Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-0

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p>f total RNA from strain 1021 was analyzed by Northern blotting hybridization with specific oligonucleotides [see Additional file ]; the molecular sizes were calculated in nucleotides (nt): > rnpB (372 nt), > tmRNA 3' end (204 nt), > 5S (120 nt), > 4.5S (95 nt), and > tmRNA 5' end (82 nt) [39]. Band > was not hybridized but its size is consistent with it being a tRNA. Exposure times were optimized for each panel and signal intensity does not indicate relative abundance of ncRNAs

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-2

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p> indicated as signal-to-noise SNR values (log2 scale), represented by a red panel. The position of each gene in the heat map is determined by its intensity. For the complementary Northern dot analysis, 10 μg of RNA, isolated from the most favourable expression condition, was spotted (in duplicate) onto a nylon membrane and hybridized with a radiolabelled specific probe [see Additional file ]

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-5

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p>f total RNA from strain 1021 was analyzed by Northern blotting hybridization with specific oligonucleotides [see Additional file ]; the molecular sizes were calculated in nucleotides (nt): > rnpB (372 nt), > tmRNA 3' end (204 nt), > 5S (120 nt), > 4.5S (95 nt), and > tmRNA 5' end (82 nt) [39]. Band > was not hybridized but its size is consistent with it being a tRNA. Exposure times were optimized for each panel and signal intensity does not indicate relative abundance of ncRNAs

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-3

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p>ted DNA oligonucleotide probes [see Additional file ] and exposed for various times (therefore the intensities of the signals do not correspond to the relative abundance of each sRNA). The positions of RNA size standards are shown on the left. B. Distribution of the genes along the chromosome. The origin of replication (= sra01) and positions of , and are also indicated. Blue and red arrows represent genes on the reverse or forward strands, respectively. Genomic islands are indicated with grey boxes (Sme21T, Sme19T and Sme80S)

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-4

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p> of 1000 replicates. B. In northern blots, a signal for the predicted was detected corresponding to lengths of 144 and 106 nucleotides in total RNA from 1021 and to 140 and 132 nt in that from and , respectively

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-1

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p>e minimal, maximal and mean values of the percentage of GC

Analyzing stochastic transcription to elucidate the nucleoid's organization-0

curve) when the plasmid is actively transcribed (and translated; data set A). The red curve shows the autocorrelation function when the genes' positions were randomly assigned. The Y-axis has been cropped at an autocorrelation of 0.15 for a clearer visual interpretation; the blue curve starts at an autocorrelation of 0.27 for a gene distance of one. Maxima (positive correlation) and minima (negative or anti-correlation) can be clearly distinguished, with a strong anti-correlation for genes that lie opposite of each other on the chromosome (a gene distance of around 650). Similarly, Figures 1b and 1c show the results for the chromosome and the megaplasmid pSymB, respectively, when both are actively transcribed (and translated; data set A). As can be seen, the autocorrelation functions for the three replicons are similar. Note: The figures are all at the same scale to better illustrate the different sizes of the three replicons. All Y-axes have been cropped at a value of 0.15 for (visual) clarity's sake.<p><b>Copyright information:</b></p><p>Taken from "Analyzing stochastic transcription to elucidate the nucleoid's organization"</p><p>http://www.biomedcentral.com/1471-2164/9/125</p><p>BMC Genomics 2008;9():125-125.</p><p>Published online 10 Mar 2008</p><p>PMCID:PMC2270832.</p><p></p

Analyzing stochastic transcription to elucidate the nucleoid's organization-2

curve) when the plasmid is actively transcribed (and translated; data set A). The red curve shows the autocorrelation function when the genes' positions were randomly assigned. The Y-axis has been cropped at an autocorrelation of 0.15 for a clearer visual interpretation; the blue curve starts at an autocorrelation of 0.27 for a gene distance of one. Maxima (positive correlation) and minima (negative or anti-correlation) can be clearly distinguished, with a strong anti-correlation for genes that lie opposite of each other on the chromosome (a gene distance of around 650). Similarly, Figures 1b and 1c show the results for the chromosome and the megaplasmid pSymB, respectively, when both are actively transcribed (and translated; data set A). As can be seen, the autocorrelation functions for the three replicons are similar. Note: The figures are all at the same scale to better illustrate the different sizes of the three replicons. All Y-axes have been cropped at a value of 0.15 for (visual) clarity's sake.<p><b>Copyright information:</b></p><p>Taken from "Analyzing stochastic transcription to elucidate the nucleoid's organization"</p><p>http://www.biomedcentral.com/1471-2164/9/125</p><p>BMC Genomics 2008;9():125-125.</p><p>Published online 10 Mar 2008</p><p>PMCID:PMC2270832.</p><p></p

Analyzing stochastic transcription to elucidate the nucleoid's organization-1

curve) when only stochastic transcription takes place (data set B). The red curve shows the autocorrelation function when the genes' positions were randomly assigned. The Y-axis has been cropped at an autocorrelation of 0.15 for a clearer visual interpretation; the blue curve starts at an autocorrelation of 0.15 for a gene distance of one. The signal becomes quickly confounded with the noise (red curve). There are minima and maxima that stand out, but only a spectral analysis can tell, whether these are significant or not. Again to serve as comparison, Figures 2b and 2c show the autocorrelation functions for the chromosome and the megaplasmid psymB, respectively, for data set B. Both replicons are actively transcribed and translated, unlike psymA, and their autocorrelation functions are comparable to those in data set A (as confirmed by the spectral and statistical analyses, see additional file ). Note: The figures are all at the same scale to better illustrate the different sizes of the three replicons. All Y-axes have been cropped at a value of 0.15 for (visual) clarity's sake.<p><b>Copyright information:</b></p><p>Taken from "Analyzing stochastic transcription to elucidate the nucleoid's organization"</p><p>http://www.biomedcentral.com/1471-2164/9/125</p><p>BMC Genomics 2008;9():125-125.</p><p>Published online 10 Mar 2008</p><p>PMCID:PMC2270832.</p><p></p