The profile for local codon usage bias and the comparison of natural gene sequences to the random sequences.

<p>The x-axis is the codon sequence and the y-axis is the local <i>CAI</i> value. The major decrease of local codon usage bias is shown with dashed square lines. The blue line is for natural gene sequence and the red line is for the average of the random sequences.</p

Results obtained from protein 1P9H.

<p>(A). The cartoon structure, with the two symmetric substructures shown in red and green respectively. (B). The profile of local codon usage bias: the region with major decreases in <i>CAI</i> value is shown with dashed square lines. (C). The comparison between the profile of the natural gene sequence and the averaged profile of the same codon sequence randomized by 10 times. The blue line is for natural gene sequence and the red line is for the average of the random sequences. (D) and (E). The profile of local folding free energy and the comparison between the natural gene sequence and the random sequences, respectively. The blue line is for natural gene sequence and the red line is for the average of the random sequences.</p

Recurrence plots for 8 proteins.

<p>The first and third horizontal panel: the recurrence plot of the nucleotide sequence; the second and the fourth horizontal panel: the recurrence plot for codon usage bias in the codon sequence of the corresponding proteins. The PDB id of the protein is given in each of the plot.</p

Results and parameters.

<p>Results and parameters.</p

Results obtained from protein 1YP2.

<p>(A). The cartoon structure: the two symmetric substructures are shown in red and green; the extended irregular structure in the middle of the helix is shown in blue. (B). The profile of local codon usage bias: the decreased region in the middle of the codon sequence is shown with dashed square lines. (C). The comparison between the profile of the natural gene sequence and the averaged profile of the same codon sequence randomized by 10 times. The blue line is for natural gene sequence and the red line is for the average of the random sequences. (D). The profile of local folding free energy, and the dashed square lines shows the region with decreased local folding free energy. (F). The comparison between the natural gene sequence and the random sequences. The blue line is for natural gene sequence and the red line is for the average of the random sequences.</p

The profile for local mRNA folding free energy and the comparison of natural gene sequences to the random sequences.

<p>The x-axis is the nucleotide sequence and the y-axis is the local folding free energy. The region with major decrease of local mRNA folding free energy is shown with dashed square lines. The blue line is for natural gene sequence and the red line is for the average of the random sequences.</p

Similarity (S) of the sequence alignment.

<p>Similarity (S) of the sequence alignment.</p

Quercetin potentiates the effect of DOX on proliferation and apoptosis in liver cancer cells, but not in normal liver cells.

<p>(A) Effect of quercetin on the proliferation of SMMC7721 and QGY7701 liver cancer cells, and L02 normal liver cells. The cells were incubated with quercetin (0 µM to 150 µM) for 48 h and subjected to an MTT assay to determine the proliferation rate. (B) Quercetin sensitized SMMC7721 cells to DOX. (C) Quercetin sensitized QGY7701 cells to DOX. (D) Quercetin partially reduced the DOX-induced growth inhibition in L02 cells. The cells were incubated with DOX (1 µM) and/or quercetin (20 µM) (B, C, and D) for 24 h, and then subjected to an MTT assay. Data are presented as mean ± S.D. of three independent experiments. (E) SMMC7721 and L02 cells were incubated with DOX (1 µM) and/or quercetin (20 µM) for 24 h, and then analyzed by flow cytometry using Annexin V/PI staining to discriminate the live cells (Annexin V−/PI−), early apoptotic cells (Annexin V+/PI−), necrosis or late apoptotic cells (Annexin V+/PI+), and dead cells (Annexin V−/PI+). *<i>P</i><0.05 vs. cells co-treated with quercetin.</p

Quercetin potentiates DOX-induced apoptosis of SMMC7721 cells in a p53-dependent manner.

<p>(A) p53 and PUMA expressions were assessed by western blot in SMMC7721 cells treated with DOX (1 µM) and/or quercetin (20 µM) for 24 h. β-actin was used as an internal control. (B) The luciferase assay of DOX- and quercetin-induced p53 activation. SMMC7721 cells were pretreated for 1 h with 2 µM of pifithrin-α, and then treated with DOX (1 µM) or quercetin (20 µM) for 12 h. p53 activity was determined by luciferase activity assay. Data are presented as mean ± S.D. of three independent experiments. *<i>P</i><0.01 vs. DOX-treated cells. **<i>P</i><0.001 vs. DOX + quercetin-treated cells. (C) SMMC7721 cells were pretreated with 2 µM of pfithrin-α for 1 h, and then treated with DOX (1 µM) and/or quercetin (20 µM) for 24 h. Apoptosis rates were assayed by Annexin V/PI staining. Data are presented as mean ± S.D. of three independent experiments. *<i>P</i><0.001 vs. DOX-treated cells. **<i>P</i><0.01 vs. DOX-treated cells. ***<i>P</i><0.001 vs. DOX + quercetin-treated cells.</p

Quercetin potentiates DOX-induced apoptosis in liver cancer cells through Bcl-xl/Bax-mediated mitochondrial pathway.

<p>(A, B) Effect of DOX and/or quercetin on the mitochondrial membrane potential breakdown in SMMC7721 cells treated with DOX (1 µM) and/or quercetin (20 µM) for 24 h. JC-1 is observed as green fluorescing monomers in the cytosol or as red fluorescing aggregates in intact mitochondria. The reduction of red fluorescence intensity indicates mitochondrial breakdown with intact membrane potential. *<i>P</i><0.01 vs. DOX-treated cells. (C) Western blot analysis of the total expression of Bid, Bcl-2, and Bcl-xl, as well as the mitochondrial distribution of Bax and the cytosol distribution of cytochrome <i>c</i> in SMMC7721 cells treated with DOX (1 µM) and/or quercetin (20 µM) for 24 h. β-actin was used as an internal control for the total protein and cytosol protein. Hsp60 was used as an internal control for the mitochondrial protein. (D) Western blot analysis of the mitochondrial distribution of Bax and the total expression of Bcl-xl in SMMC7721 cells transfected with Bcl-xl expression vector and treated with DOX (1 µM) and/or quercetin (20 µM) for 24 h. (E) Effect of DOX and/or quercetin on the apoptosis of SMMC7721/Bcl-xl and SMMC7721/neo cells assayed by PI staining after DOX (1 µM) and/or quercetin (20 µM) was administered for 24 h. *<i>P</i><0.01, SMMC7721/neo vs. SMMC7721/Bcl-xl cells. Data are presented as mean ± S.D. of three independent experiments.</p