10 research outputs found

    Genes downregulated in melioidosis and tuberculosis, arranged by pathway.

    No full text
    <p>IFN = interferon, IGF = insulin-like growth factor, IL = interleukin, NF-κB = nuclear factor kappa-light-chain-enhancer of activated B cells, PI3K = phosphoinositide 3-kinase, RNA = ribonucleic acid, TGF = transforming growth factor, TNF = tumour necrosis factor.</p><p>Note:– Genes names are those assigned by the HUGO gene nomenclature committee.</p

    Network representation of genes differentially expressed in melioidosis.

    No full text
    <p>‘Canonical’ pathways (such as those presented in a standard biochemistry textbook) are manually curated collections of protein interactions arranged in a manner that aids human understanding, and as artificial constructs the boundaries between pathways are subjective. Pathways that are conceptually distinct often have proteins in common and overlap, so in modular analysis, multiple pathways may collapse into a single module, causing other pathways and relationships to gain prominence. These two networks (<b>A</b> and <b>B</b>) represent those genes that are differentially expressed in melioidosis. For simplicity of presentation, we have used only a subset of genes in these networks. The top 221 upregulated genes (as ranked by <i>p</i>-value) are presented in <b>A</b>, and the top 155 downregulated genes are in <b>B</b>. The same clusters were found in an analysis of the whole gene set and those results are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054961#pone-0054961-t002" target="_blank">Tables 2</a> & <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054961#pone-0054961-t003" target="_blank">3</a>. <b>Network </b><b>A</b>. IFN-γ, TNF-α, IL-12 signalling pathways cluster together with the glypican network in the centre of the graph, but the complement/chemokine receptor (<b>cluster 1</b>), inflammasome (<b>cluster 2</b>) and Toll-like receptor pathways come to prominence in this analysis (<b>cluster 3</b>). <b>Network B</b>. IFN-γ, TGF-β and TNF signalling again cluster in the middle of the network. The two most prominent clusters are ribosomal proteins (<b>cluster 1</b>) and zinc finger proteins (<b>cluster 2</b>).</p

    Interferon signatures for melioidosis and tuberculosis.

    No full text
    <p>Note: The interferon signatures for melioidosis (<b>A</b>) and tuberculosis (<b>B</b>) are listed here (analysis from <a href="http://www.interferome.org" target="_blank">www.interferome.org</a>). Berry <i>et al.</i> noted that both type 1 and type 2 interferon responses were prominent in tuberculosis. We find that type 1 interferon responses appear in melioidosis also.</p

    The 86-gene signature of tuberculosis is also seen in melioidosis.

    No full text
    <p>These heat maps demonstrate the gene expression profiles for two cohorts: (A) melioidosis and (B) tuberculosis. The 86 genes displayed are those identified by Berry <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054961#pone.0054961-Berry1" target="_blank">[7]</a> as being specific for tuberculosis, after excluding genes differentially regulated in other infections (<i>Staphylococcus aureus</i> and Group A Streptococcus) and inflammatory conditions (adult onset Still’s disease and systemic lupus erythematosus). Each column in the heat map is the gene expression profile of an individual, with control subjects on the left and patients on the right. Each cell within the heat map is the expression of a single gene: orange genes are upregulated and purple genes are downregulated, with expression normalized across the rows. We used this 86-gene signature to cluster study participants into two groups (marked black and red in the coloured banner at the top of each heat map). In the tuberculosis cohort, three controls clustered with the patients, and two patients clustered with the controls. In the melioidosis cohort, the same 86-gene signature also allowed us to distinguish controls and patients, with the exception of four patients who clustered with the controls. Despite the same microarray platform being used, the two cohorts were assayed as separate batches, so the absolute fluorescence intensities are different, making a direct comparison of melioidosis and tuberculosis impossible. All patients were therefore compared to their own controls.</p

    Patient characteristics.

    No full text
    a<p>One patient in this group was lost to follow-up following discharge from hospital, and was counted as having survived to discharge.</p><p>Gb = Glibenclamide. Values reported are means, except where stated.</p

    qRT-PCR analyses of differentially expressed genes of the S.

    No full text
    <div><p><b>Typhi Δ<i>yehUT</i> mutant</b>. </p> <p>A The relative expression levels of the 15 genes found to be differentially expressed on microarray analysis of the S. Typhi Δ<i>yehUT</i> mutant when compared to <i>S</i>. Typhi in low salt LB, at mid-log phase, at 37°C (Table S6 in File S1). The 15 genes examined are listed on the <i>y</i>-axis. Grey boxes < 1.0 indicates down regulated genes and grey boxes >1.0 indicates up regulated genes relative to <i>S</i>. Typhi. B qRT-PCR analysis showing relative expression levels of genes after complementation of the Δ<i>yehUT</i> mutant compared to <i>S</i>. Typhi (Table S6 in File S1).</p></div

    A The <i>yehUT</i> operon with surrounding genes.

    No full text
    <p>The operon is 2349bp in length and located between 782210 to 784611 bp in <i>S</i>. Typhi Ty2 (Accession number AE014613) and between c2251460 to c253861 bp in <i>S</i>. Typhimurium SL1344 (Accession number FQ312003). The surrounding genes include <i>yehV</i>, <i>t0694</i>, <i>yehW</i>, <i>yehX</i> (upstream of <i>yehU</i>) and <i>yehS, t0699</i> and <i>yehR</i> (downstream from <i>yehT</i>). <b>B The domain organisation of the YehU and YehT proteins</b>. YehU protein comprises of five transmembrane (TM) alpha helical segments predicted using TMHMM webserver [17]. The intracellular signalling component consists of a GAF domain, a DHp (dimerization/histidine-containing phosphotransfer) domain that is connected to an ATP (adenosine triphosphate)-dependent Kinase domain. YehT protein consists of a Receiver domain and a LyTR-homologous DNA binding domain [16]. The phosphorylation sites are indicated (H, Histidine; D, Aspartate). The SNP positions identified in <i>yehU</i> and <i>yehT</i> genes are indicated below the proteins by grey boxes [10]. </p

    SDS-PAGE and western blot analysis of epitope-tagged YehT protein from <i>S</i>.

    No full text
    <div><p><b>Typhi BRD948</b>. </p> <p>Proteins from whole cell bacterial lysates were transferred after electrophoretic separation in a 12% SDS-PAGE gel (Invitrogen) onto a nitrocelluose membrane (Invitrogen) and probed with anti-FLAG M2 monoclonal antibodies (Sigma). Lanes: (M) protein molecular weight markers (SeeBlue Plus2 Pre-stained standard; Invitrogen); (-) proteins extracted from <i>S</i>. Typhi BRD948 (negative control); (+) proteins extracted from <i>S</i>. Typhimurium SL1344 Δ<i>fliA</i> (positive control, 27.4kDa); FLAG proteins extracted from <i>S</i>. Typhi Δ<i>yehT</i>-tagged (27.4kDa). Bacteria was grown in low salt LB; normal salt LB; SPI-2 inducing; SPI-2 + 0.5% glucose; SPI-2 + 0.25% acetate overnight, shaking at 37°C.</p></div

    SDS-PAGE and western blot analysis of epitope-tagged YehT protein from <i>S</i>.

    No full text
    <div><p><b>Typhimurium ST4/74</b>. </p> <p>Proteins from whole cell bacterial lysates were transferred after electrophoretic separation in a 12% SDS-PAGE gel (Invitrogen) onto a nitrocelluose membrane (Invitrogen) and probed with anti-FLAG M2 monoclonal antibodies (Sigma). Lanes: (M) protein molecular weight markers (SeeBlue Plus2 Pre-stained standard; Invitrogen); (-) proteins extracted from <i>S</i>. Typhimurium ST4/74 (negative control); (+) proteins extracted from <i>S</i>. Typhimurium SL1344 Δ<i>fliA</i> (positive control; 27.4kDa); FLAG proteins extracted from <i>S</i>. Typhimurium Δ<i>yehT</i>-tagged (27.4kDa). Bacteria was grown in low salt LB; normal salt LB; SPI-2 inducing; SPI-2 + 0.5% glucose; SPI-2 + 0.25% acetate overnight, shaking at 37°C.</p></div
    corecore