Percentage of infected plants infected by one or the two viral strains as determined by the RT-PCR/restriction analysis.

<p>Percentage of infected plants infected by one or the two viral strains as determined by the RT-PCR/restriction analysis.</p

Scheme of the experimental evolution procedure and virulence and <i>ID</i>₅₀ (infectivity) estimation.

<p>Seven dpi, virus accumulation (titer) was evaluated by local-lesion assays on <i>C. quinoa</i> and then concentrations were made equal so each newly infected plant received 20 LFU per evolutionary passages or to 30 LFU/µL for <i>ID</i>₅₀ determination.</p

Phase portraits obtained numerically from <b>Eqs. (1)</b>–<b>(2)</b> displaying the dynamics in the phase plane (<i>x</i>₁, <i>x</i>₂), with <i>x</i>₁+<i>x</i>₂ = 1, and the stability of the fixed points: <i>P</i>₁^*, <i>P</i>₂^*, <i>P</i>₃^*, and <i>P</i>₄^* (stable and unstable equilibria are shown, respectively, in black and white circles).

<p>In (a) we use the experimental values used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017917#pone-0017917-g004" target="_blank">Fig. 4 (a)</a> right. In (b) we use the same values of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017917#pone-0017917-g004" target="_blank">Fig. 4(b)</a> left. In both cases the origin is a repeller; <i>P</i>₃^* is a saddle; <i>P</i>₂^* (outcompetition of <i>x</i>₂ by <i>x</i>₁) is stable and the equilibrium <i>P</i>₄^* is outside the phase plane. In (c) we show the asymptotic coexistence scenario, where <i>P</i>₂^* becomes a saddle and the fixed point <i>P</i>₄^*, which is stable, is inside the phase plane (here we use <i>r_max</i>_,1 = 1.07, <i>r_max</i>_,2 = 0.621, <i>K</i>₁ = 0.8 and <i>K</i>₂ = 0.2). The arrows in all the plots indicate the directions of the flows.</p

The number of cells infected by each of the two virus variants over space and time.

<p>In Panels A–D, the observed frequencies of cellular infection in Leafs 7, 6, 5, and 3 are given for all cells infected by TEV-Venus (finely dotted green line with circles), TEV-BFP (coarsely dotted blue line with squares) and those infected by both variants (continuous red line with diamonds). The abscissae represents days post inoculation (dpi), whilst the ordinate is the frequency at which a particular infected-cell type was observed. Error bars for all panels represent ± 1 SD, and each data point represents the mean of 5 plants, with 50,000 cells measured per individual leaf. Leaf 4 was not included in this analysis because it does not become infected, probably because the host vasculature does not transport virions to this leaf (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004186#s3" target="_blank">Discussion</a>). The leaves analyzed in this study have been given different colors in the schematic representation of the plant for the sake of easy identification in the top and side views. Note that for the side of view of the tobacco plant, stem length has not been drawn to scale – being shorter than depicted here – for the sake of clarity. In panels E–F, stereomicroscopic images of Leaf 6 at 7 dpi of a plant inoculated with TEV-eGFP (green fluorescence) and TEV-mCherry (red fluorescence) are shown. Entire regions of leaf remain uninfected even though cell infection has saturated, probably because a phloem-transported virus cannot traverse the sink-source boundary. However, even prior to the boundary (panel F) there remain uninfected regions. Panel G shows confocal microscopy of a region that appears to be completely infected at higher scales (panels E and F), being a merge of the trans, eGFP and mCherry images.</p

Cellular <i>MOI</i>.

<p>The results of <i>MOI</i> model fitting and <i>MOI</i> estimates are given. In panel A, we provide estimates of <i>ψ</i>, the leaf-dependent infection aggregation parameter, for the best-supported model. In panel B, estimates of cellular <i>MOI</i>, for different times post-inoculation and in different leaves are given. Error bars represent the 95% confidence interval. Note that the reported <i>MOI</i> value is <i>m_I</i>, the <i>MOI</i> in infected cells only, which has a minimum value of 1. <i>MOI</i> is initially very low and gradually increases, never reaching 1.5. <i>MOI</i> values for the final time point (10 dpi) are similar for Leaves 3, 6 and 7, whilst it remains very low for Leaf 5, which hardly becomes infected. Panels C–E show model predictions for the frequency at which cells are infected by a certain number of virions. The blue section of the bar indicates the frequency of infection by only one virus variant, whereas striped area indicates coinfection by both virus variants, assuming a 1∶1 ratio of virus variants. Panel C gives this prediction for the lowest <i>MOI</i> (<i>m_I</i> = 1.001), panel D for the mean <i>MOI</i> (<i>m_I</i> = 1.137), and panel E for the highest <i>MOI</i> (<i>m_I</i> = 1.432). Estimated <i>MOI</i> values are low, but the number of infecting virions is assumed to follow a Poisson distribution. Hence even at the low mean <i>MOI</i> some cells will be infected by 2 or more virions, allowing for cellular coinfection.</p

The distribution of genotypic frequencies within cells and estimates of effective population size (<i>N_e</i>).

<p>In panel A, the distribution of the log-transformed TEV-Venus∶TEV-TagBFP ratio in cells infected by both variants is shown, using the combined data from days 3–10. On the abscissae is frequency of TEV-Venus in the whole leaf and on the ordinate is the value for parameters describing the distribution of the log-transformed virus ratio, with individual points representing the data and lines representing ordinary least squares regression lines. Red squares and solid line correspond to the mean, orange circles and the coarse dotted line are the variance, blue diamonds and the intermediate-grain dotted line are the kurtosis, and green triangles and fine dotted line are the skewness. There was not a significant relationship between TEV-Venus frequency and any of the distribution parameters (Model 2 regression), suggesting that the virus genotype ratio in individual coinfected cells is largely independent of infection events at the leaf level. In Panel B, we estimated <i>N_e</i> for each leaf and the whole plant, and the estimates with 95% confidence intervals from the pooled data of days 5, 7 and 10 are given (each data point represents 15 plants). <i>N_e</i> for the inoculated leaf was about 100, which corresponds well with the approximate number of primary infection foci. There were considerably smaller <i>N_e</i> values for Leaves 5 and 7. For Leaf 6, the estimated bottleneck size was about the same for the inoculated leaf, although the 95% extends to ∞ (marked by an *). <i>N_e</i> estimates therefore suggest the virus populations infecting different leaves vary in size, although <i>N_e</i> estimates are not entirely congruent with estimates of between-leaf transmission (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004186#pgen-1004186-g002" target="_blank">Figure 2B</a>) at first glance.</p

History in computer games: case study on "Valiant Hearts: The Great War"

This thesis is a case study analysis of the visualization of history in computer games. The analyzed game, Valiant Hearts: The Great War, was published by the French company Ubisoft in 2014. The game is set in The First World War and was developed in cooperation with The Centenary Parnership Proram. The main goals of the thesis are following: First, determine if the vision of history in the game reflects the current paradigms of French historiography of The First World War. Second, to identify and to interpret particularities and deformations in the way the game recreates history. The first, theoretical chapter presents the phenomenon of The First World War in the French context, the study of computer games and the methodology of the analysis. For the analysis I have created my own methodology which combines various approaches used elsewhere. Chapter 2 contains the analysis, which is further structured into the analysis of the story from the perspective of the main characters and locations (2.1), analysis of the object inventory and the in game miniencyclopedia (2.2), and the analysis of game's style and form -the graphic and audio style, along with the issue of player freedom (2.3). For greater clarity, the parts of the game are referred to through it's subchapters. The results of the analysis..

Additional file 4: Table S2. of Assessing parallel gene histories in viral genomes

Bootstrap support for the clusters identified (see Additional file 3: Figure S1 and Additional file 6: Figure S2) in the phylogenetic trees built from the concatenated sequence for the concatenated tree and the gene trees, for the TuMV and the PV nucleotide data set

Additional file 6: Figure S2. of Assessing parallel gene histories in viral genomes

Best-known ML tree (a) and phylogenetic network (d) constructed from the PV concatenated nucleotide data set. Around them, the best-known ML tree constructed for each of the genes of PV at nucleotide level. Shaded areas correspond to the supported groups refered to in the text and in Additional file 4: Table S2b

Vale-et-al-PRSB-CRISPR-Cost-Data

Data on growth rate, lag time, yield and competitive fitness of several strains of Streptococcus thermophilus. Data is provided for individual replicates, and organised separately for each set of figures.See methods section for experimental details