CpxR-mediated enhancement of multidrug resistance in <i>P</i>. <i>aeruginosa</i> is MexA-dependent, but not MuxA-dependent.

CpxR-mediated enhancement of multidrug resistance in P. aeruginosa is MexA-dependent, but not MuxA-dependent.</p

Additional file 5 of Revealing the composition of the eukaryotic microbiome of oyster spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS)

Additional file 5: Figure S2. Eukaryotic taxa representing >1% of the sequences revealed by deep-sequencing of the 18S rRNA amplicons for oyster spat samples, using "universal" 18S primers (Table S3), non-metazoan primers (Table S3), blocking primers (Table S3), or CRISPR-Cas Selective Amplicon Sequencing (CCSAS) combining "universal" 18S primers and CRISPR-Cas9 with pacific-oyster-specific sgRNA m258 (Table S2)

CpxR activates expression of target promoters.

<p>CpxR activates expression of target promoters.</p

Direct binding of CpxR to the promoter region of <i>mexA in vitro</i>.

<p>DNase I footprinting assays of the <i>mexA</i> promoter DNA fragment were performed in the absence (A) and presence (B) of purified CpxR. The FAM-labelled 322-bp DNA fragments (50 nM) pre-incubated in the absence or presence of 1.5 μM phosphorylated CpxR were subjected to DNase I digestion and fragment length analysis. The fluorescence signal of the labelled DNA fragments is plotted against the sequence of the fragment. The protected region bound by CpxR is shown with the conserved binding motif in red.</p

Additional file 7 of Revealing the composition of the eukaryotic microbiome of oyster spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS)

Additional file 7: Figure S4. Summary of the number of eukaryotic species at each D7 taxonomic level that the sgRNA can cut at the V4 region of the 18S rRNA genes that are flanked by the 18S "universal" primer set TAReuk454FWD1 / TAReukREV3 [54]. These nine sgRNAs, which are among 205242 unique taxon-specific sgRNA designed from the SILVA SSU database (version 119) [80] using CasOligo, are selected to show that some sgRNAs can target more than 1000 species and broad taxonomic groups based on an in-silico analysis (i.e. 100% match to the 18S rRNA gene sequences of the metazoan host at the gRNA-target-site, but no match for protists and fungi). Taxon names on the left side of the panel are shown as SILVA taxonomic hierarchy with levels ranging from D0 (kingdom) to D7. The D7 taxonomic level comprises eukaryotic classes and families

Additional file 4 of Revealing the composition of the eukaryotic microbiome of oyster spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS)

Additional file 4: Figure S1. Percentage of intact 18S amplicons remaining from the model organisms after cutting with one-step CRISPR-Cas9. The concentration of intact 18S amplicons was measured using Quantitative PCR for samples both with and without CRISPR-Cas9 treatment. The portion of remaining intact 18S amplicons was determined by dividing the concentration 18S amplicons in sample with CRISPR-Cas9 treatment by that of without CRISPR-Cas9 treatment. The labels on the X-axes indicate the ID of the taxon-specific sgRNA and its corresponding host

Total response time varying λ_<i>i</i> when the the computation workload of the task <i>c</i>_<i>j</i> = 75 and 200 cycles.

Total response time varying λi when the the computation workload of the task cj = 75 and 200 cycles.</p

CpxR mediates up-regulation of <i>mexAB-oprM</i> expression levels and enhancement of antibiotic resistance in isolated <i>nalB-</i>type <i>P</i>. <i>aeruginosa</i> strains <i>in vitro</i>.

CpxR mediates up-regulation of mexAB-oprM expression levels and enhancement of antibiotic resistance in isolated nalB-type P. aeruginosa strains in vitro.</p

Total response time varying λ_<i>i</i> when the bandwidth <i>β</i> = 300 and 500 Mbps.

Total response time varying λi when the bandwidth β = 300 and 500 Mbps.</p

Additional file 6 of Revealing the composition of the eukaryotic microbiome of oyster spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS)

Additional file 6: Figure S3. Distribution of the number of gRNA-target-sites of each metazoan and plant species from the SILVA SSU database v119 [80]. These gRNA-target-site oligonucleotide sequences were identified, using the Cas9.gRNA.oligo1() algorithm, from the V4 region of the 18S rRNA gene that is flanked by the 18S "universal" primer set TAReuk454FWD1 / TAReukREV3 [54], and are used for designing and synthesizing the CRISPR-Cas9-compatible sgRNA. The taxon-specific gRNA-target-sites allows the design of the sgRNA to taxon-specifically cut the 18S rRNA gene sequence of a metazoan or plant host but not microeukaryotes (protists and fungi) using CRISPR-Cas9