Repression of <i>aphA</i> by OpaR.

<p>For primer extension (a), an oligonucleotide primer was designed to be complementary to the RNA transcript of <i>aphA</i>. For EMSA (b) and DNase I footprinting (c), the DNA fragment from the 380th to 161th bp upstream of <i>aphA</i> was incubated with increasing amounts of purified His-OpaR protein. The experiments were done as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone-0034622-g005" target="_blank">Fig. 5</a>. The transcription start site of <i>aphA</i> were underlined in the DNA sequence. Lanes G, A, T, and C represented the Sanger sequencing reactions. The footprint regions were indicated with vertical bars.. The minus numbers indicated the nucleotide positions upstream of <i>aphA</i>.</p

Stimulation <i>qrr2–4</i> by OpaR.

<p>For primer extension (a1, b1, and c1), an oligonucleotide primer was designed to be complementary to the RNA transcript of each of <i>qrr2–4</i>. For EMSA (a2, b2, and c2) and DNase I footprinting (a3, b3, and c3), the upstream DNA fragments of <i>qrr2–4</i> were radioactively labeled, and then incubated with increasing amounts of purified His-OpaR protein. The experiments were done as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone-0034622-g005" target="_blank">Fig. 5</a>. The transcription start sites of <i>qrr2–4</i> were underlined in the DNA sequence. Lanes G, A, T, and C represented the Sanger sequencing reactions. The footprint regions were indicated with vertical bars. The negative or positive numbers indicated the nucleotide positions upstream or downstream of relevant <i>qr</i>r gene, respectively.</p

Phylogenetic tree of OpaR and its orthologs.

<p>Protein sequences were derived from <i>V. alginolyticus</i> ZJ-51 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Chang1" target="_blank">[60]</a>, <i>V. parahaemolyticus</i> RIMD 2210633 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Makino1" target="_blank">[16]</a>, <i>V. harveyi</i> ATCC BAA-1116 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Lin3" target="_blank">[61]</a>, <i>V. vulnificus</i> YJ016 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Chen1" target="_blank">[62]</a>, <i>V. tubiashii</i> RE22 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Hasegawa1" target="_blank">[63]</a>, <i>V. anguillarum</i> 775 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Naka1" target="_blank">[64]</a>, <i>V. cholera</i> N16961 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Heidelberg1" target="_blank">[65]</a>, and <i>V. fischeri</i> MJ11 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Mandel1" target="_blank">[66]</a>. The a.a. sequences were aligned by the CLUSTALW <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Thompson1" target="_blank">[67]</a> web server at <a href="http://align.genome.jp/" target="_blank">http://align.genome.jp/</a>. The aligned sequences were then used to construct an unrooted neighbor-joining tree using the MEGA version 5.0 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Tamura1" target="_blank">[68]</a> with a bootstrap iteration number of 1000. Shown on the branch points of phylogenic tree were the bootstrap values (%).</p

MQSR consensus constructs.

<p>(a) The sequence logo representation of the binding sites of OpaR and its orthologs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone-0034622-t002" target="_blank">Table 2</a>) was generated by the WebLogo tool <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Crooks1" target="_blank">[27]</a>. The 20-bp consensus box <u>TATTGATAAA</u>-<u>TTTATCAATA</u> was annotated as an inverted repeat sequence. (b) A position frequency matrix describes the alignment of the binding sites, and denotes the frequency of each nucleotide at each position.</p

Quorum sensing systems in <i>V. harveyi</i>/<i>V. parahaemolyticus</i>.

<p>The mode for signal transduction during QS in <i>V. harveyi</i> has been described in the text. The feedback regulatory loops are shown with dotted lines. Since all the components of <i>V. harveyi</i> quorum sensing appears to be intact in the <i>V. parahaemolyticus</i> genome <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034622#pone.0034622-Makino1" target="_blank">[16]</a>, the QS signal transduction cascades should be conserved in <i>V. harveyi</i> and <i>V. parahaemolyticus</i>.</p

Growth curves.

<p>A two-round design of bacterial seed cultivation was employed: first, the glyceric stock of bacteria was inoculated into 15 ml of the MR or HI broth for growing at 30°C for 24 h with shaking at 200 rpm, and the cell culture was subsequently diluted to an OD₆₀₀ value of about 1.0; second, the resulting culture was then 50-fold diluted into 15 ml of corresponding fresh MR or HI broth, and allowed to grow to reach an OD₆₀₀ value of about 1.2 to 1.4. The bacterial seeds were 50-fold diluted into 15 ml of corresponding fresh MR or HI broth for further cultivation, and the OD₆₀₀ values were monitored for each culture with a 1 h interval. Experiments were done in triplicate.</p

Comparative transcriptomics in : a global view of environmental modulation of gene expression-0

<p><b>Copyright information:</b></p><p>Taken from "Comparative transcriptomics in : a global view of environmental modulation of gene expression"</p><p>http://www.biomedcentral.com/1471-2180/7/96</p><p>BMC Microbiology 2007;7():96-96.</p><p>Published online 29 Oct 2007</p><p>PMCID:PMC2231364.</p><p></p>s show the transcriptional changes of the virulence genes, where columns represent different microarray experiments, and rows represent genes. Color intensities denote logratios as follows: green, negative; black, zero; red, positive; gray, missing data

Comparative transcriptomics in : a global view of environmental modulation of gene expression-5

<p><b>Copyright information:</b></p><p>Taken from "Comparative transcriptomics in : a global view of environmental modulation of gene expression"</p><p>http://www.biomedcentral.com/1471-2180/7/96</p><p>BMC Microbiology 2007;7():96-96.</p><p>Published online 29 Oct 2007</p><p>PMCID:PMC2231364.</p><p></p>s show the transcriptional changes of the virulence genes, where columns represent different microarray experiments, and rows represent genes. Color intensities denote logratios as follows: green, negative; black, zero; red, positive; gray, missing data

Ratio of every time test results vs. the first test result.

<p>*As the experiments proceeded, a calculated concentration was obtained at each time point for each of the four theoretical concentrations, then, the ratio of Log₁₀(concentration measured at each time, CET)/ Log₁₀(concentration measured at the first time, CFT) are calculated, each concentration was measured three times. The unit of concentration is copies/µl.</p

List of primers and probes used in this study.

a<p>CF/CR:short for clone forward primer and clone reverse primer.</p>b<p>F/R:forward primer and reverse primer.</p>c<p>T:TaqMan probe.</p>d<p>FAM: 6-carboxy fluorescein; TAMRA: 6-carboxy-tetra-methylrhodamine.</p>e<p>Refererring to the positions in the corresponding sequences.</p