Optimization of cDNA microarrays procedures using criteria that do not rely on external standards-4

<p><b>Copyright information:</b></p><p>Taken from "Optimization of cDNA microarrays procedures using criteria that do not rely on external standards"</p><p>http://www.biomedcentral.com/1471-2164/8/377</p><p>BMC Genomics 2007;8():377-377.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2147032.</p><p></p> lines NRK52E and AR42J) compared to self-self hybridization (rat cell line AR42J). The samples were hybridized to rat 15 k cDNA duplicates under six different blocking conditions including no blocker, 1000 ng poly(dA), and 25 to 1000 ng LNA dT blocker. Dye-swap and self self were performed for all blocking conditions (total of 24 hybridizations). Green-labelled samples are placed at the tail and red labelled samples at the head of the arrows

Optimization of cDNA microarrays procedures using criteria that do not rely on external standards-1

<p><b>Copyright information:</b></p><p>Taken from "Optimization of cDNA microarrays procedures using criteria that do not rely on external standards"</p><p>http://www.biomedcentral.com/1471-2164/8/377</p><p>BMC Genomics 2007;8():377-377.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2147032.</p><p></p

Optimization of cDNA microarrays procedures using criteria that do not rely on external standards-5

<p><b>Copyright information:</b></p><p>Taken from "Optimization of cDNA microarrays procedures using criteria that do not rely on external standards"</p><p>http://www.biomedcentral.com/1471-2164/8/377</p><p>BMC Genomics 2007;8():377-377.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2147032.</p><p></p

RBF1 and dCAP-D3 are necessary for the ability to clear bacteria <i>in vivo</i>.

<p>Adult female flies expressing RBF1 (purple) or dCAP-D3 (red) dsRNAs under the control of <i>yolk-GAL4</i> were infected with the Gram positive bacterium, <i>Staphylococcus aureus</i>. Flies expressing GFP dsRNAs under the control of <i>yolk-GAL4</i> (green) were used as “wild-type” controls. Eater mutants which are defective in phagocytosis (blue) or flies expressing IMD dsRNAs which are compromised in a major innate immune signaling pathway (yellow) were used as positive controls. Results demonstrate that at 15 hours following infection, flies expressing reduced levels of dCAP-D3 or RBF1 in the fat body cells exhibit increased numbers of bacteria in comparison to wild type controls. Three independent experiments are shown and results for each experiment are the average of three sets of three infected adults, per genotype, per timepoint. Asterisks emphasize statistical significance (p≤0.05) as determined by a students paired t-test.</p

Differentially overexpressed genes in tumour (red boxes) depicted in the Cell Cycle map from KEGG PATHWAYS (Kanehisa <i>et al</i>., 2008) (<i>P</i><0.05).

<p>21 of 21 cell cycle genes were overexpressed in mesothelioma versus normal parietal pleura tissue. Potential targets for anti-tumour treatment described in the litterature are marked (see text). Abbreviations: CDK7 = cyclin-dependent kinase 7, CHEK1 = checkpoint homolog, E2F2 = E2F transcription factor 2, ORC6L = origin recognition complex, subunit 6 like, MCM2-3-4-6 = minichromosome maintenance complex component 2-3-4-6, PCNA = proliferating cell nuclear antigen, RB1 = retinoblastoma, BUB1 = budding uninhibited by benzimidazoles 1 homolog, BUB1B = BUB1 beta, CDC7 = cell division cycle 7 homolog, APC/C = CDC23, cell division cycle 23 homolog, anaphase-promoting complex subunit 8, CCNB1 = cyclin B1, CCNB2 = cyclin B2, ESPL1 = extra spindle pole bodies homolog 1, CDC2/CDK1 = cell division cycle 2, G1 to S and G2 to M, CDC6 = cell division cycle 6 homolog, CDC20 = cell division cycle 20 homolog, CDC25A = cell division cycle 25 homolog A.</p

Top 10 overexpressed and down-regulated pathways in post- versus pre-resistance tumour in KEGG pathways map.

<p>Several interesting and important systems were deregulated after resistance. Note that overexpressed genes in GO metabolic process was 89 and in KEGG only 18. The reason is that KEGG includes new genes in a pathway only when several publications have confirmed it, and thus is more conservative but with a high level of evidence. Most pronounced were the metabolism and modification of DNA and RNA through pyrimidine and purine metabolism and aminoacyl-t-RNA biosynthesis. Interestingly, down-regulation of cell adhesion molecules and leukocyte transendothelial migration as well as cytokine-cytokine receptor interaction was pronounced, also an expression characteristic of mesothelioma versus normal pleura.</p

Thoracic computer tomography (CT) throughout the disease course.

<p>A large mediastinal tumour as well as thoracic wall infiltration was seen on the left side (CT at the same level). For details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040521#s2" target="_blank">Methods</a>.</p

RBF1 is necessary for a proper immune response to Gram positive bacterial infection.

<p>Adult female flies expressing RBF1 (purple) dsRNAs under the control of <i>yolk-GAL4</i> were infected with the Gram positive bacterium, <i>Staphylococcus aureus</i> (A) or the Gram negative bacterium, <i>Pseudomonas aeruginosa</i> (B). Flies expressing GFP dsRNAs under the control of <i>yolk-GAL4</i> (green) were used as “wild-type” controls. Eater mutants which are defective in phagocytosis (blue) or flies expressing IMD dsRNAs which are compromised in a major innate immune signaling pathway (yellow) were used as positive controls. Results demonstrate that flies expressing reduced levels of RBF1 in the fat body cells are more susceptible to infection with Gram positive bacteria (A) than wild type controls. Three independent experiments are depicted with results of each experiment shown as the average of three sets of 10 infected adults per genotype. Results are presented as cox regression models with statistical significance (p≤0.05) represented as shaded areas above and below the curves. In the third experiment in (A), which is highlighted by a star, the survival endpoint becomes significant when the confidence level is changed to 90% (p≤0.10) instead of 95% (p≤0.05). These experiments were also performed using a sterile needle dipped in PBS to rule out death as a result of wounding and survival curves matched those of yolk-GAL4 expressing flies (data not shown).</p

Serum biomarker changes over time.

<p>Ca125 and Mesothelin (SMRP) biomarkers in serum were elevated at diagnosis and decreased and increased according to the clinical and radiological regression and progression respectively. The straight horizontal dashed lines depict the maximum normal values of the two markers. CYFRA 21-1 is not shown.</p

Genes changed more than 2-fold after resistance.

<p>Expression of genes that changed more then 2-fold in the post-resistance tumour, compared to initial tumour. Down-regulated genes are shown to the left (30 in total, two not shown) and the overexpressed to the right (15, three not shown). Green bars represent the relative gene expression before and red bars after acquired resistance.</p