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WES Coding Mutations

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Drug Resistant POS Cells Emerge Following Chronic Trametinib Treatment.

Triple-negative breast cancers contain a spectrum of epithelial and mesenchymal phenotypes. SUM-229PE cells represent a model for this heterogeneity, maintaining both epithelial and mesenchymal subpopulations that are genomically similar but distinct in gene expression profiles. We identified differential regions of open chromatin in epithelial and mesenchymal cells that were strongly correlated with regions of H3K27ac. Motif analysis of these regions identified consensus sequences for transcription factors that regulate cell identity. Treatment with the MEK inhibitor trametinib induced enhancer remodeling that is associated with transcriptional regulation of genes in epithelial and mesenchymal cells. Motif analysis of enhancer peaks downregulated in response to chronic treatment with trametinib identified AP-1 motif enrichment in both epithelial and mesenchymal subpopulations. Chromatin immunoprecipitation sequencing (ChIP-seq) of JUNB identified subpopulation-specific localization, which was significantly enriched at regions of open chromatin. These results indicate that cell identity controls localization of transcription factors and chromatin-modifying enzymes to enhancers for differential control of gene expression. We identified increased H3K27ac at an enhancer region proximal to CXCR7, a G-protein–coupled receptor that increased 15-fold in expression in the epithelial subpopulation during chronic treatment. RNAi knockdown of CXCR7 inhibited proliferation in trametinib-resistant cells. Thus, adaptive resistance to chronic trametinib treatment contributes to proliferation in the presence of the drug. Acquired amplification of KRAS following trametinib dose escalation further contributed to POS cell proliferation. Adaptive followed by acquired gene expression changes contributed to proliferation in trametinib-resistant cells, suggesting inhibition of early transcriptional reprogramming could prevent resistance and the bypass of targeted therapy.Implications:We defined the differential responses to trametinib in subpopulations of a clinically relevant in vitro model of TNBC, and identified both adaptive and acquired elements that contribute to the emergence of drug resistance mediated by increased expression of CXCR7 and amplification of KRAS.

Chromosomal translocations generate oncogenic fusion proteins in approximately one-third of sarcomas, but how these proteins promote tumorigenesis is not well understood. Interestingly, some translocation-driven cancers exhibit dramatic clinical responses to therapy, such as radiotherapy, although the precise mechanism has not been elucidated. Here we reveal a molecular mechanism by which the fusion oncoprotein FUS-CHOP promotes tumor maintenance that also explains the remarkable sensitivity of myxoid liposarcomas to radiation therapy. FUS-CHOP interacted with chromatin remodeling complexes to regulate sarcoma cell proliferation. One of these chromatin remodelers, SNF2H, colocalized with FUS-CHOP genome-wide at active enhancers. Following ionizing radiation, DNA damage response kinases phosphorylated the prion-like domain of FUS-CHOP to impede these protein–protein interactions, which are required for transformation. Therefore, the DNA damage response after irradiation disrupted oncogenic targeting of chromatin remodelers required for FUS-CHOP–driven sarcomagenesis. This mechanism of disruption links phosphorylation of the prion-like domain of an oncogenic fusion protein to DNA damage after ionizing radiation and reveals that a dependence on oncogenic chromatin remodeling underlies sensitivity to radiation therapy in myxoid liposarcoma.Significance:Prion-like domains, which are frequently translocated in cancers as oncogenic fusion proteins that drive global epigenetic changes, confer sensitivity to radiation via disruption of oncogenic interactions.

Supplementary data figures, tables, and methods.

Ewing sarcoma is a cancer of children and young adults characterized by the critical translocation-associated fusion oncoprotein EWSR1::FLI1. EWSR1::FLI1 targets characteristic genetic loci where it mediates aberrant chromatin and the establishment of de novo enhancers. Ewing sarcoma thus provides a model to interrogate mechanisms underlying chromatin dysregulation in tumorigenesis. Previously, we developed a high-throughput chromatin-based screening platform based on the de novo enhancers and demonstrated its utility in identifying small molecules capable of altering chromatin accessibility. Here, we report the identification of MS0621, a molecule with previously uncharacterized mechanism of action, as a small molecule modulator of chromatin state at sites of aberrant chromatin accessibility at EWSR1::FLI1-bound loci. MS0621 suppresses cellular proliferation of Ewing sarcoma cell lines by cell cycle arrest. Proteomic studies demonstrate that MS0621 associates with EWSR1::FLI1, RNA binding and splicing proteins, as well as chromatin regulatory proteins. Surprisingly, interactions with chromatin and many RNA-binding proteins, including EWSR1::FLI1 and its known interactors, were RNA-independent. Our findings suggest that MS0621 affects EWSR1::FLI1-mediated chromatin activity by interacting with and altering the activity of RNA splicing machinery and chromatin modulating factors. Genetic modulation of these proteins similarly inhibits proliferation and alters chromatin in Ewing sarcoma cells. The use of an oncogene-associated chromatin signature as a target allows for a direct approach to screen for unrecognized modulators of epigenetic machinery and provides a framework for using chromatin-based assays for future therapeutic discovery efforts.

A new RNA virus was discovered from a horse nettle plant using high throughput sequencing (HTS) and its full genome was characterized consisting of two molecules: RNA1 and RNA2 which are 7522 and 4710 nucleotides in length, respectively. Each molecule encodes a single open reading frame flanked by 5’ and 3’ untranslated regions (UTRs) followed by a poly(A) tail at the 3’ end. Genome organization and the phylogenetic analysis revealed its close relationship with subgroup B of nepoviruses, sharing minimal similarity with any known nepoviruses, and the recombination analysis also revealed its evolutionary history within the same subgroup. These results suggest the new virus, provisionally named as horse nettle virus A, represents a new species within the genus Nepovirus.

Chromosomal translocations generate oncogenic fusion proteins in approximately one-third of sarcomas, but how these proteins promote tumorigenesis is not well understood. Interestingly, some translocation-driven cancers exhibit dramatic clinical responses to therapy, such as radiotherapy, although the precise mechanism has not been elucidated. Here we reveal a molecular mechanism by which the fusion oncoprotein FUS-CHOP promotes tumor maintenance that also explains the remarkable sensitivity of myxoid liposarcomas to radiation therapy. FUS-CHOP interacted with chromatin remodeling complexes to regulate sarcoma cell proliferation. One of these chromatin remodelers, SNF2H, colocalized with FUS-CHOP genome-wide at active enhancers. Following ionizing radiation, DNA damage response kinases phosphorylated the prion-like domain of FUS-CHOP to impede these protein–protein interactions, which are required for transformation. Therefore, the DNA damage response after irradiation disrupted oncogenic targeting of chromatin remodelers required for FUS-CHOP–driven sarcomagenesis. This mechanism of disruption links phosphorylation of the prion-like domain of an oncogenic fusion protein to DNA damage after ionizing radiation and reveals that a dependence on oncogenic chromatin remodeling underlies sensitivity to radiation therapy in myxoid liposarcoma. Significance: Prion-like domains, which are frequently translocated in cancers as oncogenic fusion proteins that drive global epigenetic changes, confer sensitivity to radiation via disruption of oncogenic interactions.

Triple-negative breast cancers contain a spectrum of epithelial and mesenchymal phenotypes. SUM-229PE cells represent a model for this heterogeneity, maintaining both epithelial and mesenchymal subpopulations that are genomically similar but distinct in gene expression profiles. We identified differential regions of open chromatin in epithelial and mesenchymal cells that were strongly correlated with regions of H3K27ac. Motif analysis of these regions identified consensus sequences for transcription factors that regulate cell identity. Treatment with the MEK inhibitor trametinib induced enhancer remodeling that is associated with transcriptional regulation of genes in epithelial and mesenchymal cells. Motif analysis of enhancer peaks downregulated in response to chronic treatment with trametinib identified AP-1 motif enrichment in both epithelial and mesenchymal subpopulations. Chromatin immunoprecipitation sequencing (ChIP-seq) of JUNB identified subpopulation-specific localization, which was significantly enriched at regions of open chromatin. These results indicate that cell identity controls localization of transcription factors and chromatin-modifying enzymes to enhancers for differential control of gene expression. We identified increased H3K27ac at an enhancer region proximal to CXCR7, a G-protein–coupled receptor that increased 15-fold in expression in the epithelial subpopulation during chronic treatment. RNAi knockdown of CXCR7 inhibited proliferation in trametinib-resistant cells. Thus, adaptive resistance to chronic trametinib treatment contributes to proliferation in the presence of the drug. Acquired amplification of KRAS following trametinib dose escalation further contributed to POS cell proliferation. Adaptive followed by acquired gene expression changes contributed to proliferation in trametinib-resistant cells, suggesting inhibition of early transcriptional reprogramming could prevent resistance and the bypass of targeted therapy. Implications: We defined the differential responses to trametinib in subpopulations of a clinically relevant in vitro model of TNBC, and identified both adaptive and acquired elements that contribute to the emergence of drug resistance mediated by increased expression of CXCR7 and amplification of KRAS.

SummaryChromosomal translocations generate oncogenic fusion proteins in approximately one-third of sarcomas, but how these proteins promote tumorigenesis and the effect of cancer therapies on their function are not well understood. Here, we reveal a molecular mechanism by which the fusion oncoprotein FUS-CHOP promotes tumor maintenance that also explains the remarkable radiation sensitivity of myxoid liposarcomas. We identified novel interactions between FUS-CHOP and chromatin remodeling complexes that regulate sarcoma cell proliferation. One of these chromatin remodelers, SNF2H, co-localizes with FUS-CHOP genome-wide at active enhancers. Following ionizing radiation, DNA damage response kinases phosphorylate the prion-like domain of FUS-CHOP to impede these protein-protein interactions, which are required for transformation. Therefore, the DNA damage response after irradiation disrupts oncogenic targeting of chromatin remodelers required for FUS-CHOP-driven sarcomagenesis.SignificancePrion-like domains translocated in cancer have been shown to drive global epigenetic changes that are oncogenic. However, some translocation-driven cancers exhibit dramatic clinical responses to therapy, though the mechanism for these responses are not well-understood. Here we show that ionizing radiation can disrupt oncogenic interactions between a fusion oncoprotein and a chromatin remodeling complex, ISWI. This mechanism of disruption links phosphorylation of the prion-like domain in an oncogenic fusion protein to DNA damage after ionizing radiation and reveals that a dependence on oncogenic chromatin remodeling underlies sensitivity to radiation therapy in myxoid liposarcoma.

Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnostic workflow of sugarcane viruses. We evaluated the impact of sequencing depth needed for the HTS-based identification of seven regulated sugarcane RNA/DNA viruses across two different growing seasons (spring and fall). Our HTS analysis revealed that viral normalized read counts (RPKM) was up to 23-times higher in spring than in the fall season for six out of the seven viruses. Random read subsampling analyses suggested that the minimum number of reads required for reliable detection of RNA viruses was 0.5 million, with a viral genome coverage of at least 92%. Using an HTS-based total RNA metagenomics approach, we identified all targeted viruses independent of the time of the year, highlighting that higher sequencing depth is needed for the identification of DNA viruses.

Though hematopoietic stem cell transplantation (HSCT) is the preferred treatment for a variety of blood malignancies, its use is limited by the development of acute graft-versus-host disease (aGvHD). Type II innate lymphoid cells (ILC2s) are immune cells that play an important role in maintaining mucosal homeostasis, and our lab has previously shown that ILC2s in the gastrointestinal tract (GI) are sensitive to conditioning therapy prior to HSCT. Strikingly, we have demonstrated that the infusion of activated donor ILC2s markedly reduces aGvHD-associated mortality. We therefore wanted to investigate the mechanism of the loss of protective ILC2s from the GI tract. We hypothesized that ILC2s fail to repopulate the gut after HSCT due to inflammatory environmental cues that convert ILC2 precursors to an alternate, ILC1- or ILC3-like fate. Thus, we evaluated the impact of cytokines associated with commitment on murine ILC2s by exposing them to cytokines that may promote differentiation to an ILC1 or ILC3 fate (IL-1b/IL-12/IFN-γ and TGF-b/IL-6/IL-23, respectively). We found ILC2 cells acquired the ability to secrete TNF and IL-17 after in vitro skewing (with these lineage-defining cytokines. To test the ability of these "ex-ILC2" cells to home to other tissues in vivo, GFP-ILC2s were infused into recipients at the time of transplantation. We tracked GFP-ILC2s to the liver and spleen, where they made IFN-g and IL-17 and expressed transcription factors associated with the ILC1 and ILC3 lineages (Figure 1). Next we assessed the ability of cytokines alter ILC2 fate via epigenetic reprogramming by using ChIP-sequencing to evaluate the presence of histone marks that may underlie cellular plasticity. We show that these changes are associated with alterations in epigenetic marks around pioneer, lineage-determining factors. We therefore chose to test a screen of compounds known to modulate a variety of epigenetic targets to ask if they can maintain or convert ILC2s to alternate fates and identified a number of compounds that target bromodomains, methyltransferases, and histonedeacetylases, respectively, that alter the viability and differentiation of ILC2s into an "ex-ILC2"-like phenotype. Preliminary work suggests that maintenance ofG9a expression is able to rescue the loss of ILC2s, which is being tested in vivo. Taken together, these data provide new insights into mechanisms by which innate lymphoid cell precursors are epigenetically regulated, providing novel approaches to treating aGvHD following HSCT. Figure 1 Disclosures Davis: Triangle Biotechnology: Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Pattenden:Triangle Biotechnology, Inc.: Equity Ownership, Other: Inventor on intellectual property. Serody:Merck: Research Funding; GlaxoSmithKline: Research Funding.

Background The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platform is designed to produce actionable mutation calls in archival material. Methods We compared calls made using the OncoScan platform with calls made using a custom designed PCR panel followed by next-generation sequencing (NGS), in order to benchmark the sensitivity and specificity of the OncoScan calls in a large cohort of fixed tumour samples. 392 fixed, clinical samples were sequenced, encompassing 641 PCR regions, 403 putative positive calls and 1528 putative negative calls. Results A small number of mutations could not be validated, either due to large indels or pseudogenes impairing parts of the NGS pipeline. For the remainder, if calls were filtered according to simple quality metrics, both sensitivity and specificity for the OncoScan platform were over 98%. This applied even to samples with poorer sample quality and lower variant allele frequency (5–10%) than product claims indicated. Conclusions This benchmarking study will be useful to users and potential users of this platform, who wish to compare technologies or interpret their own results. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0254-5) contains supplementary material, which is available to authorized users.

The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of the most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, developed by the National Center for Biotechnology Information (NCBI) as a sibling resource to PRIDE, was discontinued due to funding constraints in April 2011. A joint effort between the two teams was started soon after the Peptidome closure to ensure that data were not "lost" to the wider proteomics community by exporting it to PRIDE. As a result, data in the low terabyte range have been migrated from Peptidome to PRIDE and made publicly available under experiment accessions 17 900-18 271, representing 54 projects, ~53 million mass spectra, ~10 million peptide identifications, ~650,000 protein identifications, ~1.1 million biologically relevant protein modifications, and 28 species, from more than 30 different labs.

From Liberty to Liberality: The Transformation of the Pennsylvania Legislature, 1776-1820. By Antony Joseph. (Lanham, MD: Lexington, 2012. Pp. 220. Cloth $65.00.)Reviewed by Joseph S. FosterAnthony Joseph challenges early American historians with a new perspective on the period in which Americans went from Revolution to the nascent stages of American capitalism. He rejects the contention that capitalism guided Americans toward developing the public good through the pursuit of private interest; rather, he espouses the idea of liberality, a "generous, rational, broadminded, and moderate" set of principles that had their foundation in the birth of republicanism in 1776, and that influenced Americans to harmonize "the interests of private individuals to produce the good of all" (6).Joseph traces the traditional historiographical interpretations of the late eighteenth and early nineteenth centuries, beginning with Louis Hartz, who depicted a middling class that pursued its own interests after the war without interference from the state. This view was challenged by later historians, who suggested the emergence of a Revolutionary era "republicanism" that was "profoundly communal and state-conscious." That latter paradigm valued the protection of the individual from tyranny as its supreme responsibility. Joseph writes, however, that historians agree that republicanism was eased out of its place in American political culture and replaced with an emerging classical liberalism that stressed an individualistic, market-driven society where state and national legislatures became arenas for "clashing interests." That particular school of thought, however, had competition from historians who posited that classical liberalism, which emphasized individualism, private property, and natural rights existing independent of any government, was always the driving force behind early American political and social development. That would link the Revolutionary era and the early National period to such eighteenth-century thinkers as Adam Smith and to the early nineteenth-century Jeffersonians. Joseph finally focuses on Gordon Wood, one of the architects of the republican synthesis, and argues that Wood drops the word "liberalism" in his latest work and instead describes the post-war order as a democratic middle class, which takes the interpretation full circle back to Hartz.For Joseph, however, the entire debate has missed the point as historians mistakenly conflated the essence of classical liberalism with American liberalism, the latter having found its partial origins in "liberality," itself a body of thought and behavior that emerged from republicanism, but which is distinct from that idea. Liberality, he contends, is a classical virtue that emphasizes a rational generosity that avoids extravagance and parsimony, that comprehends an issue "in its full sweep," and that is open to a broad range of possibilities. Its opposites are parochialism and "narrow mindedness" (5-6). The argument is subtle, as he hinges his thesis on the way in which Americans perceived their role in the development of their political economy. The theory of classical liberalism, according to Joseph, was not in "widespread use" until after the American Civil War, and thus was not the operating principle for early nineteenth-century Americans; rather, they perceived that their behavior reflected an emerging sense of liberality, a perception that borrowed the republican sense of economy and suspicion of any institution's ability to become abusive in its powers, and combined it with a growing willingness to have government use its authority to fund private citizens in their individual pursuits, which, in turn, promoted the public good.To substantiate his argument, Joseph examines the changing nature of the Pennsylvania state legislature from 1776 to 1820, a period in which that institution, born in the fire of republicanism, gradually transformed itself into an entity that found liberality as its central denning core. …

The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.

Urothelial bladder cancers (UBCs) have heterogeneous clinical characteristics that are mirrored in their diverse genomic profiles. Genomic profiling of UBCs has the potential to benefit routine clinical practice by providing prognostic utility above and beyond conventional clinicopathological factors, and allowing for prediction and surveillance of treatment responses. Urinary DNAs representative of the tumour genome provide a promising resource as a liquid biopsy for non-invasive genomic profiling of UBCs. We compared the genomic profiles of urinary cellular DNA and cell-free DNA (cfDNA) from the urine with matched diagnostic formalin-fixed paraffin-embedded tumour DNAs for 23 well-characterised UBC patients. Our data show urinary DNAs to be highly representative of patient tumours, allowing for detection of recurrent clinically actionable genomic aberrations. Furthermore, a greater aberrant load (indicative of tumour genome) was observed in cfDNA over cellular DNA (P

The modeling and simulation work in this grant was directed by Prof. D. Scott Stewart, (the Stewart-Group) and the experimental work and data collection was directed by Prof. Nick Glumac (the Glumac-group). Professors Stewart and Glumac and Drs. John Bdzil and Joseph C. Foster, collaborated on experimental designs, that benefited from the concurrent theoretical and computational modeling. The effort described in this report fully integrated modeling and experiments to study the energy release processes that thermitic and/or exothermic intermetallic reactive materials experience when they are subjected to sustained shock loading.

Switchgrass (Panicum virgatum L.) is a perennial bio-based economic crop used for forage, phytoremediation, as an ornamental, and as a model biomass crop with significant cellulosic biofuel potential. In May 2016, mosaic-like leaf patterns of light and dark green areas were observed on a ‘Purple Breeze’ switchgrass clone imported into the USDA-APHIS Plant Germplasm Quarantine Program facilities from the Netherlands. Symptomatic leaf tissue was collected and total RNA was extracted from pooled leaves using an RNeasy Plant Mini Kit (Qiagen, Valencia, CA). The cDNA library was constructed from ribosomal RNA-depleted extract using the TruSeq Stranded Total RNA with Ribo-Zero Plant Kit (Illumina, San Diego, CA). Next generation sequencing (NGS) was performed on an Illumina NextSeq 500 platform, resulting in 112,000,212 single-end reads, 74 bp in length on average, after adapter trimming. Reads were de novo assembled with CLC Genomics Workbench 10.1 (CLC Bio, Qiagen), of which 275,198 mapped to Barley virus G (...

Despite the fact that data deposition is not a generalised fact yet in the field of proteomics, several mass spectrometry (MS) based proteomics repositories are publicly available for the scientific community. The main existing resources are: the Global Proteome Machine Database (GPMDB), PeptideAtlas, the PRoteomics IDEntifications database (PRIDE), Tranche, and NCBI Peptidome. In this review the capabilities of each of these will be described, paying special attention to four key properties: data types stored, applicable data submission strategies, supported formats, and available data mining and visualization tools. Additionally, the data contents from model organisms will be enumerated for each resource. There are other valuable smaller and/or more specialized repositories but they will not be covered in this review. Finally, the concept behind the ProteomeXchange consortium, a collaborative effort among the main resources in the field, will be introduced., Graphical Abstract

The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 million peptides and over 50 million spectra by September 2009. We here describe several new and improved features in PRIDE, including the revised submission process, which now includes direct submission of fragment ion annotations. Correspondingly, it is now possible to visualize spectrum fragmentation annotations on tandem mass spectra, a key feature for compliance with journal data submission requirements. We also describe recent developments in the PRIDE BioMart interface, which now allows integrative queries that can join PRIDE data to a growing number of biological resources such as Reactome, Ensembl, InterPro and UniProt. This ability to perform extremely powerful across-domain queries will certainly be a cornerstone of future bioinformatics analyses. Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium., European Union (ProDaC grant LSHG-CT-2006-036814), Burroughs Wellcome Fund (Grant WT085949MA)

The essential oil of catmint, Nepeta cataria L., contains nepetalactones, that, on hydrogenation, yield the corresponding dihydronepetalactone (DHN) diastereomers. The DHN diastereomer (4R,4aR,7S,7aS)-4,7-dimethylhexahydrocyclopenta[c]pyran-1(3H)-one, DHN 1) was evaluated as mosquito repellent, as was the mixture of diastereomers {mostly (4S,4aR,7S,7aR)-4,7-dimethylhexahydrocyclopenta[c]pyran-1(3H)-one, DHN 2} present after hydrogenation of catmint oil itself. The repellency of these materials to Aedes aegypti L. and Anopheles albimanus Wiedemann mosquitoes was tested in vitro and found to be comparable to that obtained with the well-known insect repellent active ingredient N,N-diethyl-3-methylbenzamide (DEET). DHN 1 and DHN 2 also repelled the stable fly, Stomoxys calcitrans L., in this study. DHN 1, DHN 2, and p-menthane-3,8-diol (PMD), another natural monoterpenoid repellent, gave comparable levels of repellency against An. albimanus and S. calcitrans. Laboratory testing of DHN 1 and DHN 2 using human subjects with An. albimanus mosquitoes was carried out. Both DHN 1 and DHN 2 at 10% (wt:vol) conferred complete protection from bites for significant periods of time (3.5 and 5 h, respectively), with DHN2 conferring protection statistically equivalent to DEET. The DHN 1 and DHN 2 diastereomers were also efficaceous against black-legged tick (Ixodes scapularis Say) nymphs.

The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across-domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy-to-use, platform-independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium.

Background Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations. Methods In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan® formalin fixed paraffin embedded assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations. Where available, somatic mutation data was compared to data from orthogonal technologies (pyro/sanger sequencing). Results Cross site comparisons of genome-wide copy number and loss of heterozygosity profiles showed greater than 95% average agreement between sites. Somatic mutations pre-validated by orthogonal technologies showed greater than 90% agreement with OncoScan® somatic mutation calls and somatic mutation concordance between sites averaged 97%. Conclusions Reproducibility of whole-genome copy number, loss of heterozygosity and somatic mutation data using the OncoScan® assay has been demonstrated with comparatively low DNA inputs from a range of highly degraded formalin fixed paraffin embedded samples. In addition, our data shows examples of clinically-relevant aberrations that demonstrate the potential utility of the OncoScan® assay as a robust clinical tool for guiding tumour therapy. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0079-z) contains supplementary material, which is available to authorized users.

ISMS Practice Prize Competition Chairman Gary L. Lilien: "Special Section Introduction by the ISMS Practice Prize Competition Chairman"Finalists Joseph A. Foster, Peter N. Golder, Gerard J. Tellis: "Predicting Sales Takeoff for Whirlpool's New Personal Valet"John H. Roberts, Pamela D. Morrison, Charles J. Nelson: "Implementing a Prelaunch Diffusion Model: Measurement and Management Challenges of the Telstra Switching Study"

Cure cast plastic bonded explosives (PBXs) consist of relatively hard particles in a soft binder. Under compressive loading, the explosive cyrstals come into contact that causes high stress concentrations. The lines along which the crystals are loaded are called stress chains. Damage done to these particle beds during compressive loading can lead to reaction. The photoelastic effect of PMMA is exploited to examine the stress state within a two-dimensional particle bed. Stress chain development within the bed is recorded and is shown to increase the stress state within some particles while leaving others unloaded. These concentrations form early in the loading process, leading to fracture along the stress bridges and generating likely reaction initiation sites. Through material point method simulations, contact friction is shown to have a large effect on the stress distribution within the particle bed.

Simple conservation relationships (jump conditions) in conjunction with postulated material constitutive behavior are applied to steady plastic strain waves propagating in problems of uniaxial stress and Taylor Cylinder Impact. These problems are simulated with a two-dimensional Lagrangian continuum mechanics code for the purpose of numerically validating the jump relationships as an accurate analytical representation of plastic wave propagation. The constitutive behavior used in this effort assumes isotropy and models the thermodynamic response with a Mie-Grunisen Equation-of-State and the mechanical response with the rate-dependent Johnson-Cook and MTS flow stress models. The jump relationships successfully replicate the results produced by continuum code simulations of plastic wave propagation and provide a methodology for constructing mechanical constitutive models from experimental plastic wave speed information. Comparisons are also presented between experimental speeds from Taylor Cylinder Impact tests with jump relationships and continuum code predictions, indicating that the above mentioned flow stress models may not accurately capture plastic wave propagation speeds in annealed and hardened copper.

A new one-dimensional analysis of the Taylor impact test is presented. This analysis differs from any previously presented in that the wave mechanics are separated from the calculation of dynamic stress. The new results utilize post test measurements to estimate key parameters in the plastic wave propagation. However, these measurements are incorporated into the analysis in a very unconventional way. A comparison with continuum code calculations shows very good agreement has been achieved.

Correction: Whole-exome sequencing efficiently detects rare mutations in autosomal recessive nonsyndromic hearing loss. (PLoS ONE)

Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.

We characterized the "design" of explosive materials as represented by the complete suite of engineering specifications on ingredients and processes used in the manufacture of specific components used in various applications. The detonation of explosive materials and the associated high power density of this process have historically been accepted as essential elements of the design. Evolving requirements such as the desire for insensitive munitions and the broadened demands of controlling the power output are producing a new class on energetic materials whose thermo-chemical response to specific intentional trigger mechanisms result in reactive behavior far removed the classical detonation modeling represented by the physics and chemistry of Chapman-Jouguet [CJ] or Zel'dovich, VonNeuman, Doering [ZND] detonation models. Experimental studies of representative designs and analysis of the role of processes controlled by the mesostructure suggest functional paths to establishing the desired output.

PRIDE Inspector thus provides a user-friendly, comprehensive tool for the browsing, inspection, and evaluation of data in the PRIDE database, or in a compatible standard file format. As such, we believe that PRIDE Inspector will substantially increase the ability of researchers, editors and peer-reviewers to explore, review, evaluate, and reuse proteomics data. This work was supported by the Wellcome Trust (grant number WT085949MA) and EMBL core funding. R.G.C. is supported by EU FP7 grant SLING (grant number 226073). J.A.V. is supported by the EU FP7 grants LipidomicNet (grant number 202272) and ProteomeXchange (grant number 260558). A.F. was partially supported by the Spanish network COMBIOMED (RD07/0067/0006, ISCIII-FIS). L.M. would like to acknowledge support from the EU FP7 PRIME-XS grant (grant number 262067).

Condensed phase high explosives convert potential energy stored in the electro-magnetic field structure of complex molecules to high power output during the detonation process. Historically, the explosive design problem has focused on intramolecular energy storage. The molecules of interest are derived via molecular synthesis providing near stoichiometric balance on the physical scale of the molecule. This approach provides prompt reactions based on transport physics at the molecular scale. Modern material design has evolved to approaches that employ intermolecular ingredients to alter the spatial and temporal distribution of energy release. State of the art continuum methods have been used to study this approach to the materials design. Cheetah has been used to produce data for a set of fictitious explosive formulations based on C-4 to study the partitioning of the available energy between internal and kinetic energy in the detonation. The equation of state information from Cheetah has been used in ALE3D to develop an understanding of the relationship between variations in the formulation parameters and the internal energy cycle in the products.