Increased Functional Constraints Are Associated with All Types of Tissue-Switched Exons

<div><p>(A) The fraction of exons conserved between human and mouse for each exon category. All types of tissue-switched exons (usually major, intermediate, usually minor) showed a high rate of conservation.</p><p>(B) The frame-preservation ratio for each category of exons. Protein reading frame preservation is associated with all types of tissue-switched exons and conserved, always minor exons. Conserved, always major exons showed no evidence for increased protein reading frame preservation.</p><p>(C) The percent nucleotide substitution density for each exon category. All types of tissue-switched exons showed a reduced nucleotide-sequence substitution density between human and mouse, similar to what is observed for conserved, always minor exons. Error bars represent 95% confidence intervals obtained from nonparametric bootstrapping.</p><p>(D) The nucleotide substitution rate calculated for synonymous sites <i>(Ks)</i> from human and mouse orthologous exon sequences (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010034#s4" target="_blank">Materials and Methods</a>). All types of tissue-switched exons showed reduced <i>K</i>s rates between human and mouse, similar to what is observed for conserved, always minor exons. Error bars represent 95% confidence intervals obtained from nonparametric bootstrapping.</p></div

Enhanced Promiscuity of Lipase-Inorganic Nanocrystal Composites in the Epoxidation of Fatty Acids in Organic Media

In the present study, <i>Candida antarctica</i> lipase B (CALB) was encapsulated in inorganic nanocrystal composites with flower-like shapes, retaining 92% of its catalytic activity compared to that of native lipase. Surprisingly, CALB-inorganic crystal nanoflowers exhibited promiscuous activity at levels 25- and 4-fold higher than those of native lipase and the commercial immobilized lipase Novozym 435, respectively, as demonstrated by the chemoenzymatic epoxidation of fatty acids conducted in organic media. To the best of our knowledge, we showed for the first time that the promiscuity of enzymes can be significantly improved by enzyme immobilization, suggesting that the enzyme-inorganic nanocrystal composites are a very promising type of immobilized enzyme that can be used to address the challenge of the extremely low efficiency of enzymatic promiscuity

Effects of probe selection on genes differentially expressed between liver and muscle.

<div><p>(<b>A</b>) 438 transcript clusters were defined as overexpressed in liver relative to muscle, based on 3′ expression array data (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000088#s2" target="_blank">Materials and Methods</a>).</p> <p>Using gene expression indexes computed from all core probes or the selected core probes, we calculated the average gene expression fold change in three liver samples over three muscle samples.</p> <p>The X-axis shows the fold change using all core probes, and the Y-axis shows the fold change using selected core probes.</p> <p>The red line indicates the 45-degree line (Y = X).</p> <p>(<b>B</b>) A magnification of (A) when the fold change computed from all core probes was less than 6.</p> <p>(<b>C</b>) 500 transcript clusters were defined as overexpressed in muscle relative to liver, based on 3′ expression array data (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000088#s2" target="_blank">Materials and Methods</a>).</p> <p>Using gene expression indexes computed from all core probes or the selected core probes, we calculated the average gene expression fold change in three muscle samples over three liver samples.</p> <p>The X-axis shows the fold change using all core probes, and the Y-axis shows the fold change using selected core probes.</p> <p>The red line indicates the 45-degree line (Y = X).</p> <p>(<b>D</b>) A magnification of (C) when the fold change computed from all core probes was less than 6.</p></div

Hierarchical clustering of probe intensities of CD44 core probes.

<div><p>Core probes of CD44 are clustered by average linkage hierarchical clustering based on their intensities in 11 tissues (a total of 33 samples).</p> <p>The distance metric is (1-Pearson correlation coefficient).</p> <p>A total of 44 core probes are selected when we cut the clustering dendrogram at <i>h</i> = 0.1 (indicated by the dashed horizontal line).</p></div

Gene expression indexes computed using all probes, all core probes, and selected core probes.

<div><p>(<b>A</b>) Gene expression indexes of transcript cluster 2899110 (HFE) are computed using all probes (black circles), all core probes (red triangles) and selected probes (green rectangles).</p> <p>Probe selection increases the gene expression indexes computed for all the samples.</p> <p>The relative expression levels in different tissues remain unaltered.</p> <p>(<b>B</b>) Gene expression indexes of transcript cluster 3833500 (SPTBN4, a gene known to be overexpressed in brain and cerebellum).</p> <p>Probe selection strengthens the pattern of overexpression in cerebellum (sample #4, #5 and #6).</p></div

Probe design of exon arrays.

<div><p>(<b>A</b>) Exon-intron structure of a gene.</p> <p>Black boxes represent exons. Gray boxes represent introns. Introns are not drawn to scale.</p> <p>(<b>B</b>) Probe design of exon arrays.</p> <p>Exon arrays have four probes targeting each exon of the gene.</p> <p>(<b>C</b>) Probe design of 3′ expression arrays.</p> <p>Probes on 3′ expression arrays target 3′ end of the mRNA sequence.</p></div

Heatmap visualization of exon array pairwise probe correlations.

<div><p>(<b>A</b>) Heatmap visualization of probe intensities of HLA-DMB (transcript cluster 2950263).</p> <p>Each cell of the heatmap shows the correlation of two probes in 11 tissues.</p> <p>The top color bar indicates the probe type.</p> <p>Core probes are colored in red.</p> <p>Extended probes are colored in blue.</p> <p>The signal intensities of core probes usually have a high correlation (the top right corner of the heatmap).</p> <p>(<b>B</b>) Heatmap visualization of probe intensities of core probes in CD44 (transcript cluster 3326635).</p> <p>Probes targeting the 5′ and 3′ regions (constitutive exons) of CD44 show highly correlated signals in 11 tissues (the top right corner of the heatmap).</p> <p>(<b>C</b>) Heatmap visualization of probe intensities of core probes in CD44 (transcript cluster 3326635).</p> <p>Probes are ordered from top to bottom based on their genomic coordinates (5′ to 3′).</p></div

The impact of gene expression levels on probe selection.

<div><p>We grouped 17056 transcript clusters into ten distinct bins according to the height where we cut the clustering dendrogram (<i>h_final</i>).</p> <p>For each transcript cluster, we calculated its peak gene expression index in the 11 tissues using selected probes.</p> <p>Then we took an average for each bin.</p> <p>The values of tree cutoff (X-axis) were negatively correlated with average peak gene expression levels in the 11 tissues (Y-axis).</p></div

Low-temperature SCR NO_x removal experimental apparatus.

<p>Low-temperature SCR NO_x removal experimental apparatus.</p

Influence of different reaction temperatures on three preparation methods.

<p>Influence of different reaction temperatures on three preparation methods.</p