La Charente

25 juin 18861886/06/25 (A15,N5592)-1886/06/25.Appartient à l’ensemble documentaire : PoitouCh

Additional file 2: of Genomic exaptation enables Lasius niger adaptation to urban environments

Phylogenetic tree of ants fatty acid desaturases. 1 - hymenoptera-specific desaturases, 2 D. melanogaster CG9747 orthologs, 3 — D. melanogaster CG9743 orthologs, 4 — D. melanogaster desat1 orthologs, 5 — D. melanogaster CG8630 orthologs, 6 — D. melanogaster CG15331 orthologs. (PDF 2930 kb

Additional file 1: Tables S1-13. of Genomic exaptation enables Lasius niger adaptation to urban environments

Samples, number of CYP, OR, OBP and desturases genes, results of selection detection, neuropeptides. (XLSX 47 kb

Additional file 1: Table S1. of Glucose transporter 4 promotes head and neck squamous cell carcinoma metastasis through the TRIM24-DDX58 axis

Demographic features of HNCC patient cohort. Table S2. GLUT overexpression activated transcription factors and their downstream targets ranked by Z-Score. Table S3. GLUT overexpression inhibited transcription factors and their downstream targets ranked by Z-Score. Table S4. List of TRIM24 downstream genes and their fold changes. Table S5. List of primers and knockdown clones’ information. Table S6. List of candidate probes >2.0-fold change cutoff by GLUT4 vs. control in FaDu cells. Figure S1. Box plot showing the expression of the GLUT family members correlated with the survival rate of the patients in the Petel HNSCC cohort (E-MTAB-1328, n = 89) in the SurvExpress database (HR = 3.37, P = 0.043). Figure S2. Forest plot of GLUT family members and their corresponding hazard ratios, probes and Cox-P values. Figure S3. GLUT4 overexpression model in vitro and in vivo. (A) Cell proliferation rate and (B) tumorigenicity ability in animal model GLUT4-overexpressing FaDu cells. Figure S4. Glucose uptake and lactate production in a panel of HNSCC cell lines. Figure S5. The migration abilities of with or without GLUT4 knockdown combined DDX58 or OASL knockdown in HSC-2 cells. Figure S6. Correlation plot of GLUT4 expression with the (A) OASL or (B) DDX58 RNA level in a clinical cohort (Pearson r = −0.7146, P < 0.001 and Pearson r = −0.6246, P < 0.001, respectively). (DOCX 2697 kb

A Versatile Method for Cell-Specific Profiling of Translated mRNAs in <em>Drosophila</em>

<div><p>In <em>Drosophila melanogaster</em> few methods exist to perform rapid cell-type or tissue-specific expression profiling. A translating ribosome affinity purification (TRAP) method to profile actively translated mRNAs has been developed for use in a number of multicellular organisms although it has only been implemented to examine limited sets of cell- or tissue-types in these organisms. We have adapted the TRAP method for use in the versatile <em>GAL4/UAS</em> system of <em>Drosophila</em> allowing profiling of almost any tissue/cell-type with a single genetic cross. We created transgenic strains expressing a GFP-tagged ribosomal protein, RpL10A, under the control of the <em>UAS</em> promoter to perform cell-type specific translatome profiling. The GFP::RpL10A fusion protein incorporates efficiently into ribosomes and polysomes. Polysome affinity purification strongly enriches mRNAs from expected genes in the targeted tissues with sufficient sensitivity to analyze expression in small cell populations. This method can be used to determine the unique translatome profiles in different cell-types under varied physiological, pharmacological and pathological conditions.</p> </div

Polysome incorporation of GFP tagged RpL10A.

<p>(A) Sucrose gradient polysome fractionation from heads of <i>Elav-GAL4>UAS-GFP::RpL10A</i> flies shows the different ribosomal and polysomal fractions. Protein extracts were run on Western blots and probed with GFP and RpS6 antibodies, showing that the GFP-tagged RpL10A displays qualitatively similar incorporation into the polysomes but not into the small 40S ribosomal unit. (B) Immunoprecipitation from lysted made from 50 adult heads of <i>Elav-GAL4>UAS-GFP::RpL10A</i> flies following polysome immunoprecipitation with PAS beads coated with GFP antibodies (IP) or mouse IgG antibodies as a mock control (m). Lysate from the input fraction without the immunoprecipitation step was also loaded on the gel. The GFP-tagged fusion protein is efficiently precipitated from the GFP coated beads but not from the mock coated beads. Actin is only present in the unprecipitated lysate and not in the IP fraction. (C) Western blot of lysates from heads of the <i>Elav-GAL4</i> (c155) strain and flies expressing GFP or GFP-tagged RpL10A (strain BF14; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040276#pone.0040276.s005" target="_blank">Table S1</a>) with the <i>Elav-GAL4</i> driver. All total lysates (16% input) show strong signal for the small ribosomal protein RpS6. After polysome affinity purification, only the immunoprecipitate from <i>Elav-GAL4>UAS-GFP::RpL10A</i> flies (strain BF14) show staining for RpS6, showing that whole ribosomes are precipitated.</p

Tissue specific expression levels of significantly enriched or depleted genes in the neuronal translatome compared to whole head mRNA.

<p>Comparison of the lists of genes that have transcripts that are significantly and substantially enriched (A; 872 genes) or depleted (B; 1,755 genes) in the polysome-enriched fraction (q<0.05, >2-fold enriched or depleted, respectively) to Flyatlas microarray expression data. For this analysis we generated two lists of genes: those that are either significantly enriched or depleted in the polysome pull-down fraction relative to mRNA derived from whole heads. The two lists were uploaded to Flymine <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040276#pone.0040276-Lyne1" target="_blank">[21]</a>, which generated the graphs presented that shows the number of genes from each list for which the levels of expression are significantly high or low, in several tissues of the fly, according to FlyAtlas <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040276#pone.0040276-Chintapalli1" target="_blank">[4]</a> microarray data analysis. The genes with transcripts enriched in the polysome-enriched fraction have a greater number of genes with high expression in neuronal tissues as compared to low expression (A; see adult brain, eye, larval CNS, thoracicoabdominal ganglion), and this is not seen in the polyosme-depleted fraction. In other tissues examined by Flyatlas, the polysome-enriched and -depleted fractions do not show this pattern of substantially more genes with high expression in that tissue.</p

Enrichment of <i>dIlp2</i> and depletion of <i>NPF</i> from the <i>PI</i> translatome.

<p>qRT-PCR from total RNA extracts from affinity purified polysome fractions from neurons in the <i>pars intercerebralis</i> (from <i>50Y>UAS-GFP::RpL10A</i> flies) compared to whole head extracts from control flies. (A) <i>dIlp2</i> is expressed in <i>PI</i> neurons and shows ∼55 fold higher expression in the immunoprecipitate from <i>PI</i> neurons (<i>PI-IP</i>) as compared to whole head extract (<i>Head</i>). (B) NPF is not expressed in <i>PI</i> neurons and shows the opposite pattern: ∼80 fold lower in <i>PI-IP</i> than in whole head extract. Data are means +/− S.E.M. averaged from three replicates from 2 biological repeats.</p

The average gain in number of days for each delivery method for cases where one record arrived before the other.

<p>The average gain in number of days for each delivery method for cases where one record arrived before the other.</p

Diplay of mobile phone with received laboratory results via SMS.

<p>Diplay of mobile phone with received laboratory results via SMS.</p