Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid-1

<p><b>Copyright information:</b></p><p>Taken from "Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid"</p><p>http://www.biomedcentral.com/1471-2105/8/375</p><p>BMC Bioinformatics 2007;8():375-375.</p><p>Published online 9 Oct 2007</p><p>PMCID:PMC2099448.</p><p></p>gLen. In the second, these intermediate fragments are further digested and the respective ALFFs are calculated. The longest ALFF is selected, shown as the dotted line. FgLen is changed from 50 to 80, the longest ALFF at different FgLen is collected into a set, and the average of the set is used to evaluate the resistance of the protein to gastric fluid digestion

Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid-2

<p><b>Copyright information:</b></p><p>Taken from "Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid"</p><p>http://www.biomedcentral.com/1471-2105/8/375</p><p>BMC Bioinformatics 2007;8():375-375.</p><p>Published online 9 Oct 2007</p><p>PMCID:PMC2099448.</p><p></p>of which the digestibility is lower than the threshold while to the right it is higher. The unit for digestibility is the amino acid residue

Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid-3

<p><b>Copyright information:</b></p><p>Taken from "Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid"</p><p>http://www.biomedcentral.com/1471-2105/8/375</p><p>BMC Bioinformatics 2007;8():375-375.</p><p>Published online 9 Oct 2007</p><p>PMCID:PMC2099448.</p><p></p

Pathway enrichment analysis showed several pathways were enriched by salinity and ecotype effects.

1<p>NF: Normalized frequency  =  sample frequency of each category in this experiment/background frequency of each category in the Arabidopsis genome.</p><p>Genes with P-value <0.05 and fold change >2.0 were loaded and annotated in the Classification SuperViewer Tool (<a href="http://bar.utoronto.ca/ntools/cgi-bin/ntools_classification_superviewer.cgi" target="_blank">http://bar.utoronto.ca/ntools/cgi-bin/ntools_classification_superviewer.cgi</a>). MapMan was used as the classification source to assign functional categories for each gene. Group 1: pathways enriched by both salt and ecotype effects; Group 2: pathways enriched by salt effect and ecotype effect in the presence of salt; Group 3: pathways mainly enriched by salt effect; –: no significant enrichment. The color scales indicated different normalized frequencies which were described in Materials and Methods.</p

Adult phenotypes analysis among Col, Ler and Sha after salt stress treatment.

<p><b>Salt treatments were initiated at 14 DAS (<u>D</u>ay-<u>A</u>fter-<u>S</u>owing).</b> (A) 2-week-old seedlings of Col, Ler and Sha were treated with indicated concentrations of NaCl for 14 days. Plants were photographed after 2 weeks treatments. (B) Survival rates were calculated from the results of above three independent experiments (n = 20). The values indicated means + SEs. * indicated significant difference with <i>P</i><0.05 (<i>t-test</i>) in relative to Ler. (C) Relative dry weight comparison after salt treatment. The values indicated means + SEs of four independent experimental repeats (n = 30). * indicated significant difference with <i>P</i><0.05 (<i>t-test</i>) in relative to Ler. (D) Plants were grown for 2 weeks under normal condition and exposed to different concentrations of NaCl treatments. At 10 days after treatment, aerial plants were harvested for measurement of relative electrolyte leakage. The values indicated means + SEs of four independent experimental repeats (n = 15). * indicated significant difference with <i>P</i><0.05 (<i>t-test</i>) in relative to Ler.</p

Quantitative comparison of superoxide contents and antioxidant enzyme activities (SOD and CAT) among Col, Ler and Sha after salt stress treatment.

<p>Two-week-old plants were started to be treated with the indicated concentrations of NaCl for 10 days before measurement in (B), (C) & (D). The values indicated means + SEs of two independent experimental repeats in (B), (C) & (D) (n = 15). * indicated significant difference with <i>P</i><0.05 (t-test) in relative to Ler. (A) Visualization of superoxide radical and hydrogen peroxide detected by NBT and DAB staining. Detections have been done on 2-week-old MS-grown plants subjected to subsequent treatment with 200 mM NaCl for the indicated time. Bar = 1 cm. (B) Changes in H₂O₂ content were analyzed with different salt treatment. (C) Changes in SOD activity were analyzed with different salt treatment. (D) Changes in CAT activity were analyzed with different salt treatment.</p

Model of salt effect and ecotype effects.

<p>Model of salt effect and ecotype effects.</p

Cluster analyses of transcripts involved in specific pathway.

<p> Red, increase in transcript abundance (up-regulation); green, decrease in transcript abundance (down-regulation); yellow, no change. The color scales were also indicated. Hierarchical cluster analysis was applied for differentially expressed transcripts (P < 0.05 and log 2 fold change > 1 or < −1) with Cluster 3.0 software. The resulting tree figures were displayed using the software package, Java TreeView.</p

Numbers of gene changed by Sha ecotype effect and salt effect.

<p>Numbers of gene changed by Sha ecotype effect and salt effect.</p

Stress-related GO term enrichment analysis.

<p>Term enrichment analysis was performed using AmiGO software.</p>1<p>NF: Normalized frequency  =  sample frequency of each category in this experiment/background frequency of each category in the Arabidopsis genome.</p