MOESM1 of Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid short- and branched-chain alkyl esters biodiesel

Additional file 1. Supplementary tables and figures. Table S1. List of primers used in this study. Table S2. Codon optimized sequence of wax ester synthase genes used in this study. Table S3. Growth parameters of engineered yeast strains. Figure S1. Relative FAEEs, FABEs or FAIEs production with exogenous alcohol feeding. Figure S2. Production of fatty acid esters in engineered yeast expressing ws2. Figure S3. Relative phospholipid concentration of engineered yeast strains. Figure S4. Production of fatty acid esters in engineered yeast expressing Maqu_0168. Figure S5. Growth curves for engineered cells. Figure S6. OD600 for high cell density fermentation. Figure S7. FASBEs production yield corresponding to Fig. 6

Performance in 6-fold cross-validation (CV) using phased CEU data of HapMap Project.

<p>Performance in 6-fold cross-validation (CV) using phased CEU data of HapMap Project.</p

Proportion of “phase-known genotypes” and “predictable genotypes” growths with the increase of reference panel size.

<p>The y-axis show proportion of different genotype categories in GWAS data; number of individuals involved in reference panel was shown on x-axis. “unknown genotype” is only a very small proportion.</p

An Engineered Probiotic Produces a Type III Interferon IFNL1 and Reduces Inflammations in <i>in vitro</i> Inflammatory Bowel Disease Models

The etiology of inflammatory bowel diseases (IBDs) frequently results in the uncontrolled inflammation of intestinal epithelial linings and the local environment. Here, we hypothesized that interferon-driven immunomodulation could promote anti-inflammatory effects. To test this hypothesis, we engineered probiotic Escherichia coli Nissle 1917 (EcN) to produce and secrete a type III interferon, interferon lambda 1 (IFNL1), in response to nitric oxide (NO), a well-known colorectal inflammation marker. We then validated the anti-inflammatory effects of the engineered EcN strains in two in vitro models: a Caco-2/Jurkat T cell coculture model and a scaffold-based 3D coculture IBD model that comprises intestinal epithelial cells, myofibroblasts, and T cells. The IFNL1-expressing EcN strains upregulated Foxp3 expression in T cells and thereafter reduced the production of pro-inflammatory cytokines such as IL-13 and -33, significantly ameliorating inflammation. The engineered strains also rescued the integrity of the inflamed epithelial cell monolayer, protecting epithelial barrier integrity even under inflammation. In the 3D coculture model, IFNL1-expressing EcN treatment enhanced the population of regulatory T cells and increased anti-inflammatory cytokine IL-10. Taken together, our study showed the anti-inflammatory effects of IFNL1-expressing probiotics in two in vitro IBD models, demonstrating their potential as live biotherapeutics for IBD immunotherapy

An example for haplotype identification with selected SNP cluster and phase-known reference population.

<p>An example for haplotype identification with selected SNP cluster and phase-known reference population.</p

MOESM2 of Engineering transcription factors to improve tolerance against alkane biofuels in Saccharomyces cerevisiae

Additional file 2. Additional tables.Table S1. M values of reference gene candidates derived from qPCR data. Table S2. Fold changes of PDR genes expressed in BYL13 stains as compared to BY4741. Table S3. Primers used in this study

Comparison of results from single-SNP and Haplotype-based analysis.

<p>A. Histograms of single SNPs and SNP clusters with p-value less than 1.0×10⁻⁷ in analyses for male and female data sets, respectively. B. Venn Diagrams showed the sharing of significant single SNPs and SNP clusters in association studies for male and female data sets, respectively. A single-SNP or haplotype finding was shared with the other approach when the significant SNP appeared in any of the significant SNP clusters or any SNP of the cluster appeared in findings of single-SNP analysis, respectively.</p

Haplotype-based analysis is more powerful than single-SNP analysis.

<p>Upper panel shows results from single-SNP analysis; lower panel presents results of haplotype-based analysis.</p

Q-Q plot of p-values in −log10 scale.

<p>Quartile of p-values from our approach was shown on y-axis and x-axis presented quantile of p-values from analysis on raw haplotype data.</p

Performance of Haplominer and Beagle-based approach in association study with simulated data.

<p>A. Percentage of accordant p-values in the valuation with simulation data. B. Contributions of different approaches to the total discordant p-values.</p