Comparison of phospholipase C encoding genes in <i>C. novyi sensu lato</i> genomes.

<p>Comparison of phospholipase C genes found in <i>C. novyi sensu lato</i> genomes to the characterized beta toxin gene (accession number AF525415) of <i>C. haemolyticum</i> strain 7170. Chromosomal phospholipase C genes were found in all strains in this study and this table shows only representatives of the different species in the different lineages.</p><p>Comparison of phospholipase C encoding genes in <i>C. novyi sensu lato</i> genomes.</p

Average whole genome similarity of <i>C. novyi sensu lato</i> genomes.

<p>A similarity matrix based on normalized average BLASTN sores for fragmented comparisons covering the whole genomes (200 bp fragment size) illustrated by a heat-plot. Four lineages were identified (I–IV) and are framed with black squares. The geographical origins of the strains are listed with two-digit country codes. Strains isolated more than 50 years ago are marked with a star.</p

Alignment of chimeric <i>bont</i> sequences in comparison with non-chimeric sequences.

<p>Chimeric sequences are aligned against non-chimeric sequences from type C strain C-Stockholm (lineage II) and type D strain 16868 (lineage I). The chimeric sequences are from type C/D strains BKT015925 and BKT75002, and type D/C strain DC5 (all from lineage I). In the H_N domain, nucleotides that are conserved are not colored, whereas unique nucleotides are marked in green, nucleotides corresponding to the C-sequence are marked in blue, and nucleotides corresponding to the D-sequence are in red. The light chain and the H_C domain are not represented according to scale and they are colored as the closest related sequence. Estimated recombination sites are indicated.</p

Comparative analysis of <i>C. novyi sensu lato</i> plasmids.

<p>A heat-plot of the relative amount of shared genetic material between plasmids (40% normalized BLASTN score threshold). Thirteen plasmid groups (PG1–PG13), framed by black squares, were identified from these results and from analysis of plasmid replication and partitioning genes. Some of the plasmids in lineage I strains (PG1–PG3) shared several IS elements, and this resulted in an apparent increase in the background level of shared genetic content between otherwise dissimilar plasmids within this lineage. Uncompleted plasmids are marked with a star.</p

Sequence comparison between the C-St BoNT-encoding phage and the p1Ch9693 phage from a <i>C. haemolyticum</i> strain.

<p>Artemis Comparison Tool (ACT) plot of an alignment between the C-St BoNT-encoding phage from <i>C. botulinum</i> strain C-Stockholm and p1Ch9693 from <i>C. haemolyticum</i> strain NCTC 9693. Regions of similarity are indicated in red (same direction) or blue (opposite direction). Genes in the <i>bont</i> cluster are green, genes homologous between the two replicons are orange, and remaining genes are gray.</p

Representation of plasmid groups and the plasmid distribution in analyzed strains.

<p>The table headings represent Lineage (L), Species (Sp), Type and Strain name (Type/Strain) and number of plasmids predicted in each strain (No). The species are represented by B (<i>Clostridium botulinum</i>), N (<i>Clostridium novyi</i>) or H (<i>Clostridium haemolyticum</i>).</p><p>*The sequenced strain lacked the plasmid but was previously confirmed positive for it.</p><p>Representation of plasmid groups and the plasmid distribution in analyzed strains.</p

Circular representation of the <i>T. pedis</i> T A4 genome and complete genome alignment with <i>T. denticola</i>.

<p>(A.) Circular representation of the <i>T. pedis</i> T A4 genome. The CDSs are shown in violet where the outer circle represents predictions on the plus strand and the second circle those on the minus strand. CDSs with a best BLASTP hit in <i>T. denticola</i> ATCC 35405 are colored red and shown in the third circle. The fourth circle represents genes with best BLASTP hits in <i>T. brennaborense</i> (black), <i>F. nucleatum</i> (green), <i>F. alocis</i> (blue) and <i>T. succinifaciens</i> (grey). G+C skew is drawn in the inner circle. (B.) Complete genome alignment between <i>T. pedis</i> T A4 and <i>T. denticola</i> ATCC 35405. Dots represent maximum unique matches (MUMs) between the genomes. MUMs oriented in the same direction are depicted as red dots and reverse complemented MUMs are depicted as blue dots.</p

The strand bias of mivaRNA association with RISC differs between HAds.

<p>293-Flag-Ago2 cells were infected with the indicated viruses, 24 hpi the RISC-associated small RNAs were immunopurified using an anti-FLAG resin. The Flag-Ago2 associated 5′-mivaRNAI (<b>A</b>), 3′-mivaRNAI (<b>B</b>), 5′-mivaRNAII (<b>C</b>) and 3′-mivaRNAII (<b>D</b>) were detected by Northern blot using mixtures of ³²P-labelled oligonucleotide probes complementary to the corresponding mivaRNA sequences (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105746#pone.0105746.s007" target="_blank">Table S2</a>). The different panels were repeated at least two times.</p

Distribution of functional categories in <i>T. pedis</i> strain T A4 and <i>T. denticola</i> strain ATCC 35405 according to the COG classification.

<p>Distribution of functional categories in <i>T. pedis</i> strain T A4 and <i>T. denticola</i> strain ATCC 35405 according to the COG classification.</p

The impact of different HAd infections on RNAi/miRNA-pathway proteins.

<p>(<b>A</b>) Efficiency of different HAd infections. HeLa cells were infected with the indicated viruses, followed by a ³⁵S-methionine pulse labeling after 24 and 48 hpi. Total protein lysates were separated on an SDS-PAGE and protein synthesis visualized by autoradiography. Accumulation of late viral hexon protein is indicated by an arrow. (<b>B</b>) HAd infections do not affect RNAi/miRNA-pathway protein levels. Western blot analysis on the same protein samples as in panel A was used to monitor the levels of RNAi/miRNA-pathway proteins Exportin 5, Dicer, TRBP and Ago2. Detection of the Lamin B protein served as a loading control. Letter “M” denotes mock, non-infected samples. The different panels were repeated at least two times.</p