Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates.

BACKGROUND: Burkholderia thailandensis is a non-pathogenic environmental saprophyte closely related to Burkholderia pseudomallei, the causative agent of the often fatal animal and human disease melioidosis. To study B. thailandensis genomic variation, we profiled 50 isolates using a pan-genome microarray comprising genomic elements from 28 Burkholderia strains and species. RESULTS: Of 39 genomic regions variably present across the B. thailandensis strains, 13 regions corresponded to known genomic islands, while 26 regions were novel. Variant B. thailandensis isolates exhibited isolated acquisition of a capsular polysaccharide biosynthesis gene cluster (B. pseudomallei-like capsular polysaccharide) closely resembling a similar cluster in B. pseudomallei that is essential for virulence in mammals; presence of this cluster was confirmed by whole genome sequencing of a representative variant strain (B. thailandensis E555). Both whole-genome microarray and multi-locus sequence typing analysis revealed that the variant strains formed part of a phylogenetic subgroup distinct from the ancestral B. thailandensis population and were associated with atypical isolation sources when compared to the majority of previously described B. thailandensis strains. In functional assays, B. thailandensis E555 exhibited several B. pseudomallei-like phenotypes, including colony wrinkling, resistance to human complement binding, and intracellular macrophage survival. However, in murine infection assays, B. thailandensis E555 did not exhibit enhanced virulence relative to other B. thailandensis strains, suggesting that additional factors are required to successfully colonize and infect mammals. CONCLUSIONS: The discovery of such novel variant strains demonstrates how unbiased genomic surveys of non-pathogenic isolates can reveal insights into the development and emergence of new pathogenic species.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Spatiotemporal Genomic Profiling of Intestinal Metaplasia Reveals Clonal Dynamics of Gastric Cancer Progression

Intestinal metaplasia (IM) is a pre-malignant condition of the gastric mucosa associated with increased gastric cancer (GC) risk. Analyzing 1,256 gastric samples (1,152 IMs) across 692 subjects from a prospective 10-year study, we identify 26 IM driver genes in diverse pathways including chromatin regulation (ARID1A) and intestinal homeostasis (SOX9). Single-cell and spatial profiles highlight changes in tissue ecology and IM lineage heterogeneity, including an intestinal stem-cell dominant cellular compartment linked to early malignancy. Expanded transcriptome profiling reveals expression-based molecular subtypes of IM associated with incomplete histology, antral/intestinal cell types, ARID1A mutations, inflammation, and microbial communities normally associated with the healthy oral tract. We demonstrate that combined clinical-genomic models outperform clinical-only models in predicting IMs likely to transform to GC. By highlighting strategies for accurately identifying IM patients at high GC risk and a role for microbial dysbiosis in IM progression, our results raise opportunities for GC precision prevention and interception

DISSECTING THE HETEROGENEITY OF GASTRIC CANCER AT THE SINGLE CELL LEVEL

Ph.DDOCTOR OF PHILOSOPHY (SOM

Increase in local protein concentration by field-inversion gel electrophoresis-2

<p><b>Copyright information:</b></p><p>Taken from "Increase in local protein concentration by field-inversion gel electrophoresis"</p><p>http://www.proteomesci.com/content/5/1/18</p><p>Proteome Science 2007;5():18-18.</p><p>Published online 26 Sep 2007</p><p>PMCID:PMC2211458.</p><p></p>ditions. Each gel represents 100 μg of rat liver lysate separated by isoelectric focusing (IEF) using a non-linear pH 3–10 IPG strip in the first dimension and a Criterion precast SDS-10–20% PAG in the second dimension at room temperature. Control denotes CFE and pulsed denotes FIGE with a a/r of 400/106 msec in the second-dimension separation. Gels were stained with Coomassie blue. Spots selected for LC-MS/MS analysis are denoted by numbers, and A denotes the internal calibrator (see also Table 3). The internal calibrator is the internal controls for equivalent sample loading in both control and pulsed conditions

Increase in local protein concentration by field-inversion gel electrophoresis-4

<p><b>Copyright information:</b></p><p>Taken from "Increase in local protein concentration by field-inversion gel electrophoresis"</p><p>http://www.proteomesci.com/content/5/1/18</p><p>Proteome Science 2007;5():18-18.</p><p>Published online 26 Sep 2007</p><p>PMCID:PMC2211458.</p><p></p>resting within glass plates in room temperature for 12 hours (a III). Lanes 1 to 6 are 2 μL, 4 μL, 6 μL, 8 μL, 10 μL, and 12 μL of Mark12 protein standards, respectively, in a self-cast Bio-Rad 14% SDS-PAGE 1 mm × 7 cm gel followed by Coomassie blue staining. a I) Gel was run with a pulsed-field at (4 sec/3.4 sec) at 200 V for 13 hours, with an average buffer temperature of 30°C. A II) Gel was run at a constant field of 200 V for one hour and an average buffer temperature of 25°C. a III) Gel was run at a constant field of 200 V for one hour and left at rest for another 12 hours within the glass plates to permit diffusion prior to staining. b) Densitometry analysis of protein bands in the gels of the three conditions tested. Molecular mass was represented by alphabet A to K, where A = 200 kDa, B = 116.3 kDa, C = 97.4 kDa, D = 66.3 kDa, E = 55.4 kDa, F = 36.3 kDa, G = 31.0 kDa, H = 21.5 kDa, I = 14.4 kDa, J = 6.0 kDa, and K = unresolved 3.5/2.0 kDa bands, respectively. Migration distance relative to the dye front (R) and intensity of bands from lane 6 of all three gels was densitometrically analyzed using Quantity One software. The graph results were the average of two independent experiments. The graph results were subsequently employed in the calculation of peak variance, σ, in Table 1

Increase in local protein concentration by field-inversion gel electrophoresis-1

<p><b>Copyright information:</b></p><p>Taken from "Increase in local protein concentration by field-inversion gel electrophoresis"</p><p>http://www.proteomesci.com/content/5/1/18</p><p>Proteome Science 2007;5():18-18.</p><p>Published online 26 Sep 2007</p><p>PMCID:PMC2211458.</p><p></p>ons in 6% (a), 10% (b), 14% (c) and 18% (d) cross-linked polyacrylamide concentration self-cast Bio-Rad SDS-PAG (1 mm × 7 cm). Different concentrations of polyacrylamide were casted in a mini-Protean 3 apparatus. Five microliters of Mark12 protein standards were used. Relative mobility was measured as a ratio of the migration distance of the target protein to that of the resolving front (% R). The graphs were generated using Quantity One software. The y-axis denotes the percent differences of % Rin pulsed conditions compared to the CFE control. Each data point was the average of two separate experiments. All gels were run at 200 V with the average buffer temperature of 10°C. Positive values denote shorter migration distance and negative values denote longer migration distance with respect to CFE control. Error bar denotes the standard deviation of two separate experiments. Error bar cannot be showed if the range is smaller than the label

Increase in local protein concentration by field-inversion gel electrophoresis-3

<p><b>Copyright information:</b></p><p>Taken from "Increase in local protein concentration by field-inversion gel electrophoresis"</p><p>http://www.proteomesci.com/content/5/1/18</p><p>Proteome Science 2007;5():18-18.</p><p>Published online 26 Sep 2007</p><p>PMCID:PMC2211458.</p><p></p>(b) in native PAG between CFE and FIGE conditions. FIGE was the left panel. CFE control was the right panel. The gels were 1 mm × 7 cm native 6% PAG casted in a mini-Protean 3 apparatus. Run time was 2 hrs 15 min in control condition. Pulsed condition run time was 5 hrs 30 min with a a/r of 400/100 msec. Lane 1, native MW markers (10 μg total); Lane 2, 10 μg purified GroEL native complex (14-mer, 840 kDa). The band at 300 kDa could be a minor cofactor associated with GroEL during purification. The gel was stained with Coomassie blue. Proteins were purposefully overloaded to best represent the effect of "detrapping" of native proteins under pulsing conditions. In panel b), MCF-7 nuclear extracted were run through native 2–5% PAG. The run time was 10 hrs for CFE control condition. Pulsed condition run time was 14 hrs with /tof 900 msec/240 msec. Lane 1, 5.6 μg MCF-7 cell nuclear extract; Lane 2, 7.5 μg MCF-7 cell nuclear extract; Lane 3, native protein MW markers. The gels were silver stained

Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer

10.1186/s13059-021-02261-xGenome Biology2214