Amphioxus functional genomics and the origins of vertebrate gene regulation

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that—in vertebrates—over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations

Measurement of double-differential charged-current Drell-Yan cross-sections at high transverse masses in pp collisions at √s = 13 TeV with the ATLAS detector

This paper presents a first measurement of the cross-section for the charged-current Drell-Yan process $pp\rightarrow W^{\pm} \rightarrow \ell^{\pm} \nu$ above the resonance region, where $\ell$ is an electron or muon. The measurement is performed for transverse masses, $m_{\text{T}}^{\text{W}}$, between 200 GeV and 5000 GeV, using a sample of 140 fb$^{-1}$ of $pp$ collision data at a centre-of-mass energy of $\sqrt{s}$ = 13 TeV collected by the ATLAS detector at the LHC during 2015-2018. The data are presented single differentially in transverse mass and double differentially in transverse mass and absolute lepton pseudorapidity. A test of lepton flavour universality shows no significant deviations from the Standard Model. The electron and muon channel measurements are combined to achieve a total experimental precision of 3% at low $m_{\text{T}}^{\text{W}}$. The single- and double differential $W$-boson charge asymmetries are evaluated from the measurements. A comparison to next-to-next-to-leading-order perturbative QCD predictions using several recent parton distribution functions and including next-to-leading-order electroweak effects indicates the potential of the data to constrain parton distribution functions. The data are also used to constrain four fermion operators in the Standard Model Effective Field Theory formalism, in particular the lepton-quark operator Wilson coefficient $c_{\ell q}^{(3)}.

Charged-hadron and identified-hadron (K0 S, , −) yield measurements in photonuclear Pb+Pband p+Pbcollisions at √ sNN = 5.02TeV with ATLAS

This paper presents the measurement of charged-hadron and identified-hadron (K0 S, , −) yields in photonuclear collisions using 1.7nb−1 of √ sNN = 5.02TeV Pb+Pb data collected in 2018 with the ATLAS detector at the Large Hadron Collider. Candidate photonuclear events are selected using a combination of tracking and calorimeter information, including the zero-degree calorimeter. The yields as a function of transverse momentum and rapidity are measured in these photonuclear collisions as a function of charged-particle multiplicity. These photonuclear results are compared with 0.1nb−1 of √ sNN = 5.02TeV p+Pbdata collected in 2016 by ATLAS using similar charged-particle multiplicity selections. These photonuclear measurements shed light on potential quark-gluon plasma formation in photonuclear collisions via observables sensitive to radial flow, enhanced baryon-to-meson ratios, and strangeness enhancement. The results are also compared with the Monte Carlo DPMJET-III generator and hydrodynamic calculations to test whether such photonuclear collisions may produce small droplets of quark-gluon plasma that flow collectively

Search for long-lived charged particles using large specific ionisation loss and time of flight in 140 fb−1 of pp collisions at = 13 TeV with the ATLAS detector

This paper presents a search for massive, charged, long-lived particles with the ATLAS detector at the Large Hadron Collider using an integrated luminosity of 140 f b−1 of proton-proton collisions at √ s = 13 TeV. These particles are expected to move signifcantly slower than the speed of light. In this paper, two signal regions provide complementary sensitivity. In one region, events are selected with at least one charged-particle track with high transverse momentum, large specifc ionisation measured in the pixel detector, and time of fight to the hadronic calorimeter inconsistent with the speed of light. In the other region, events are selected with at least two tracks of opposite charge which both have a high transverse momentum and an anomalously large specifc ionisation. The search is sensitive to particles with lifetimes greater than about 3 ns with masses ranging from 200 GeV to 3 TeV. The results are interpreted to set constraints on the supersymmetric pair production of long-lived R-hadrons, charginos and staus, with mass limits extending beyond those from previous searches in broad ranges of lifetime

Measurement of W±-boson differential cross-sections in proton–proton collisions with low pile-up data at √s = 5.02TeV and 13TeV with the ATLAS detector

High precision single-differential W±-boson production cross-sections as a function of electron or muon transverse momentum pT or their pseudorapity η, as well as double-differential cross-sections as functions of these variables, are measured in proton–proton collisions at centre-of mass energies √s = 5.02TeV and 13TeV. The W-boson charge asymmetry as a function of lepton η is also measured. The data, collected in dedicated runs at reduced instantaneous luminosity with the ATLAS detector at the Large Hadron Collider, correspond to integrated luminosities of 255pb−1 at 5.02TeV and 338pb−1 at 13TeV. The measurements are in agreement with Standard-Model predictions calculated at next-to-next-to-leading-order in the strong coupling constant αs including transverse-momentum resummation at next-to next-to-leading logarithmic accuracy using several parton distribution functions. The impact of the measured differential cross-sections as a function of lepton η on the determination of these functions is studied using a profiling technique

Structural studies of the four-way helical DNA junction

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