Monitoring of transcriptional regulation in under protein production conditions-1

<p><b>Copyright information:</b></p><p>Taken from "Monitoring of transcriptional regulation in under protein production conditions"</p><p>http://www.biomedcentral.com/1471-2164/8/179</p><p>BMC Genomics 2007;8():179-179.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1919374.</p><p></p>ndend up- or downregulatated genes are highlighted; B: Logratio of cultures producing 2F5 Fab under control of the GAP promoter compared to the wild type, in the same order as A. Red bars: change in transcript up > 2-fold; yellow bars: up > 1.5 fold; white bars: unchanged; blue bars: down > 1.5 fold

Monitoring of transcriptional regulation in under protein production conditions-4

<p><b>Copyright information:</b></p><p>Taken from "Monitoring of transcriptional regulation in under protein production conditions"</p><p>http://www.biomedcentral.com/1471-2164/8/179</p><p>BMC Genomics 2007;8():179-179.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1919374.</p><p></p>steady state; Blue bars: 20 °C steady state. BiP: intracellular signals for the UPR marker BiP/Kar2p (detected with anti-Grp78/BiP specific IgG). HC: intracellular signals for Fab heavy chain (obtained with anti-h-Fab specific IgG); LC: intracellular signals for light chain (analyzed with anti-kappa light chain IgG)

Monitoring of transcriptional regulation in under protein production conditions-0

<p><b>Copyright information:</b></p><p>Taken from "Monitoring of transcriptional regulation in under protein production conditions"</p><p>http://www.biomedcentral.com/1471-2164/8/179</p><p>BMC Genomics 2007;8():179-179.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1919374.</p><p></p>mparison to the wild type. Data from were taken from [21], where UPR was induced with DTT or tunicamycin. ScD60 (treatment with DTT after 60 min); ScD120 (treatment with DTT after 120 min); ScT60 (treatment with tunicamycin after 60 min), all compared to a non-treated culture. Cluster analysis was made using EPClust [], Euklidian distance with complete linkage. Subclusters are shown for the following: A: genes induced in both yeasts; B: upregulated in , down-regulated in ; C: down-regulated to unchanged in , upregulated in ; D: reduced in both yeasts. Subclusters of genes that are unchanged in both organisms are not displayed. The brightest colouring corresponds to the logregulation ≥ ± 2

Monitoring of transcriptional regulation in under protein production conditions-2

<p><b>Copyright information:</b></p><p>Taken from "Monitoring of transcriptional regulation in under protein production conditions"</p><p>http://www.biomedcentral.com/1471-2164/8/179</p><p>BMC Genomics 2007;8():179-179.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1919374.</p><p></p>ts control strain (containing only the Fab expression cassette). B: 2F5 Fab producing SMD1168 co-expressing compared to the control strain. Both diagrams are ordered from the lowest to the highest logratio. Colour legend as in figure 2

Metabolic Pathways Retained in wBm

<p>Pathways shared by <i>Wolbachia</i> and <i>Rickettsia</i> are shown with black arrows. Pathways present in <i>Wolbachia</i> but not in <i>Rickettsia</i> are shown with green arrows. Numbering alongside pathway arrows reflects enzyme annotation, a table of which is available at <a href="http://tools.neb.com/wolbachia/" target="_blank">http://tools.neb.com/wolbachia/</a>.</p

Absence of Gene Order Colinearity between <i>w</i>Bm and <i>Rickettsia</i> and Disruption of Gene Colinearity between <i>w</i>Bm and <i>w</i>Mel

<div><p>Each dot represents a pair of probable orthologs defined as reciprocal BLAST best hits with E-value less than 0.001.</p> <p>(A) Genome dot-plot comparison of <i>w</i>Bm <i>(Wolbachia</i> from <i>B. malayi)</i> and <i>Rpro (R. prowazekii).</i></p> <p>(B) Genome dot-plot comparison of <i>w</i>Bm <i>(Wolbachia</i> from <i>B. malayi)</i> and <i>Rcon (R. conorii).</i></p> <p>(C) Genome dot-plot comparison of <i>Rpro (R. prowazekii)</i> and <i>Rcon (R. conorii).</i></p> <p>(D) Genome dot-plot comparison of <i>w</i>Bm and <i>w</i>Mel.</p></div

Venn Diagram Showing Comparison of Conserved and Unique Genes and Pseudogenes in <i>w</i>Bm <i>(Wolbachia</i> from <i>B. malayi), Rickettsia prowazekii, Rickettsia conorii,</i> and in <i>w</i>Bm and <i>w</i>Mel (among Those Assigned to COGs)

<div><p>(A) Predicted functional protein-coding genes.</p> <p>(B) Pseudogenes.</p> <p>(C) Combined results for comparison between <i>wBm</i> and <i>w</i>Mel.</p> <p>G, intact gene; P, pseudogene.</p></div

Organization of Direct and Palindromic Repeats in <i>w</i>Bm

<p>Circles represent the complete genomic sequence of <i>w</i>Bm. Repeats were identified using the REPuter program [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030121#pbio-0030121-b182" target="_blank">182</a>] and are connected by line segments. Direct repeats are shown in the graphs in the top row, while palindromic repeats are shown in the lower row of graphs. The left column graphs display repeats of 50 to 500 bp in length. The rightmost graphs display repeats of greater than 500 bp in length.</p

Genogram of the Complete Circular Genome of <i>w</i>Bm

<p>The scale indicates coordinates in kilobase pairs (kbp) with the putative origin of replication positioned at 0 kbp. The outermost ring indicates the GC-skew over all bases in the forward strand using a window size of 40 kbp and a step size of 1 kbp. Positive and negative skew are shaded gold and blue, respectively. Features are shown as paired rings separated by a circular baseline. In each pair, the outer and inner rings represent the forward and reverse DNA strands, respectively. Working inward from the scale, the features displayed are as follows: identified genes and their broad functional classification (multihued, as listed); tRNA (blue)/rRNA (red) genes; putative pseudogenes (green); repeated sequences (red) and transposon-related repeats (blue).</p