adopting comparative transcriptomic approach, we investigated the gene expression of wood decomposing Basidiomycota fungus Phlebia radiata. Our aim was to reveal how hypoxia and lignocellulose structure affect primary metabolism and the expression of wood decomposition related genes. RESULTS: Hypoxia was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides by the fungus. Our results manifest how oxygen depletion affects not only over 200 genes of fungal primary metabolism but also plays central role in regulation of secreted CAZyme (carbohydrate-active enzyme) encoding genes. Based on these findings, we present a hypoxia-response mechanism in wood-decaying fungi divergent from the regulation described for Ascomycota fermenting yeasts and animal-pathogenic species of Basidiomycota.
