Site-dependent microbial diversity associated with PWN.

<p>Microbial community associated with the pinewood nematodes, isolated from the three forest areas (A-Oliveira do Hospital, M-Arganil and Z-Grândola) where Pine wilt disease was detected.</p

Microbial diversity of bacteria carried by <i>B. xylophilus</i> and other nematodes isolated in Portugal.

<p>Phylogenetic relationship of partial 16S rRNA gene sequences from isolated bacteria with selected reference sequences from identified bacteria in the database were obtained. A – <i>Gammaproteobacteria</i> classe - <i>Enterobacteriaceae</i> family; B – <i>Betaproteobacteria</i> classe <i>Burkholderiaceae</i> and <i>Oxalobacteriaceae</i> families; C - <i>Gammaproteobacteria</i> classe - <i>Pseudomonadaceae</i> family.</p

Bacterial colonies from nematode trails.

<p>Infected wood piece placed on Petri dish with R2A medium and incubated at 25°C, for three days (A). Bacterial colonies from the trails made by the nematodes on the medium were selected for characterization (B).</p

Assignment of taxonomic groups to uncultured bacterial clones from molecular nematode-associated bacteria clone libraries and the closest sequence match in database.

<p>Assignment of taxonomic groups to uncultured bacterial clones from molecular nematode-associated bacteria clone libraries and the closest sequence match in database.</p

Expression signatures of antisense PIN RNAs and corresponding PIN RNA-overlapped exon pairs relative to their 3' protein-coding exons

<p><b>Copyright information:</b></p><p>Taken from "Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription"</p><p>http://genomebiology.com/2007/8/3/R43</p><p>Genome Biology 2007;8(3):R43-R43.</p><p>Published online 26 Mar 2007</p><p>PMCID:PMC1868932.</p><p></p> A subset of 64 pairs of antisense PIN RNAs and corresponding PIN RNA-overlapped exons were identified among the tissue signatures shown in Figure 10 as having correlated patterns of expression: 49 pairs were identified in which the 3' exon of the protein-coding transcript (right panel) follows a similar expression pattern to that of the PIN RNA/PIN RNA-overlapped exon pair (left and central panels); 9 pairs were identified in which the 3' exon of the protein-coding transcript (right panel) does not follow the pattern of tissue expression of the PIN RNA and the corresponding PIN RNA-overlapped exon (left and central panels); 6 pairs in which the PIN RNA (left panel) has an expression pattern inverted in relation to that of the PIN RNA-overlapped exon (central panel). Each line represents a genomic locus covered by three different types of probes (antisense PIN RNA, PIN RNA-overlapped protein-coding exon and 3' protein-coding exon). For each line, expression intensities among the three tissues were normalized within each type of probe and colored as a function of the number of standard deviations from the mean value

Frequency of exon skipping and abundance of wholly intronic noncoding transcription in RefSeq genes

<p><b>Copyright information:</b></p><p>Taken from "Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription"</p><p>http://genomebiology.com/2007/8/3/R43</p><p>Genome Biology 2007;8(3):R43-R43.</p><p>Published online 26 Mar 2007</p><p>PMCID:PMC1868932.</p><p></p> Distribution of exon skipping events along spliced RefSeq genes with 7, 8, 9 or 10 exons. Filled squares indicate the average frequency of skipping per exon for genes with evidence of TIN RNAs mapping to their introns. Open squares indicate the average frequency of skipping per exon for genes with no evidence in GenBank that TIN RNAs map to their introns. A significantly higher (< 0.002) frequency of exon skipping was observed for RefSeq genes with TIN RNA transcription. Distribution of TIN transcripts among the introns of RefSeq sequences with 7, 8, 9 or 10 introns selected from GenBank as being outside the 95% confidence level of significance (not correlated) in a Pearson correlation analysis between the abundance of TIN contigs per intron and the intron size (in nt). Bars indicate the average intron size (nt) for this selected set of genes. Triangles indicate the number of TIN contigs per intron for RefSeq genes for the same set

Number of protein-coding, TIN and PIN transcripts expressed in three human tissues

<p><b>Copyright information:</b></p><p>Taken from "Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription"</p><p>http://genomebiology.com/2007/8/3/R43</p><p>Genome Biology 2007;8(3):R43-R43.</p><p>Published online 26 Mar 2007</p><p>PMCID:PMC1868932.</p><p></p> Different types of transcripts are shown in each panel, and are color-coded as in Figure 3: protein-coding exonic (red bars), antisense TIN (black bars), antisense PIN (blue bars) or sense TIN transcripts (hashed black bars). The total number of probes present in the microarray for each type of transcript is shown with bars marked as 'M'. The number of transcripts expressed in at least one of the three tissues tested is shown with bars marked as 'One'. Transcripts exclusively expressed in each of the three tissues are shown with bars marked as 'L' for liver; 'P' for prostate; or 'K' for kidney. The percentage of expressed transcripts relative to the total number of transcripts probed in the array is indicated at the top of each bar

Expression signature of intronic and protein-coding transcripts in human liver, prostate and kidney

<p><b>Copyright information:</b></p><p>Taken from "Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription"</p><p>http://genomebiology.com/2007/8/3/R43</p><p>Genome Biology 2007;8(3):R43-R43.</p><p>Published online 26 Mar 2007</p><p>PMCID:PMC1868932.</p><p></p> Transcripts with significantly different levels among prostate, kidney and liver samples were selected by a SAM multi-class test (FD

Most highly expressed TIN transcripts map to genes related to regulation of transcription

<p><b>Copyright information:</b></p><p>Taken from "Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription"</p><p>http://genomebiology.com/2007/8/3/R43</p><p>Genome Biology 2007;8(3):R43-R43.</p><p>Published online 26 Mar 2007</p><p>PMCID:PMC1868932.</p><p></p> TIN RNA expression data from three different human tissues (prostate, liver and kidney) were used to select the protein-coding genes to which the top 40% most highly expressed TIN transcripts map. The BiNGO program was used to identify significantly (≤ 0.05) enriched GO terms within the set of selected protein-coding genes. GO-enriched categories for prostate are shown in color, which is related to the value as indicated by the color-code bar. The exact values for all significantly enriched GO categories are shown in Additional data file 4. GO category 'Regulation of transcription, DNA-dependent' (GO:006355) is the most significantly enriched (= 0.002). Similar results were obtained for liver and kidney (see Additional data file 4). Venn diagram for the 123 unique protein-coding genes belonging to GO:006355 category 'Regulation of transcription, DNA-dependent'. The number of genes in each tissue for which intronic transcription was detected is shown in parenthesis; the numbers of coincident and dissimilar genes among kidney, prostate and liver are shown in the circles

Expression signatures of wholly intronic RNAs relative to their 3' protein-coding exons

<p><b>Copyright information:</b></p><p>Taken from "Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription"</p><p>http://genomebiology.com/2007/8/3/R43</p><p>Genome Biology 2007;8(3):R43-R43.</p><p>Published online 26 Mar 2007</p><p>PMCID:PMC1868932.</p><p></p> Cross-referencing of the tissue signatures shown in Figure 10 identified subsets of TIN RNAs that have correlated patterns of expression relative to the 3' protein-coding exon signature from the corresponding genomic loci: 38 pairs were identified in which the 3' exon of the protein-coding transcript (right panel) follows a similar expression pattern to that of the antisense TIN RNA (left panel); 16 pairs were identified in which the 3' exon of the protein-coding transcript (right panel) follows a pattern of tissue expression inverted in relation to that of the antisense TIN RNA (left panel); 64 pairs were identified in which the 3' exon of the protein-coding transcript (right panel) follows a similar expression pattern as that of the sense TIN RNA (left panel); 22 pairs were identified where the 3' exon of the protein-coding transcript (right panel) follows a pattern of tissue expression inverted in relation to that of the sense TIN RNA (left panel). For each line in each panel, expression intensities among the three tissues were normalized within each type of probe and colored as a function of the number of standard deviations from the mean value