Autozygome Sequencing Expands the Horizon of Human Knockout Research and Provides Novel Insights into Human Phenotypic Variation

<div><p>The use of autozygosity as a mapping tool in the search for autosomal recessive disease genes is well established. We hypothesized that autozygosity not only unmasks the recessiveness of disease causing variants, but can also reveal natural knockouts of genes with less obvious phenotypic consequences. To test this hypothesis, we exome sequenced 77 well phenotyped individuals born to first cousin parents in search of genes that are biallelically inactivated. Using a very conservative estimate, we show that each of these individuals carries biallelic inactivation of 22.8 genes on average. For many of the 169 genes that appear to be biallelically inactivated, available data support involvement in modulating metabolism, immunity, perception, external appearance and other phenotypic aspects, and appear therefore to contribute to human phenotypic variation. Other genes with biallelic inactivation may contribute in yet unknown mechanisms or may be on their way to conversion into pseudogenes due to true recent dispensability. We conclude that sequencing the autozygome is an efficient way to map the contribution of genes to human phenotypic variation that goes beyond the classical definition of disease.</p></div

Summary of genes with biallelic LoF (please refer to Supp. Table S2 for a full list of the LoF alleles, and to Supp. Table S4 for a full list of the reported function for each of these genes and the score of the LoF allele).

<p>Summary of genes with biallelic LoF (please refer to Supp. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004030#pgen.1004030.s004" target="_blank">Table S2</a> for a full list of the LoF alleles, and to Supp. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004030#pgen.1004030.s006" target="_blank">Table S4</a> for a full list of the reported function for each of these genes and the score of the LoF allele).</p

LoF alleles that are significantly biased (at p<0.1 using a one-tailed binomial test, see Text S1 for details) to be within the autozygome (when called at a minimum ROH cutoff of 2MB) are rarer compared to alleles biased to be outside of the autozygome.

<p>The boxes and whiskers represent allele frequency distributions as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004030#pgen-1004030-g001" target="_blank">Fig. 1</a>. The two groups have a significantly different median at p<0.0005 (Mann-Whitney non parametric test).</p

Longer ROHs are more enriched for homozygous LoFs.

<p>Solid line: Percentage of LoFs found within an ROH of indicated length or longer. Dashed line: Percentage of autosomal genome bases included (on average) in ROHs at the indicated length or longer. Dotted line: Percentage of gain in LoF recovery compared to genomic coverage at the indicated ROH length or longer (the percent ratio of the two curves minus one).</p

Allele frequency distribution according to mutation type.

<p>Each box represents the 25^th to 75^th percentiles, with the median shown as a line and the mean as a cross. The whiskers represent the 5^th and 95^th percentiles. Non-parametric ANOVA (Kruskal-Wallis test) indicates significant differences in the group medians at p<0.0001 and all pairwise median comparisons were also significant (p<0.0001, Mann-Whitney non parametric test), except for frameshift vs. nonsense.</p

In Vitro Antioxidant, Cytotoxic Activities, and Phenolic Profile of Senecio glaucus from Saudi Arabia

Current treatments for complex diseases have remarkable side effects that negatively impact patients’ quality of life. Thus, natural compounds with fewer side effects represent a promising source for safe drugs. The genus Senecio is widely used in folk medicine due to its various pharmacological properties. In the present study, the total phenolic content of Senecio glaucus, which is grown in Saudi Arabia, was assessed using the Folin-Ciocalteau colorimetric method. Scavenging DPPH and ABTS assays were utilized to determine the antioxidant properties of S. glaucus fractions, and MTT assay was used to screen the cytotoxic activity of S. glaucus against various cancer cells. In addition, HPLC-UV was utilized to detect the presence of two phenolic acids, namely, vanillic acid (VA) and gallic acid (GA). Among all fractions tested, S. glaucus chloroform fraction (SGCF) yielded the highest value (125.3 mg·GA/g) in terms of total phenolic content. SGCF also exhibited the highest scavenging activities (76.7 and 74.1%) on both DPPH and ABTS assays, respectively. Similarly, SGCF also possessed the most potent cytotoxic activity against the MCF-7 cell line, with an IC50 value of 41.8 μg/ml. The validated HPLC method confirmed the presence of VA (4.8 μg/mg DW) and GA (3.9 μg/mg DW) in SGCF. Overall, our data show that S. glaucus had antioxidant and cytotoxic properties. A developed validated HPLC method which could be helpful for quantifying phenolic compounds in S. glaucus was established

Cichorins D–F: Three New Compounds from Cichorium intybus and Their Biological Effects

Cichorium intybus L., (chicory) is employed in various traditional medicines to treat a wide range of diseases and disorders. In the current investigation, two new naphthalane derivatives viz., cichorins D (1) and E (2), along with one new anthraquinone cichorin F (3), were isolated from Cichorium intybus. In addition, three previously reported compounds viz., &beta;-sitosterol (4), &beta;-sitosterol &beta;-glucopyranoside (5), and stigmasterol (6) were also isolated from Cichorium intybus. Their structures were established via extensive spectroscopic data, including 1D (1H and 13C) and 2D NMR (COSY, HSQC and HMBC), and ESIMS. Cichorin E (2) has a weak cytotoxic effect on breast cancer cells (MDA-MB-468: IC50: 85.9 &micro;M) and Ewing&rsquo;s sarcoma cells (SK-N-MC: IC50: 71.1 &micro;M); cichorin F (3) also illustrated weak cytotoxic effects on breast cancer cells (MDA-MB-468: IC50: 41.0 &micro;M and MDA-MB-231: IC50: 45.6 &micro;M), and SK-N-MC cells (IC50: 71.9 &micro;M). Moreover compounds 1&ndash;3 did not show any promising anthelmintic effects