The relationship between proportion of duplicate gene pairs with different exon-intron structure and sequence divergence.

<p>Synonymous divergence is used to represent sequence divergence. Each point represents 200 gene pairs.</p

The relationship between Pearson’s correlation coefficient of gene expression and structural divergence.

<p>(A) Four different types of duplicate gene pairs: not structurally divergent (NSD), structurally divergent (SD), not structurally divergent cattle-specific (NSD cattle-specific), structurally divergent cattle-specific (SD cattle-specific). (B) The linear regression model with expression similarity as the dependent variable and the synonymous divergence as explanatory variable was constructed for both structurally divergent duplicate gene pairs and not structurally divergent duplicate gene pairs.</p

Percentage of differentially expressed duplicate gene pairs by tissue.

<p>Percentage of differentially expressed duplicate gene pairs by tissue.</p

The relationship between Pearson’s correlation coefficient of gene expression and sequence divergence.

<p>(A) A significant negative correlation implies a positive correlation between <i>d_s</i> and expression divergence because can be regarded as expression divergence. Each point represents five gene pairs. (B) A negative correlation between transformed r and <i>d_N</i> with . Each point represents five gene pairs. (C) No correlation between transformed r and <i>d_N</i> with . Each point represents five gene pairs.</p

Genetic Association Analysis of Common Variants in <i>FOXO3</i> Related to Longevity in a Chinese Population

<div><p>Recent studies suggested that forkhead box class O3 (FOXO3) functions as a key regulator for the insulin/insulin-like growth factor-1signaling pathway that influence aging and longevity. This study aimed to comprehensively elucidate the association of common genetic variants in <i>FOXO3</i> with human longevity in a Chinese population. Eighteen single-nucleotide polymorphisms (SNPs) in <i>FOXO3</i> were successfully genotyped in 616 unrelated long-lived individuals and 846 younger controls. No nominally significant effects were found. However, when stratifying by gender, four SNPs (rs10499051, rs7762395, rs4946933 and rs3800230) previously reported to be associated with longevity and one novel SNP (rs4945815) showed significant association with male longevity (<i>P</i>-values: 0.007–0.032), but all SNPs were not associated with female longevity. Correspondingly, males carrying the <b><i>G</i></b>-G-<b><i>T</i></b>-<b><i>G</i></b> haplotype of rs10499051, rs7762395, rs4945815 and rs3800230 tended to have longer lifespan than those carrying the most common haplotype A-G-C-T (odds ratio = 2.36, 95% confidence interval = 1.20–4.63, <i>P</i> = 0.013). However, none of the associated SNPs and haplotype remained significant after Bonferroni correction. In conclusion, our findings revealed that the <i>FOXO3</i> variants we tested in our population of Chinese men and women were associated with longevity in men only. None of these associations passed Bonferroni correction. Bonferroni correction is very stringent for association studies. We therefore believe the effects of these nominally significant variants on human longevity will be confirmed by future studies.</p></div

Genotype and allele frequencies of longevity-associated <i>FOXO3</i> polymorphisms in the long-lived individuals and controls.

<p>Genotype and allele frequencies of longevity-associated <i>FOXO3</i> polymorphisms in the long-lived individuals and controls.</p

Haplotype analysis of male-longevity-associated SNPs in <i>FOXO3</i>.

<p>Haplotype analysis of male-longevity-associated SNPs in <i>FOXO3</i>.</p

Linkage disequilibrium plot of the 18 <i>FOXO3</i> SNPs genotyped.

<p>Linkage disequilibrium was quantified as D' (A) and <i>r</i>² (B), calculated in all subjects with the web tool SHEsis. Note: the darker the color, the higher the values.</p

Additional file 1: Table S1. of Common variants in SIRT1 and human longevity in a Chinese population

Details for single-nucleotide polymorphisms (SNPs) tagged by genotyped SNPs. Table S2. Genotype and allele frequencies of SIRT1 polymorphisms in the Chinese Han long-lived individuals and controls. Table S3. Association of SIRT1 haplotypes with human longevity in the Chinese Han long-lived individuals and controls. Table S4. Genotype and allele frequencies of SIRT1 polymorphisms in the long-lived individuals and controls when stratified by gender. Table S5. Association of SIRT1 haplotypes with human longevity when stratified by gender. Table S6. Association studies of SIRT1 with human longevity. (DOC 226 kb

EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in <i>E. coli</i>

Developing computational tools for a chassis-centered biosynthetic pathway design is very important for a productive heterologous biosynthesis system by considering enormous foreign biosynthetic reactions. For many cases, a pathway to produce a target molecule consists of both native and heterologous reactions when utilizing a microbial organism as the host organism. Due to tens of thousands of biosynthetic reactions existing in nature, it is not trivial to identify which could be served as heterologous ones to produce the target molecule in a specific organism. In the present work, we integrate more than 10,000 <i>E. coli</i> non-native reactions and utilize a probability-based algorithm to search pathways. Moreover, we built a user-friendly Web server named EcoSynther. It is able to explore the precursors and heterologous reactions needed to produce a target molecule in <i>Escherichia coli K12 MG1655</i> and then applies flux balance analysis to calculate theoretical yields of each candidate pathway. Compared with other chassis-centered biosynthetic pathway design tools, EcoSynther has two unique features: (1) allow for automatic search without knowing a precursor in <i>E. coli</i> and (2) evaluate the candidate pathways under constraints from <i>E. coli</i> physiological states and growth conditions. EcoSynther is available at http://www.rxnfinder.org/ecosynther/