第768回千葉医学会例会・第3回磯野外科例会 83.

List of the sequences used in the analyses. (XLSX 67 kb

Distribution of pairwise genetic/evolutionary distances of the same set of 25 mastrevirus full genome sequences in the context of progressively larger sequence datasets.

<p>The constant frequency distribution (represented by red graph) illustrates the consistency of pairwise distance calculation based on pairwise alignments while the changing frequency distributions (represented by blue and green graphs) indicate how pairwise distance scores based on multiple sequence alignment tend to become inflated as dataset sizes get larger.</p

Speed-ups achieved with the parallelised versions of SDT.

<p>Speed-ups achieved with the parallelised versions of SDT.</p

The SDT interface.

<p>(<b>A</b>) Colour-coded pairwise identity matrix generated from 29 <i>Chickpea chlorotic dwarf virus</i> genomes. Each coloured cell represents a percentage identity score between two sequences (one indicated horizontally to the left and the other vertically at the bottom). A coloured key indicates the correspondence between pairwise identities and the colours displayed in the matrix. (<b>B</b>) Pairwise identity frequency distribution plot. The horizontal axis indicates percentage pairwise identities, and the vertical axis indicates proportions of these identities within the distribution. While peaks on the graph indicate pairwise sequence identity thresholds that would yield the most ambiguous classifications, troughs indicate thresholds that would yield the least ambiguous classifications and could therefore be tentatively used as relatively conflict free operational taxonomic unit demarcation cut-offs.</p

Estimated growth rates.

<p>Average daily growth rate estimates (with 95% CI) from best model (i.e., model with lowest AIC_c) relating growth rates of morphological characteristics and mass to sex, year, brood size, chick hatching order; and sample sizes (n) for male and female Adélie Penguin chicks measured, and weighed during 2012–13 (2012) and 2013–14 (2013) on Ross Island, Antarctica. Sex was not supported as an important variable for foot growth so only means by year (best model results) are reported.</p

Growth model parameter estimates.

<p>Parameter estimates (with 95% CI) for the sex effect on growth from the best model (i.e., lowest AIC_c) for each morphological measurement of Adélie Penguin chicks during 2012–13 and 2013–14 on Ross Island, Antarctica. Plus signs denote additive effects and asterisks denote interactions. Sex was not supported as an important factor associated with foot growth.</p

Measurement diagram.

<p>Schematic illustrating the location of morphological measurements collected from male and female Adélie Penguin chicks during Austral summers of 2012–13 and 2013–14 on Ross Island, Antarctica. Bill was measured to the nearest hundredth mm and remaining measurements to the nearest mm. Dashed line indicates humeral head on underside of the flipper.</p

PHYLOGENETIC JAE DATA

The file contains the plant-herbivore interaction metaweb, the herbivore-parasitoid interaction metaweb, parasitoid species abundance by sampling plot, plant species biomass by sampling plot, herbivore species abundance by sampling plot, and the native herbivore-parasitoid interactions present on the different sampling plots

Vertical box-and-whisker plots summarising real-time PCR data on all constructs bombarded at a 5∶1 weight ratio with infectious clones of diverse MSV strains and another mastrevirus species.

<p>A) MSV-Kom. The plots were constructed as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105932#pone-0105932-g006" target="_blank">Figure 6</a>. The number of replicates (i.e. the number of bombarded samples) were as follows: pSK, 34; pSPLITGusUbi, 18; pSPLIT<i>rep</i>^1-219Rb-UbiΔI, 18; pSPLIT<i>rep</i>^1-219Rb-Ubi, 14; pSPLIT<i>rep</i>^III-Rb-Ubi, 8; p<i>rep</i>^1-219Rb-, 9; pMSV-<i>Pst</i>I, 11. Plots in B-C) were constructed as described for A), but this time either pSPLIT<i>rep</i>^III-Rb-Ubi or pSK were co-bombarded with infectious clones of: B) the MSV-B strain isolate VW; and C) the PanSV strain A isolate Kar. The number of replicates for B) were: pSK, 11; pSPLIT<i>rep</i>^III-Rb-Ubi, 14. The number of replicates for C) were: pSK, 16; pSPLIT<i>rep</i>^III-Rb-Ubi, 25. All real-time PCRs were performed on total DNA extracted from BMS cells four days post-bombardment.</p

Lengths, numbers of reads and BlastX analysis results for siRNA <i>de novo</i> contigs from sugarcane plant VARX with detectable homology to mastreviral sequences.

<p>Acronyms used are as follows: SSEV (Sugarcane streak Egypt virus), SWSV (Sugarcane white streak virus), SacSV (Saccharum streak virus), WDIV (Wheat dwarf India virus), SSRV (Sugarcane streak Reunion virus).</p