Unraveling the effect of silent, intronic and missense mutations on VWF splicing: contribution of next generation sequencing in the study of mRNA

Large studies in von Willebrand disease patients, including Spanish and Portuguese registries, led to the identification of >250 different mutations. It is a challenge to determine the pathogenic effect of potential splice site mutations on VWF mRNA. This study aimed to elucidate the true effects of 18 mutations on VWF mRNA processing, investigate the contribution of next-generation sequencing to in vivo mRNA study in von Willebrand disease, and compare the findings with in silico prediction. RNA extracted from patient platelets and leukocytes was amplified by RT-PCR and sequenced using Sanger and next generation sequencing techniques. Eight mutations affected VWF splicing: c.1533+1G>A, c.5664+2T>C and c.546G>A (p.=) prompted exon skipping; c.3223-7_3236dup and c.7082-2A>G resulted in activation of cryptic sites; c.3379+1G>A and c.7437G>A) demonstrated both molecular pathogenic mechanisms simultaneously; and the p.Cys370Tyr missense mutation generated two aberrant transcripts. Of note, the complete effect of three mutations was provided by next generation sequencing alone because of low expression of the aberrant transcripts. In the remaining 10 mutations, no effect was elucidated in the experiments. However, the differential findings obtained in platelets and leukocytes provided substantial evidence that four of these would have an effect on VWF levels. In this first report using next generation sequencing technology to unravel the effects of VWF mutations on splicing, the technique yielded valuable information. Our data bring to light the importance of studying the effect of synonymous and missense mutations on VWF splicing to improve the current knowledge of the molecular mechanisms behind von Willebrand disease. clinicaltrials.gov identifier:02869074

Combined measurement of differential and total cross sections in the H → γγ and the H → ZZ* → 4ℓ decay channels at s=13 TeV with the ATLAS detector

A combined measurement of differential and inclusive total cross sections of Higgs boson production is performed using 36.1 fb−1 of 13 TeV proton–proton collision data produced by the LHC and recorded by the ATLAS detector in 2015 and 2016. Cross sections are obtained from measured H→γγ and H→ZZ*(→4ℓ event yields, which are combined taking into account detector efficiencies, resolution, acceptances and branching fractions. The total Higgs boson production cross section is measured to be 57.0−5.9 +6.0 (stat.) −3.3 +4.0 (syst.) pb, in agreement with the Standard Model prediction. Differential cross-section measurements are presented for the Higgs boson transverse momentum distribution, Higgs boson rapidity, number of jets produced together with the Higgs boson, and the transverse momentum of the leading jet. The results from the two decay channels are found to be compatible, and their combination agrees with the Standard Model predictions

Measurement of the t¯tZ and t¯tW cross sections in proton-proton collisions at √s=13 TeV with the ATLAS detector

A measurement of the associated production of a top-quark pair (t¯t) with a vector boson (W, Z) in proton-proton collisions at a center-of-mass energy of 13 TeV is presented, using 36.1  fb−1 of integrated luminosity collected by the ATLAS detector at the Large Hadron Collider. Events are selected in channels with two same- or opposite-sign leptons (electrons or muons), three leptons or four leptons, and each channel is further divided into multiple regions to maximize the sensitivity of the measurement. The t¯tZ and t¯tW production cross sections are simultaneously measured using a combined fit to all regions. The best-fit values of the production cross sections are σt¯tZ=0.95±0.08stat±0.10syst pb and σt¯tW=0.87±0.13stat±0.14syst pb in agreement with the Standard Model predictions. The measurement of the t¯tZ cross section is used to set constraints on effective field theory operators which modify the t¯tZ vertex

Search for flavour-changing neutral current top-quark decays t → qZ in proton-proton collisions at \sqrt{s} = 13 TeV with the ATLAS detector

A search for flavour-changing neutral-current processes in top-quark decays is presented. Data collected with the ATLAS detector from proton-proton collisions at the Large Hadron Collider at a centre-of-mass energy of s√=13 TeV, corresponding to an integrated luminosity of 36.1 fb−1, are analysed. The search is performed using top-quark pair events, with one top quark decaying through the t → qZ (q = u, c) flavour-changing neutral-current channel, and the other through the dominant Standard Model mode t → bW. Only Z boson decays into charged leptons and leptonic W boson decays are considered as signal. Consequently, the final-state topology is characterized by the presence of three isolated charged leptons (electrons or muons), at least two jets, one of the jets originating from a b-quark, and missing transverse momentum from the undetected neutrino. The data are consistent with Standard Model background contributions, and at 95% confidence level the search sets observed (expected) upper limits of 1.7 × 10−4 (2.4 × 10−4) on the t → uZ branching ratio and 2.4 × 10−4 (3.2 × 10−4) on the t → cZ branching ratio, constituting the most stringent limits to date. Open image in new windo

Measurement of the inclusive isolated-photon cross section at √s = 13 TeV using fb⁻¹ of ATLAS data

The differential cross section for isolated-photon production in pp collisions is measured at a centre-of-mass energy of 13 TeV with the ATLAS detector at the LHC using an integrated luminosity of 36.1 fb−1. The differential cross section is presented as a function of the photon transverse energy in different regions of photon pseudorapidity. The differential cross section as a function of the absolute value of the photon pseudorapidity is also presented in different regions of photon transverse energy. Next-to-leading-order QCD calculations from Jetphox and Sherpa as well as next-to-next-to-leading-order QCD calculations from Nnlojet are compared with the measurement, using several parameterisations of the proton parton distribution functions. The predictions provide a good description of the data within the experimental and theoretical uncertainties

Observation of electroweak production of two jets and a Z-boson pair

Electroweak symmetry breaking explains the origin of the masses of elementary particles through their interactions with the Higgs field. Besides the measurements of the Higgs boson properties, the study of the scattering of massive vector bosons with spin 1 allows the nature of electroweak symmetry breaking to be probed. Among all processes related to vector-boson scattering, the electroweak production of two jets and a Z-boson pair is a rare and important one. Here we report the observation of this process from proton–proton collision data corresponding to an integrated luminosity of 139 fb−1 recorded at a centre-of-mass energy of 13 TeV with the ATLAS detector at the Large Hadron Collider. We consider two different final states originating from the decays of the Z-boson pair: one containing four charged leptons and another containing two charged leptons and two neutrinos. The hypothesis of no electroweak production is rejected with a statistical significance of 5.7σ, and the measured cross-section for electroweak production is consistent with the Standard Model prediction. In addition, we report cross-sections for inclusive production of a Z-boson pair and two jets for the two final states

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Probing the Quantum Interference between Singly and Doubly Resonant Top-Quark Production in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector.

This Letter presents a normalized differential cross-section measurement in a fiducial phase-space region where interference effects between top-quark pair production and associated production of a single top quark with a W boson and a b-quark are significant. Events with exactly two leptons (ee, μμ, or eμ) and two b-tagged jets that satisfy a multiparticle invariant mass requirement are selected from 36.1  fb^{-1} of proton-proton collision data taken at sqrt[s]=13  TeV with the ATLAS detector at the LHC in 2015 and 2016. The results are compared with predictions from simulations using various strategies for the interference. The standard prescriptions for interference modeling are significantly different from each other but are within 2σ of the data. State-of-the-art predictions that naturally incorporate interference effects provide the best description of the data in the measured region of phase space most sensitive to these effects. These results provide an important constraint on interference models and will guide future model development and tuning

Erratum to: Search for diboson resonances in hadronic final states in 139 fb⁻¹ of pp collisions at s = 13 TeV with the ATLAS detector (Journal of High Energy Physics, (2019), 2019, 9, (91), 10.1007/JHEP09(2019)091)

A mistake was identified for the paper [1] in the treatment of the radion [2] cross-sections, which resulted in multiple changes