This study was designed as a replication and extension of the classic study of vowel acoustics by Peterson and Barney (PB) [J. Acoust. Soc. Am. 24, 175–184 (1952)]. Recordings were made of 50 men, 50 women, and 50 children producing the vowels /i, i, eh, æ, hooked backward eh, inverted vee), a, open oh, u, u/ in h–V–d syllables. Formant contours for F1–F4 were measured from LPC spectra using a custom interactive editing tool. For comparison with the PB data, formant patterns were sampled at a time that was judged by visual inspection to be maximally steady. Preliminary analysis shows numerous differences between the present data and those of PB, both in terms of average formant frequencies for vowels, and the degree of overlap among adjacent vowels. As with the original study, listening tests showed that the signals were nearly always identified as the vowel intended by the talker.

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Whole exome sequencing by high-throughput sequencing of target-enriched genomic DNA (exome-seq) has become common in basic and translational research as a means of interrogating the interpretable part of the human genome at relatively low cost. Presented here is a comparison of three major commercial exome sequencing platforms from Agilent, Illumina and Nimblegen applied to the same human blood sample. The Nimblegen platform, which is the only one to use high-density overlapping baits, provides increased efficiency of enrichment and sensitivity for detecting variants but covers fewer genomic regions than the other platforms. As a result, Nimblegen requires the least amount of sequencing to sensitively detect small variants, but Agilent and Illumina are able to detect a greater total number of variants with additional sequencing. Illumina in particular captures the untranslated regions, which are missing from the Nimblegen and Agilent platforms. Exome sequencing and whole genome sequencing (WGS) of the same sample were also compared, demonstrating that exome-seq allows for the detection of additional small variants missed by WGS. These data suggest that WGS experiments benefit from being supplemented with targeted exome-seq data. This study serves to assist the community in selecting the optimal exome-seq platform for their experiments, as well as proving that exome-seq is capable of identifying important coding variations that are missed by a typical WGS experiment.

Oxidized phospholipids are thought to promote atherogenesis by stimulating endothelial cells (ECs) to produce inflammatory cytokines, such as IL-8. In studies with mouse models, we previously demonstrated that genetic variation in inflammatory responses of endothelial cells to oxidized lipids contributes importantly to atherosclerosis susceptibility. We now show that similar variations occur in cultured aortic ECs derived from multiple heart transplant donors. These variations were stably maintained between passages and, thus, reflect either genetic or epigenetic regulatory differences. Expression array analysis of aortic EC cultures derived from 12 individuals revealed that >1,000 genes were regulated by oxidized phospholipids. We have used the observed variations in the sampled population to construct a gene coexpression network comprised of 15 modules of highly connected genes. We show that several identified modules are significantly enriched in genes for known pathways and confirm a module enriched for unfolded protein response (UPR) genes using siRNA and the UPR inducer tunicamycin. On the basis of the constructed network, we predicted that a gene of unknown function (MGC4504) present in the UPR module is a target for UPR transcriptional activator ATF4. Our data also indicate that IL-8 is present in the UPR module and is regulated, in part, by the UPR. We validate these by using siRNA. In conclusion, we show that interindividual variability can be used to group genes into pathways and predict gene-gene regulatory relationships, thus identifying targets potentially involved in susceptibility to common diseases such as atherosclerosis.genetic ͉ interleukin 8 ͉ atherosclerosis ͉ unfolded protein response ͉ network A therosclerosis, the major cause of heart disease, is characterized by the accumulation of cholesterol, inflammatory cells, smooth muscle cells, and fibrous elements beneath the endothelial cell (EC) monolayer that lines the artery wall (1). Although numerous risk factors for atherosclerosis, such as elevated blood pressure, hypercholesterolemia, and smoking, have been recognized, these factors do not alone account for the genetic contribution to risk (2). An important mechanism contributing to the recruitment of inflammatory cells in atherosclerosis is the induction of adhesion molecules, growth factors, and cytokines in vascular ECs by oxidized phospholipids, such as oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycero-phosphorylcholine (oxPAPC) derived from lipoproteins trapped in the vessel wall (3).We have previously demonstrated that ECs from different strains of mice show differences in the induction of inflammatory genes when treated with oxidized lipoproteins, and that these differences segregate with susceptibility to atherosclerosis (4, 5). Studies in human populations show significant variability in the plasma levels of inflammatory mediators associated with atherosclerosis, including IL-8 and C-reactive protein (6-8). The plasma levels of cytokines are influenced by genetic and environmenta...

Objective-Oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycero-phosphorylcholine (oxPAPC) accumulates in atherosclerotic lesions and in vitro studies suggest that it mediates chronic inflammatory response in endothelial cells (ECs). The goal of our studies was to identify pathways mediating the induction of inflammatory genes by oxPAPC. Methods and Results-Using expression arrays, quantitative polymerase chain reaction (PCR), and immunoblotting we demonstrate that oxPAPC leads to endoplasmic reticulum stress and activation of the unfolded protein response (UPR) in human aortic ECs. Immunohistochemistry analysis of human atherosclerotic lesions indicated that UPR is induced in areas containing oxidized phospholipids. Using the UPR inducing agent tunicamycin and selective siRNA targeting of the ATF4 and XBP1 branches of the UPR, we demonstrate that these transcription factors are essential mediators of IL8, IL6, and MCP1 expression in human aortic ECs required for maximal inflammatory gene expression in the basal state and after oxPAPC treatment. We also identify a novel oxPAPC-induced chemokine, the CXC motif ligand 3 (CXCL3), and show that its expression requires XBP1. Conclusions-These

Genetic screens for dominant second-site mutations that suppress the lethality of Abl mutations in Drosophila identified alleles of only one gene, enabled (ena). We report that the ena protein contains proline-rich motifs and binds to Abl and Src SH3 domains, ena is also a substrate for the Abl kinase; tyrosine phosphorylation of ena is increased when it is coexpressed in cells with human or Drosophila Abl and endogenous ena tyrosine phosphorylation is reduced in Abl mutant animals. Like Abl, ena is expressed at highest levels in the axons of the embryonic nervous system and ena mutant embryos have defects in axonal architecture. We conclude that a critical function of Drosophila Abl is to phosphorylate and negatively regulate ena protein during neural development.

Whole-genome sequencing is becoming commonplace, but the accuracy and completeness of variant calling by the most widely used platforms from Illumina and Complete Genomics have not been reported. Here we sequenced the genome of an individual with both technologies to a high average coverage of ~76×, and compared their performance with respect to sequence coverage and calling of single-nucleotide variants (SNVs), insertions and deletions (indels). Although 88.1% of the ~3.7 million unique SNVs were concordant between platforms, there were tens of thousands of platform-specific calls located in genes and other genomic regions. In contrast, 26.5% of indels were concordant between platforms. Target enrichment validated 92.7% of the concordant SNVs, whereas validation by genotyping array revealed a sensitivity of 99.3%. The validation experiments also suggested that >60% of the platform-specific variants were indeed present in the genome. Our results have important implications for understanding the accuracy and completeness of the genome sequencing platforms.

Purpose The endoplasmic reticulum-associated degradation (ERAD) pathway is responsible for the translocation of misfolded proteins across the ER membrane into the cytosol for subsequent degradation by the proteasome. In order to understand the spectrum of clinical and molecular findings in a complex neurological syndrome, we studied a series of eight patients with inherited deficiency of N-glycanase 1 (NGLY1), a novel disorder of cytosolic ERAD dysfunction. Methods Whole-genome, whole-exome or standard Sanger sequencing techniques were employed. Retrospective chart reviews were performed in order to obtain clinical data. Results All patients had global developmental delay, a movement disorder, and hypotonia. Other common findings included hypo- or alacrima (7/8), elevated liver transaminases (6/7), microcephaly (6/8), diminished reflexes (6/8), hepatocyte cytoplasmic storage material or vacuolization (5/6), and seizures (4/8). The nonsense mutation c.1201A>T (p.R401X) was the most common deleterious allele. Conclusions NGLY1 deficiency is a novel autosomal recessive disorder of the ERAD pathway associated with neurological dysfunction, abnormal tear production, and liver disease. The majority of patients detected to date carry a specific nonsense mutation that appears to be associated with severe disease. The phenotypic spectrum is likely to enlarge as cases with a more broad range of mutations are detected.