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Roy, B.

Publications and source records attributed to Roy, B..

2 recordsLinked to original sources

An agent-based model of the Foraging Ascomycete Hypothesis

Most trees host hundreds of species of fungi asymptomatically in their internal tissues, known collectively as fungal endophytes. The Foraging Ascomycete (FA) hypothesis proposes that some fungal endophytes inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia during periods of environmental stress. This dispersal strategy has been termed viaphytism. Following the FA hypothesis, many fungi may therefore be in continuous and cyclical flux between life stages as endophytes in the forest canopy and as wood-decomposing fungi on the forest floor. This cycle may represent a very common and previously-ignored process in the ecology of forests, with implications for forest health. The ecological consequences of the FA hypothesis are complex, so we constructed an agent-based model of the FA hypothesis. Our model is intended to serve as both an explicit conceptual explanation of the FA hypothesis, and as an exploration of the conditions in which a strategy of endophytism accompanied by leaf dispersal may be advantageous for fungi. In a scenario of a viaphytic fungal species on a model forest landscape, without fungal competitors, viaphytism is predicted to be a plausible alternative to dispersal to substrates by spores alone, allowing the fungus to persist reliably on the landscape. In a scenario that allows competition from aggressively dispersed non-viaphytic fungi, the model predicts some competitive benefits to fungal dispersal via leaves. However, these benefits are conditional, requiring sufficient retention through time of endophyte infections by host trees, and sufficient host trees on the landscape. In the model, loss of these fungal populations can result from increased local disturbances of forest canopy, and deforestation.

ecology

Whole exome sequencing study of colorectal cancer in Chinese population reveals novel prevalently mutated genes and decreased mutation frequency of APC and Wnt signaling in lymph node positive cancer

Colorectal cancer is the fifth prevalent cancer in China. Nevertheless, a large-scale characterization of Chinese colorectal cancer mutation spectrum has not been carried out. In this study, we have performed whole exome-sequencing analysis of 98 patients tumor samples with matched pairs of normal colon tissues using Illumina and Complete Genomics high-throughput sequencing platforms. Canonical CRC somatic gene mutations with high prevalence (>10%) have been verified, including TP53, APC, KRAS, SMAD4, FBXW7 and PIK3CA. PEG3 is identified as a novel frequently mutated gene (10.6%). APC and Wnt signaling exhibit significantly lower mutation frequencies than those in TCGA data. Analysis with clinical characteristics indicates that APC gene and Wnt signaling display lower mutation rate in lymph node positive cancer than negative ones, which are not observed in TCGA data. APC gene and Wnt signaling are considered as the key molecule and pathway for colorectal cancer initiation, and these findings greatly undermine their importance in tumor progression for Chinese patients. Taken together, the application of next-generation sequencing has led to the determination of novel somatic mutations and alternative disease mechanisms in colorectal cancer progression, which may be useful for understanding disease mechanism and personalizing treatment for Chinese patients.

genomics