Primers used to validate microarray results by Real-Time PCR.

<p>Primers used to validate microarray results by Real-Time PCR.</p

Number of up and down-regulated genes in rat CP in response to ovariectomy or orchidectomy.

<p>Number of up and down-regulated genes in rat CP in response to ovariectomy or orchidectomy.</p

Expression of <i>S. cerevisiae</i> tRNA^leu in <i>C. albicans.</i>

<p>A) Aminoacylation <i>in vivo</i> in <i>C. albicans</i> of <i>S. cerevisiae</i> tRNA_UAG/CAG^Leu and tRNA_AGA^Ser was monitored by Acidic Page and Northern Blot analysis. For this, total tRNAs were extracted under acidic conditions from pUA13, pUA14, pUA15, and pUA16 clones and fractionated on an acidic polyacrylamide gel, as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000996#s4" target="_blank">materials and methods</a>. These gels separated deacylated (-AA) from aminoacylated tRNAs (+AA), which were detected using a tDNA_Leu/Ser probe labeled with [³²P]. B) Transformation efficiencies of plasmids encoding tRNA^Leu, which decoded the <i>C. albicans</i> serine CUG codons as leucine, was significantly lower that that of control plasmids (pUA12 and pUA16), indicating that the leucine tRNAs were slightly toxic. C) However, clones that survived the transformation procedure adapted readily to CUG ambiguity and showed growth rates similar to control clones (pUA12).</p

OGD increases REST expression in mature hippocampal neurons.

<p>(<b>A</b>) Quantitative PCR analysis showed the OGD insult induced a marked increase in Nrse (Rest) mRNA. Total RNA was extracted with TriZol 7 h and 24 h after the OGD insult. Quantitative PCR analysis was performed using cDNA prepared from 1 µg of total RNA and specific primers for each selected gene. Fold change in mRNA levels was normalized to Gapdh and Actb. Bars represent the mean ± SEM of three independent experiments, performed in distinct preparations. *Significantly different from control (*<i>p</i><0.05, Student's <i>t</i>-test on log-transformed data). (<b>B</b>) Representative Western blot shows a marked increase in REST protein levels, both in the cytoplasmic and nuclear fractions of hippocampal neurons submitted to OGD followed by 24 h of incubation in culture conditioned medium (n = 3). Actin was used as loading control. (<b>C</b>) Putative RE-1 sequence(s)/REST-binding site(s) in synaptic genes (according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099958#pone.0099958-Otto1" target="_blank">[35]</a>) found to be down-regulated after OGD. (D) Genes with enrichment of REST after ischemia (according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099958#pone.0099958-Noh1" target="_blank">[33]</a>) found to be differently expressed after OGD.</p

Ambiguous CUG decoding induced karyotype rearrangements and ploidy-shift.

<p>A) In ambiguous cell lines (pUA15) polyploidy was predominant and very high ploidy was often detected (>32N). Aneuploidy was also observed (6N). B) However, after plating cells several consecutive times on fresh agar chromosome numbers were reduced indicating that most cells returned to low ploidy (2N or 4N). Ploidy reduction after mating normally occurs by chromosome loss in <i>C. albicans</i> and it is likely that such mechanism also played a role in ploidy reduction in pUA15 transformed cells. C) CUG ambiguity also promoted extensive rearrangements of the R-chromosome (highlighted in white circles). Chromosomes were separated by PFGE on 0.6% agarose gels under the following conditions: 120–300 s for 24h at 80 V, then 420–900 s for 48 h at 80 V. The numbers 1–7 and R identify <i>C. albicans</i> chromosomes.</p

Ischemic insults affect the protein levels of the AMPAR subunits GluA1 and GluA2.

<p>(<b>A</b>) Total protein extracts were prepared 7 h and 24 h after the OGD insult and Western blot analysis were performed. Total GluA1 is decreased after 24 h, whereas GluA2 levels remain unaltered following both periods of recovery. The left panel shows a representative Western blot for total GluA1 and GluA2 present in cell lysates after OGD. The right panel represents the quantification of the Western blots. Bars represent the mean ± SEM of five independent experiments, performed in ditinct preparations. (<b>B</b>) GluA1 and GluA2 surface levels were analyzed after biotinylation of cultured hippocampal neurons, 24 h after the OGD insult. At this time point after OGD GluA1 is removed from the surface, whereas GluA2 surface levels remain unaltered. The left panel shows a representative Western blot for surface GluA1 and GluA2 after the insult. Total actin (from the total extract) was used as loading control. Bars represent the mean ± SEM of 3–4 independent experiments, performed in distinct preparations. *<i>p</i><0.05, as determined by the Student's <i>t</i>-test.</p

KEGG pathways with significant association with genes differentially expressed in female and male rat choroid plexus.

<p>KEGG pathways with significant association with genes differentially expressed in female and male rat choroid plexus.</p

Comparison of microarray and Real-Time PCR fold-changes of 15 selected genes differentially expressed in choroid plexus of gonadectomized female and male rats.

<p>Comparison of microarray and Real-Time PCR fold-changes of 15 selected genes differentially expressed in choroid plexus of gonadectomized female and male rats.</p

Time course analysis of OGD-induced differential gene expression within each functional gene category.

<p>The number of genes that were up-regulated (black bars) or down-regulated (white bars) at each period of recovery after the OGD insult is plotted for each functional gene category. Gene ontology analyses were performed using GoMiner and functional groups were selected manually.</p

Consensus tree of 16 <i>Saccharomyces cerevisiae</i> populations (285 strains) from the Vinho Verde and Bairrada wine regions, shown as a neighbor-joining tree of allelic frequencies.

<p>Numbers on nodes are percentages of bootstrap values out of 1000. Populations from the same grape variety (8_D/9_D; 11_E/12_E; 2_A/3_A) are indicated by full circles, whereas groups of strains from the same vineyard (1_I/1_C/1_G; 11_I/11_E) and from grape variety I (10_I/11_I/13_I, collected in vineyards from both winemaking regions), are indicated by dotted and dashed circles, respectively.</p