Aquasplatche network simulation settings

Ten folders corresponding to the ten networks described in Fourcade et al. Simulations can be performed using Aquasplatche

dataset for all 114 strains

The whole dataset is available for download(114 strains). Note that the observed 106 unique haplotypes (i.e. the clone-corrected dataset used for all the analyses; see the Methods section) are labeled with a "0". Excluded clones are labeled with a "1"

Pairwise correlations between phenotypic traits.

<p>Scatter plots indicating the degree of correlation between traits (below diagonal) and pairwise Pearson's correlation R values (above diagonal). Pearson’s correlation coefficients were calculated from averaged data from each strain for sporulation capacity, spore size and hyphal growth. Statistical significant correlation coefficients are indicated as following: ** P-value < 0.01 and *** P-value < 0.001. Calculations were performed for domestic (A panel) and wild (B panel) populations, respectively.</p

Quantitative distribution of life history trait variables.

<p>Distribution of quantitative variables: hyphal growth 24 days after deposits on agar (cm), germination rate (in logit units), sporulation capacity (in Log₁₀ units), and spore size (μm). Blue histograms correspond to the wild population and green ones correspond to the domestic population.</p

Quantitative distribution of life history trait variables between wild (blue) and domestic population (green).

<p>The horizontal line in boxplots represents the median. A significant difference between populations is observed for the sporulation capacity and spore size. Sporulation average in wild population: 122,400 spores mL^-1; and in domestic population: 199,955 spores mL^-1. Spore size average is 9.2 μm in the wild population and is 9.5 μm in the domestic population.</p

DRYAD_DATASET_GLADIEUX

DRYAD_DATASET_GLADIEU

Citrinin induces apoptosis in human HCT116 colon cancer cells through endoplasmic reticulum stress

<p>The mycotoxin citrinin (CTN) is a natural contaminant of various human foods that may produce serious adverse health problems. Several studies demonstrated that citrinin exerts cytotoxic and genotoxic effects in both <i>in vivo</i> and <i>in vitro</i> systems. However, the precise mechanisms of action (MOA), particularly in intestinal cells remain unclear. The aim of the present study was to examine the precise MOA of citrinin <i>in vitro</i>. Data demonstrated that CTN significantly decreased the number of viable human intestinal HCT116 cells and induced apoptotic events including (1) decrease in ΔѰm indicative of mitochondrial membrane permeabilization, (2) activation of caspase 3, (3) elevated production of reactive oxygen species (ROS) and (4) relative persistence of plasma membrane integrity. Further, the genetic deficiency of the pro-apoptotic protein Bax protected cells against CTN-induced apoptosis, indicating that Bax is required for CTN-mediated toxicity. It was also found that CTN triggered endoplasmic reticulum (ER) stress and activated different arms of the unfolded protein response (UPR) as demonstrated by increase in expression of GRP78 (glucose-regulated protein-78), GRP94 (glucose-regulated protein-94), GADD34 (growth arrest and DNA damage-inducible protein-34), the protein disulfide isomerase associated 6 (PDIA6), CHOP (C/EBP-homologous protein) and the splicing of XBP1 (X-Box Binding Protein 1). Pretreatment of cells with the chemical chaperone 4-phenylbutyrate (PBA), known to alleviate ER stress, prevented significantly the apoptotic process triggered by CTN. Taken together, these results suggest that CTN exerts its cytotoxic effects in HCT116 cells by inducing apoptosis, at least in part, through induction of ER stress.</p

Inferences on transfer of VA genes possibly involved in host specificity.

<p>The repertoires of 107 genes encoding MCPs, sensors, adhesins, and T3Es were previously determined for each strain of the collection <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058474#pone.0058474-Hajri1" target="_blank">[27]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058474#pone.0058474-MhedbiHajri1" target="_blank">[28]</a>. Using a parsimony approach implemented in Mesquite 2.5 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058474#pone.0058474-Maddison1" target="_blank">[61]</a>, repertoires of genes at nodes of the ClonalFrame genealogy were inferred. Comparison of repertoires at ancestral nodes provided hypotheses on horizontal transfers concomitant to migration events identified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058474#pone-0058474-g002" target="_blank">Figure 2</a>. Populations 9.1 to 9.6 refer to genetic groups in <i>X. axonopodis</i> and A1 to A5 refer to ancestral populations. Four of the migration events detected by IMa2 may be associated to transfers of genes encoding MCP (<i>xac3768, xcv1954</i>), adhesins (<i>fhaB1</i>, <i>fhaB2</i>), sensors (<i>xac0852</i>, <i>xac2152, xac2155, xac3050</i>, <i>xac3498</i>, <i>xac4062</i>), and T3Es (<i>avrXccA2</i>, <i>xopC1, xopE1, xopF2, xopJ5, xopL, xopP, xopAJ, xopAF</i>).</p

Mutation rate per gene and per year inferred from EBSP analysis in BEAST for each of the six housekeeping genes in each of the six groups within <i>X. axonopodis</i>.

<p>Mutation rate per gene and per year inferred from EBSP analysis in BEAST for each of the six housekeeping genes in each of the six groups within <i>X. axonopodis</i>.</p

Primers characteristics.

<p>Primers characteristics.</p