Hierarchical cluster analysis with bootstrap resampling method was performed on the complete set of organisms (columns of the phylogenetic profile matrix)

<p><b>Copyright information:</b></p><p>Taken from "A global gene evolution analysis on family using phylogenetic profile"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S23</p><p>BMC Bioinformatics 2007;8(Suppl 1):S23-S23.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885853.</p><p></p> The number of genes identified in each organism (with a similarity measure greater than zero) is reported as a gray histogram below the dendrogram. Organism taxonomies are highlighted with different colors: proteobacteria in blue, proteobacteria in red, proteobacteria in green, proteobacteria in light blue and others in black

Number of gene clusters identified only in family; the number of genomes is reported on the x axis and the amount of shared genes is reported on the y axis

<p><b>Copyright information:</b></p><p>Taken from "A global gene evolution analysis on family using phylogenetic profile"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S23</p><p>BMC Bioinformatics 2007;8(Suppl 1):S23-S23.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885853.</p><p></p> In the first histogram, for example, there are 11 groups of each composed by 2 genomes

The blue line represents the number of genes, while the red line reports the number of gene clusters shared by an increasing number of genomes

<p><b>Copyright information:</b></p><p>Taken from "A global gene evolution analysis on family using phylogenetic profile"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S23</p><p>BMC Bioinformatics 2007;8(Suppl 1):S23-S23.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885853.</p><p></p

Two-way hierarchical cluster analysis performed on prophage and transposase proteins

<p><b>Copyright information:</b></p><p>Taken from "A global gene evolution analysis on family using phylogenetic profile"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S23</p><p>BMC Bioinformatics 2007;8(Suppl 1):S23-S23.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885853.</p><p></p> The blue bars highlight the more interesting clusters of genes such as for example the CTX prophage

Two-way hierarchical cluster analysis of the entire phylogenetic profile matrix (panel A)

<p><b>Copyright information:</b></p><p>Taken from "A global gene evolution analysis on family using phylogenetic profile"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S23</p><p>BMC Bioinformatics 2007;8(Suppl 1):S23-S23.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885853.</p><p></p> Panel B: dendrogram selection zoom of highly conserved genes shared among all the organisms; panel C: genes conserved mostly among ; panel D: genes specific of family

Percentage of strains, for each of the six clusters of recorded plant root response types, that display the tested PGP traits.

<p>Percentage of strains, for each of the six clusters of recorded plant root response types, that display the tested PGP traits.</p

Representative <i>Arabidopsis</i> root hairs distribution.

<p>The morphology on maturation zone is compared among the six clusters to a) non-inoculated roots and e) 50 nM IAA-treated seedlings. b) seedling roots grouped in cluster 1 and 2, c) seedling roots grouped in cluster 3–4; d) seedling roots grouped in clusters 5 and 6. Scale bars: 500 μm.</p

Effects of bacterial strains on <i>Arabidopsis</i> root architecture.

<p>a-c) supervised model based clustering performed on the variables a) length b) diameter and c) area of the roots. d) <i>Arabidopsis</i> plantlet phenotypes (after two weeks of growing) grouped in different clusters obtained from “model based cluster” analysis in comparison with non-inoculated (control) and 50nM IAA-treated seedlings. Scale bars: 1 cm.</p

Revertant Fibers in the <i>mdx</i> Murine Model of Duchenne Muscular Dystrophy: An Age- and Muscle-Related Reappraisal

<div><p>Muscles in Duchenne dystrophy patients are characterized by the absence of dystrophin, yet transverse sections show a small percentage of fibers (termed “revertant fibers”) positive for dystrophin expression. This phenomenon, whose biological bases have not been fully elucidated, is present also in the murine and canine models of DMD and can confound the evaluation of therapeutic approaches. We analyzed 11 different muscles in a cohort of 40 <i>mdx</i> mice, the most commonly model used in pre-clinical studies, belonging to four age groups; such number of animals allowed us to perform solid ANOVA statistical analysis. We assessed the average number of dystrophin-positive fibers, both absolute and normalized for muscle size, and the correlation between their formation and the ageing process. Our results indicate that various muscles develop different numbers of revertant fibers, with different time trends; besides, they suggest that the biological mechanism(s) behind dystrophin re-expression might not be limited to the early development phases but could actually continue during adulthood. Importantly, such finding was seen also in cardiac muscle, a fact that does not fit into the current hypothesis of the clonal origin of “revertant” myonuclei from satellite cells. This work represents the largest, statistically significant analysis of revertant fibers in <i>mdx</i> mice so far, which can now be used as a reference point for improving the evaluation of therapeutic approaches for DMD. At the same time, it provides new clues about the formation of revertant fibers/cardiomyocytes in dystrophic skeletal and cardiac muscle.</p></div

Assayed PGP traits of selected strain, their cluster attribution and their taxonomical identification.

<p>Assayed PGP traits of selected strain, their cluster attribution and their taxonomical identification.</p