Using BUSCO to Assess Insect Genomic Resources

The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships amongst different species or orders and to build ‘omics’ resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of critical importance to understanding the potential limitations on the types of questions that these data can be reliably used to address. This chapter details the use of the Benchmarking Universal Single-Copy Orthologue (BUSCO) assessment tool to estimate the completeness of transcriptomes, genome assemblies, and annotated gene sets in terms of their expected gene content

Diminished macrophage apoptosis and reactive oxygen species generation after phorbol ester stimulation in Crohn's disease.

BACKGROUND: Crohn's Disease (CD) is a chronic relapsing disorder characterized by granulomatous inflammation of the gastrointestinal tract. Although its pathogenesis is complex, we have recently shown that CD patients have a systemic defect in macrophage function, which results in the defective clearance of bacteria from inflammatory sites. METHODOLOGY/PRINCIPAL FINDINGS: Here we have identified a number of additional macrophage defects in CD following diacylglycerol (DAG) homolog phorbol-12-myristate-13-acetate (PMA) activation. We provide evidence for decreased DNA fragmentation, reduced mitochondrial membrane depolarization, impaired reactive oxygen species production, diminished cytochrome c release and increased IL-6 production compared to healthy subjects after PMA exposure. The observed macrophage defects in CD were stimulus-specific, as normal responses were observed following p53 activation and endoplasmic reticulum stress. CONCLUSION: These findings add to a growing body of evidence highlighting disordered macrophage function in CD and, given their pivotal role in orchestrating inflammatory responses, defective apoptosis could potentially contribute to the pathogenesis of CD

Loss of susceptibility as a novel breeding strategy for durable and broad-spectrum resistance

Recent studies on plant immunity have suggested that a pathogen should suppress induced plant defense in order to infect a plant species, which otherwise would have been a nonhost to the pathogen. For this purpose, pathogens exploit effector molecules to interfere with different layers of plant defense responses. In this review, we summarize the latest findings on plant factors that are activated by pathogen effectors to suppress plant immunity. By looking from a different point of view into host and nonhost resistance, we propose a novel breeding strategy: disabling plant disease susceptibility genes (S-genes) to achieve durable and broad-spectrum resistance

Combination of searches for heavy spin-1 resonances using 139 fb−1 of proton-proton collision data at s = 13 TeV with the ATLAS detector

A combination of searches for new heavy spin-1 resonances decaying into different pairings of W, Z, or Higgs bosons, as well as directly into leptons or quarks, is presented. The data sample used corresponds to 139 fb−1 of proton-proton collisions at = 13 TeV collected during 2015–2018 with the ATLAS detector at the CERN Large Hadron Collider. Analyses selecting quark pairs (qq, bb, , and tb) or third-generation leptons (τν and ττ) are included in this kind of combination for the first time. A simplified model predicting a spin-1 heavy vector-boson triplet is used. Cross-section limits are set at the 95% confidence level and are compared with predictions for the benchmark model. These limits are also expressed in terms of constraints on couplings of the heavy vector-boson triplet to quarks, leptons, and the Higgs boson. The complementarity of the various analyses increases the sensitivity to new physics, and the resulting constraints are stronger than those from any individual analysis considered. The data exclude a heavy vector-boson triplet with mass below 5.8 TeV in a weakly coupled scenario, below 4.4 TeV in a strongly coupled scenario, and up to 1.5 TeV in the case of production via vector-boson fusion

Accuracy versus precision in boosted top tagging with the ATLAS detector

Abstract The identification of top quark decays where the top quark has a large momentum transverse to the beam axis, known as top tagging, is a crucial component in many measurements of Standard Model processes and searches for beyond the Standard Model physics at the Large Hadron Collider. Machine learning techniques have improved the performance of top tagging algorithms, but the size of the systematic uncertainties for all proposed algorithms has not been systematically studied. This paper presents the performance of several machine learning based top tagging algorithms on a dataset constructed from simulated proton-proton collision events measured with the ATLAS detector at √ s = 13 TeV. The systematic uncertainties associated with these algorithms are estimated through an approximate procedure that is not meant to be used in a physics analysis, but is appropriate for the level of precision required for this study. The most performant algorithms are found to have the largest uncertainties, motivating the development of methods to reduce these uncertainties without compromising performance. To enable such efforts in the wider scientific community, the datasets used in this paper are made publicly available.</jats:p

Parasitoid complex of diamondback moth in south-east Queensland: first records of Oomyzus sokolowskii (Hymenoptera : Eulophidae) in Australia

Surveys for parasitoids attacking larvae and pupae of Plutella xylostella L. (Lepidoptera: Plutellidae) were conducted in the Brassica agro-ecosystem of the Lockyer valley, south-east Queensland between 1999 and 2002. Parasitised hosts were collected from infested plants placed in Brassica crops during the growing season (February-October) and from the natural P. xylostella population on the common weed Rapistrum rugosum L. (Brassicaceae) during the summer production break (November-January). Five species of primary parasitoids were recorded and they ranked in order of abundance: Diadegma semiclausum Hellen (Hymenoptera: Ichneumonidae) > Diadromus collaris Gravenhorst (Hymenoptera: Ichneumonidae) = Apanteles ippeus Nixon (Hymenoptera: Braconidae) > Brachymeria phya Walker (Hymenoptera: Chalcididae) = Oomyzus sokolowskii Kurdjumov (Hymenoptera: Eulophidae). In crops, parasitoids were reared from 23 of the 30 P. xylostella cohorts studied; D. semiclausum was collected at 21 sites, O. sokolowskii at eight sites, D. collaris at six sites, A. ippeus at three sites and B. phya at a single site. The incidence and abundance of hosts parasitised by D. semiclausum increased markedly in winter and early spring months and parasitism rates as high as 95% were recorded. Diadromus collaris and O. sokolowskii were recovered at low levels throughout 2000 and 2001 but parasitism rates never exceeded 11% or 8%, respectively. Parasitism rates are compared with other mortality factors and the contribution that each species of parasitoid makes to the biological control of the pest in the region is considered. Oomyzus sokolowskii has also been reared from P. xylostella collected in Tasmania and Western Australia. This study is the first report of the incidence O. sokolowskii in Australia; however, its wide distribution indicates that its establishment is not a recent event