Secondary structure evolution, as a function of time, for the LOX-1 region (140–165) including strands 0 (red bar with middle point around 150) and 1 (red bar with middle point around 156)

<p><b>Copyright information:</b></p><p>Taken from "Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant"</p><p>http://www.biomedcentral.com/1472-6807/7/73</p><p>BMC Structural Biology 2007;7():73-73.</p><p>Published online 7 Nov 2007</p><p>PMCID:PMC2194713.</p><p></p> Colour code identifying the secondary structure is shown in the figure

Dynamic cross-correlation maps calculated for the wild-type and the mutant LOX-1 proteins

<p><b>Copyright information:</b></p><p>Taken from "Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant"</p><p>http://www.biomedcentral.com/1472-6807/7/73</p><p>BMC Structural Biology 2007;7():73-73.</p><p>Published online 7 Nov 2007</p><p>PMCID:PMC2194713.</p><p></p> Panels A and C reports the intra-subunit motion correlations in the wild-type, while panels B and D the intra-subunit motion correlations in the mutant. The black and grey squares represent the Cmotion correlations wit

Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells-1

<p><b>Copyright information:</b></p><p>Taken from "Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells"</p><p>http://www.molecular-cancer.com/content/6/1/38</p><p>Molecular Cancer 2007;6():38-38.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904238.</p><p></p>presence of Dox (, + Dox) the tetracycline Tet repressor (tetR) is released from the TetO2 sequence in the promoter of the lentiviral construct containing the gene. The dissociation of the tetR allows induction of transcription for the gene of interest. LNCaP-DDC and LNCaP-pDEST (vector control) cell lines were plated in medium containing 5% charcoal-stripped serum and incubated overnight. The next day, cells were treated for 48 hours under mock-induced (-Dox) and Dox-induced (+Dox) conditions, 24 h of which was in the presence or absence of 0.1 nM R1881. Total RNA samples were isolated from each condition, labeled and hybridized on the microarrays. The relative mRNA abundance of each gene was calculated as a ratio between hormone-treated (+R1881) and hormone-untreated (- R1881) samples. The comparison of the expression data obtained from LNCaP-DDC+Dox stable cells () with the expression data from the three LNCaP control cells (: LNCaP-DDC-Dox, LNCaP-pDEST- Dox, and LNCaP-pDEST+Dox) yielded the identification of genes that are androgen- and DDC-regulated

Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells-0

<p><b>Copyright information:</b></p><p>Taken from "Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells"</p><p>http://www.molecular-cancer.com/content/6/1/38</p><p>Molecular Cancer 2007;6():38-38.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904238.</p><p></p> In LNCaP-DDC and LNCaP-pDEST (vector control) cells were treated for 48 hours under mock-induced (-Dox) and Dox-induced (+Dox) conditions before protein lysate preparation. No visible expression was detected in the LNCaP-pDEST control cells regardless of Dox treatment status (lines 3–4). A 6 fold increased DDC expression level was detected in the Dox-induced LNCaP-DDC cells compared to the mock-induced cells (lines 1–2), after β-actin normalization. In total cellular RNA was isolated from LNCaP-DDC and LNCaP-pDEST cells after 48 hours of Dox treatment. After reverse transcription, PCR was performed with DDC and β-actin specific primers. The up-regulation of the 209-bp DDC-specific band was detected in LNCaP-DDC cells (line 2). A 100 bp DNA ladder (Promega) was used for size markers

Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells-2

<p><b>Copyright information:</b></p><p>Taken from "Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells"</p><p>http://www.molecular-cancer.com/content/6/1/38</p><p>Molecular Cancer 2007;6():38-38.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904238.</p><p></p>lized average signal intensity under the DDC overexpression conditions are shown on the x and y axes (controls = no DDC overexpression and DDC = DDC overexpression). The middle line indicates values that represent a DDC/controls ratio of 1.0 (similar levels of expression in both cell lines). The outer lines represent a DDC/controls ratio of 2.0 (upper line; 2-fold greater expression in DDC compared to controls) and of 0.5 (lower line; 2-fold greater expression in controls compared to DDC)

A Venn diagram analysis showing in yellow, the genes (130) with two fold induction in response to R1881 treatment in DDC overexpressing and control cells

<p><b>Copyright information:</b></p><p>Taken from "Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells"</p><p>http://www.molecular-cancer.com/content/6/1/38</p><p>Molecular Cancer 2007;6():38-38.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904238.</p><p></p> The genes up- and down-regulated only in DDC overexpressing cells are represented in red (DDC; ) and the genes up- and down-regulated only in the control cells are represented in the green (controls; ). Reported here are 35 androgen-regulated genes differentially expressed at least 2-fold in DDC overexpressing cells (LNCaP-DDC) compared with the controls cells (LNCaP-CTRLs). The colors represent the ratio of gene expression levels in each cell line after R1881 treatment (red = hormone up-regulated and green = hormone down-regulated)

eGFP expression increased after 5-Aza-2′-Deoxycytidine treatment.

<p>A) Bright field (upper row) and fluorescent (bottom row) images of D1 sorted corrected cells at different experimental time (scale bar: 150 µm). B) eGFP expression, analyzed by Real Time PCR, after 24 h and 48 h of treatment with 0.5 µM 5-Aza-2′-Deoxycytidine respect to untreated (0 h) (*p = 0.002); untreated cells, at 24 h and 48 h, usually showed a decreasing relative eGFP expression (data not shown).</p

Southern blot analysis.

<p>A) Probe design. A 566 bp probe was used, recognizing a region of eGFP gene. Dashed box correspond to pCEP4-eGFP locus integrated within genomic DNA. <i>BtsI</i> site recovery highlight the correction of the eGFP gene. After <i>SalI/BtsI</i> genomic DNA digestion, two different restriction pattern can be obtained, according to the presence/absence of <i>BtsI</i> restriction site. B) Southern blot. A 1111 bp band was obtained only in cells in which <i>BtsI</i> site is present (D1 sorted positive and C1 clone).</p

<i>HpaII</i> and <i>AciI</i> methylation analyses of integrated eGFP in C1 and D1 clones.

<p>A) Experimental design showing the amplicon regions and their length within eGFP locus integrated in genomic DNA. <i>HpaII</i> and <i>AciI</i> site are indicated. B) Densitometric analyses of parental C1 clone methylation pattern on eGFP⁺ more positive, eGFP⁺ less positive and eGFP⁻ cells (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030851#pone.0030851.s009" target="_blank">Fig. S9B</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030851#pone.0030851.s010" target="_blank">Fig. S10B</a>). ANOVA test gave a statistical significance of p<0.001 and p<0.005 respectively for <i>HpaII</i> and <i>AciI</i> panels. C) Densitometric analysis of methylation pattern of D1 SFHR-modified clone on both fluorescent and non fluorescent cells (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030851#pone.0030851.s009" target="_blank">Fig. S9C and S10</a>C). ANOVA test gave a statistical significance of p<0.001 for both panels.</p

Molecular analyses of sorted D1 cells.

<p>A) Modification efficiency in D1 cells transfected with 12×10⁶ SDF-PCR-WT/cell. Positive cells (0.5%) were sorted and soon after reanalyzed (right panel) to asses population purity (>99%). B) PCR/RFLP analysis design. C) Amplicon is generated using RFLP primer pair. Cells transfected with mutated SDF represent our control (D1 CTR, lane 2). All amplification products were digested with <i>BtsI</i>, except lane 4. Restriction patterns of Sorted positive D1 clone (lane 1) and of parental eGFP C1 cells (lane 5) were identical. No restriction bands were present in D1 CTR (lane 2) and in sorted negative cells (lane 3). M is ladder 50 bp. D) Sequence analysis of D1 cells (sorted positive, sorted negative and CTR). The site-specific T-to-C conversion was present only in sorted positive cells.</p