SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences-0

<p><b>Copyright information:</b></p><p>Taken from "SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences"</p><p>http://www.biomedcentral.com/1471-2105/8/354</p><p>BMC Bioinformatics 2007;8():354-354.</p><p>Published online 20 Sep 2007</p><p>PMCID:PMC2082047.</p><p></p>and the value for the maximum length of the pattern (from 7 to 35); and we record its running time and the total number of patterns. At right, we run Searchpattool on four random input sequences with respectively 10, 20, 50 and 100 sequences (400 bp for each sequence). For each input sequence we choose a minimum support value of 80% and a maximum length pattern value of 24, execute Searchpattool and record its running time and the total number of patterns

DNA immunization with HA, HA+NP, and HA+NP+M2 induces similar protection after A/Vietnam/1203/2004 virus challenge in mice.

<p>(A) Survival data is shown as a percentage comparing the final animal number at day 21 with the initial animal number in each group. All HA-containing groups showed significant survival compared to controls. There is no statistical difference between the HA, HA+NP and HA+NP+M2 groups (<i>p</i> = 0.317 between HA and HA+NP; <i>p</i> = 0.146 between HA and HA+NP+M2; <i>p</i> = 0.515 between HA+NP and HA+NP+M2 by log-rank test); NP and the control groups were not statistically different from each other. (B) Body weights of the mice were also monitored and the total body weight of all of the surviving animals in each group was compared with the respective initial body weights. As expected, the HA group showed the least amount of body weight loss, with the other HA-containing groups showing similar patterns. However, the NP-immunized group demonstrated severe weight loss, similar to controls.</p

Protection of DNA/rAd5 vaccines encoding HA or HA+NP+M2, but not NP, NP+M2, or M2, against A/Vietnam/1203/2004 virus challenge.

<p>(A) Ferrets immunized three times with DNA followed by a single rAd5 boost were challenged under anesthesia with 10⁷ EID₅₀/ferret of influenza virus A/Vietnam/1203/2004. The animals were monitored 7 days for survival, shown as a percentage comparing the initial animal number to the final animal number in the same group (left panel). There was no statistical difference between the control group and groups immunized with NP, NP+M2, or M2. Both the HA and HA+NP+M2 groups showed 100% survival (right panel), whereas the vector control group showed 0% survival after the viral challenge. There was no statistically significant difference between the HA and HA+NP+M2 groups (<i>p</i> = 1.00), but there was a significant difference between these groups and the control (<i>p</i> = 0.008), by a log-rank test. (B) Body weights of the ferrets were also monitored and the total body weight of all of the surviving animals in each group was compared with the respective initial body weight (left panel). Ferrets immunized with HA and HA+NP+M2 groups showed no weight loss, while the control group ferrets showed rapid weight loss (right panel). The survival and initial animal numbers in each group on the last day of body weight data collection are indicated next to the curve labels. The survival percentage for each group was analyzed statistically by a log-rank test.</p

Neutralizing Antibody Responses of HA-Vaccinated Mice and Ferrets.

<p>*UD = Undetectable; NA = Not Assessed.</p><p>Neutralization was determined by lentiviral inhibition assay, hemagglutinin inhibition assay, and microneutralization assay. Sera from the indicated mouse and ferret immunizations with the indicated viral antigens by DNA alone or DNA/rAd5 before the viral challenge were evaluated by pseudotyped lentiviral inhibition, hemagglutinin inhibition (HAI), and microneutralization assays (MN). UD represents serum samples with undetectable neutralization activities even at the lowest dilutions, while NA represents samples that were not available, and therefore not assessed. In both mice and ferrets, only HA-containing groups stimulated strong humoral responses.</p

Expression of immunogens using DNA and rAd5 vectors in cell culture.

<p>(A) Western blot analysis confirmed the expression of HA protein of A/Thailand/1/KAN-1/2004 (lane 2), NP protein of A/PR/8/34 (lane 3) and A/Thailand/1/KAN-1/2004 (lane 4), and M2 protein of A/Thailand/1/KAN-1/2004 (lane 6) in 293T cells transfected by eukaryotic plasmid expression vectors. (B) Expression of rAd5 vectors was confirmed in A549 cells after transduction with vectors encoding HA (KAN-1) (lane 8), NP (KAN-1) (lane 9), and M2 (KAN-1) (lane 11). Arrows indicate the relevant predicted size of the indicated viral proteins. Bands refer to the right predicted size of different viral proteins that were detected in each lane as indicated. Molecular weight markers were used for protein size reference.</p

Humoral immune responses to HA, NP and M2 confirmed by ELISA after DNA/rAd5 immunization in ferrets.

<p>(A) Sera from the HA, HA+NP+M2 or vector control immunized ferrets were collected 14 days after the third DNA immunization (white bars), and 14 days after the recombinant adenovirus boost (solid bars), and subjected to ELISA assays to determine their end-point titer levels against HA(KAN-1), NP(KAN-1), and M2(KAN-1) antigens. Each bar represents the group mean for the end-point titers of total IgG and IgM, determined in duplicate by series dilution of ELISA assay with the error bars indicating the standard deviation. ANOVA tests were significant for only the responses against HA at the first time point, and for all three antigens after the rAd5 boost. For HA and M2, significant pairs of groups are noted on the graph. Only <i>p</i>-values less than 0.05 are indicated. * represents a <i>p</i>-value between 0.05 and 0.001, while ** indicates <0.001, and *** indicates <0.0001. As expected, the HA alone group elicited significant anti-HA immunity that increased after rAd5 HA boost (left panel) compared to controls (<i>p</i><0.0001). The HA+NP+M2 group elicited similar anti-HA ELISA antibodies, as well as significant anti-NP humoral responses (<i>p</i> = 0.0006) and anti-M2 responses (<i>p</i><0.0001) after the rAd boost (middle and right panels). (B) Sera from the NP, M2, NP+M2 or vector controls were collected 14 days after the third DNA immunization (white bars), and the sera from the same animals were also collected 14 days after the recombinant adenovirus boost (solid bars). ANOVA tests were not significant for any of the antigens at the first time point, and for NP and M2 after the rAd5 boost. For NP and M2, significant pairs of groups are noted on the graph. Only <i>p</i>-values less than 0.008 are indicated. * represents a <i>p</i>-value between 0.008 and 0.001, while ** indicates <0.001, and *** indicates <0.0001. For both NP and NP+M2 immunized groups, significant anti-NP humoral responses were observed after the rAd boost (<i>p</i><0.0001) (middle panel). Significant anti-M2 humoral responses were detected in animals immunized with NP+M2 post-rAd boost (<i>p</i> = 0.0005), but not in the M2 alone group (right panel).</p

Seroprevalence of Ad14, Ad28 and Ad41 in HIV-infected, Ad5 seropositive and HIV-uninfected, Ad5 seropositive participants is similar.

*<p>Fisher's exact test.</p

Pre-existing anti-Ad5 fiber neutralizing antibodies reduced immune responses generated by MRKAd5 HIV-1 gag/pol/nef vaccine, especially HIV specific CD8+ immune responses.

<p>Median (25%–75% percentile),</p>*<p>: p<0.05;</p>**<p>: p<0.01,</p>***<p>: p<0.001.</p

Pre-existing anti-Ad5 capsid neutralizing antibodies reduced immune responses generated by MRKAd5 HIV-1 gag/pol/nef vaccine, especially HIV-specific CD8+ immune responses.

<p>Median (25%–75% percentile),</p>*<p>: p<0.05;</p>**<p>: p<0.01,</p>***<p>: p<0.001.</p

Seroprevalence of Ad35 in HIV-infected, Ad5 seropositive participants is lower compared to that in HIV-uninfected, Ad5 seropositive participants.

*<p>values used for Fisher's exact test, p = 0.002.</p