The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes

Circoviruses (family Circoviridae) are small, non-enveloped viruses that have short, single-stranded DNA genomes. Circovirus sequences are frequently recovered in metagenomic investigations, indicating that these viruses are widespread, yet they remain relatively poorly understood. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in vertebrate genomes. CVe are a useful source of information about the biology and evolution of circoviruses. In this study, we screened 362 vertebrate genome assemblies in silico to generate a catalog of CVe loci. We identified a total of 179 CVe sequences, most of which have not been reported previously. We show that these CVe loci reflect at least 19 distinct germline integration events. We determine the structure of CVe loci, identifying some that show evidence of potential functionalization. We also identify orthologous copies of CVe in snakes, fish, birds, and mammals, allowing us to add new calibrations to the timeline of circovirus evolution. Finally, we observed that some ancient CVe group robustly with contemporary circoviruses in phylogenies, with all sequences within these groups being derived from the same host class or order, implying a hitherto underappreciated stability in circovirus-host relationships. The openly available dataset constructed in this investigation provides new insights into circovirus evolution, and can be used to facilitate further studies of circoviruses and CVe

Insights into circovirus host range from the genomic fossil record

A diverse range of DNA sequences derived from circoviruses (family Circoviridae) have been identified in samples obtained from humans and domestic animals, often in association with pathological conditions. In the majority of cases, however, little is known about the natural biology of the viruses from which these sequences are derived. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in animal genomes and provide a useful source of information about circovirus-host relationships. In this study we screened genome assemblies of 675 animal species and identified numerous circovirus-related sequences, including the first examples of CVe derived from cycloviruses. We confirmed the presence of these CVe in the germline of the elongate twig ant (Pseudomyrmex gracilis), thereby establishing that cycloviruses infect insects. We examined the evolutionary relationships between CVe and contemporary circoviruses, showing that CVe from ants and mites group relatively closely with cycloviruses in phylogenies. Furthermore, the relatively random interspersal of CVe from insect genomes with cyclovirus sequences recovered from vertebrate samples, suggested that contamination might be an important consideration in studies reporting these viruses. Our study demonstrates how endogenous viral sequences can inform metagenomics-based virus discovery. In addition, it raises doubts about the role of cycloviruses as pathogens of humans and other vertebrates

Evolution of the pairing pseudogap in the spectral function with interplane anisotropy

We study the pairing pseudogap in the spectral function as a function of interplane coupling. The analytical expressions for the self-energy in the critical regime are obtained for any degree of anisotropy. The frequency dependence of the self-energy is found to be qualitatively different in two and three dimensions, and the crossover from two to three dimensional behavior is discussed. In particular, by considering the anisotropy of the Fermi velocity and gap along the Fermi surface, we can qualitatively explain recent photoemission experiments on high temperature superconductors concerning the temperature dependent Fermi arcs seen in the pseudogap phase.Comment: 20 pages, revtex, 5 encapsulated postscript figures include

Stability of metallic stripes in the extended one-band Hubbard model

Based on an unrestricted Gutzwiller approximation (GA) we investigate the stripe orientation and periodicity in an extended one-band Hubbard model. A negative ratio between next-nearest and nearest neighbor hopping t'/t, as appropriate for cuprates, favors partially filled (metallic) stripes for both vertical and diagonal configurations. At around optimal doping diagonal stripes, site centered (SC) and bond centered (BC) vertical stripes become degenerate suggesting strong lateral and orientational fluctuations. We find that within the GA the resulting phase diagram is in agreement with experiment whereas it is not in the Hartree-Fock approximation due to a strong overestimation of the stripe filling. Results are in agreement with previous calculations within the three-band Hubbard model but with the role of SC and BC stripes interchanged.Comment: 10 pages, 8 figure

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

The underlying causes of military outsourcing in the USA and UK: bridging the persistent gap between ends, ways and means since the beginning of the Cold War

This article reappraises the two most-studied country cases of military outsourcing: the USA and the UK. It argues that the contemporary wave of military contracting stretches back to the beginning of the cold war and not only to the demobilisation of armies in the 1990s or the neoliberal reforms introduced since the 1980s. It traces the political, technological and ideational developments that laid the groundwork for these reforms and practices since the early cold war and account for its endurance today. Importantly, it argues that a persistent gap between strategic objectives and resources, i.e. the challenge to reconcile ends and means, is an underlying driver of military contracting in both countries. Contemporary contracting is thus most closely tied to military support functions in support of wider foreign and defence political objectives. Security services in either state may not have been outsourced so swiftly, if at all, without decades of experience in outsourcing military logistics functions and the resultant vehicles, processes and familiarities with public-private partnerships. The article thus provides a wider and deeper understanding of the drivers of contractualisation, thereby improving our understanding of both its historical trajectory and the determinants of its present and potential futures

Epithelial IL-6 trans-signaling defines a new asthma phenotype with increased airway inflammation

Background: Although several studies link high levels of IL-6 and soluble IL-6 receptor (sIL-6R) to asthma severity and decreased lung function, the role of IL-6 trans-signaling (IL-6TS) in asthmatic patients is unclear. Objective: We sought to explore the association between epithelial IL-6TS pathway activation and molecular and clinical phenotypes in asthmatic patients. Methods: An IL-6TS gene signature obtained from air-liquid interface cultures of human bronchial epithelial cells stimulated with IL-6 and sIL-6R was used to stratify lung epithelial transcriptomic data (Unbiased Biomarkers in Prediction of Respiratory Disease Outcomes [U-BIOPRED] cohorts) by means of hierarchical clustering. IL-6TS-specific protein markers were used to stratify sputum biomarker data (Wessex cohort). Molecular phenotyping was based on transcriptional profiling of epithelial brushings, pathway analysis, and immunohistochemical analysis of bronchial biopsy specimens. Results: Activation of IL-6TS in air-liquid interface cultures reduced epithelial integrity and induced a specific gene signature enriched in genes associated with airway remodeling. The IL-6TS signature identified a subset of patients with IL-6TS-high asthma with increased epithelial expression of IL-6TS-inducible genes in the absence of systemic inflammation. The IL-6TS-high subset had an overrepresentation of frequent exacerbators, blood eosinophilia, and submucosal infiltration of T cells and macrophages. In bronchial brushings Toll-like receptor pathway genes were upregulated, whereas expression of cell junction genes was reduced. Sputum sIL-6R and IL-6 levels correlated with sputum markers of remodeling and innate immune activation, in particular YKL-40, matrix metalloproteinase 3, macrophage inflammatory protein 1 beta, IL-8, and IL-1 beta. Conclusions: Local lung epithelial IL-6TS activation in the absence of type 2 airway inflammation defines a novel subset of asthmatic patients and might drive airway inflammation and epithelial dysfunction in these patients.Peer reviewe

Voices of the Governed: towards a theory of the translocal

In this article I want to interrogate the political, economic, and social conditions that enable the extraction of natural and mineral resources from Indigenous and rural communities in Africa, the Americas, and the Asia-Pacific. The end of direct colonialism and the emergence of the development state did not necessarily translate into forms of local sovereignty for these communities who bore the brunt of development. I describe the emergence of resource wars in the postcolonial era and how organizational technologies of extraction, exclusion and expulsion lead to dispossession and death. I conclude by discussing possibilities of resistance and develop the notion of translocal resistance where local actors most affected by development are able to forge a series of temporary coalitions with international and national groups in an attempt to promote some form of participatory democracy. The article advance debates on postcolonialism by developing theoretical insights from translocal modes of resistance that open up new analytical spaces marked by particular configurations of market, state and civil society actors

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy