Gene fusions and gene duplications: relevance to genomic annotation and functional analysis

BACKGROUND: Escherichia coli a model organism provides information for annotation of other genomes. Our analysis of its genome has shown that proteins encoded by fused genes need special attention. Such composite (multimodular) proteins consist of two or more components (modules) encoding distinct functions. Multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. Previous work overstated the number of multimodular proteins in E. coli. This work corrects the identification of modules by including sequence information from proteins in 50 sequenced microbial genomes. RESULTS: Multimodular E. coli K-12 proteins were identified from sequence similarities between their component modules and non-fused proteins in 50 genomes and from the literature. We found 109 multimodular proteins in E. coli containing either two or three modules. Most modules had standalone sequence relatives in other genomes. The separated modules together with all the single (un-fused) proteins constitute the sum of all unimodular proteins of E. coli. Pairwise sequence relationships among all E. coli unimodular proteins generated 490 sequence similar, paralogous groups. Groups ranged in size from 92 to 2 members and had varying degrees of relatedness among their members. Some E. coli enzyme groups were compared to homologs in other bacterial genomes. CONCLUSION: The deleterious effects of multimodular proteins on annotation and on the formation of groups of paralogs are emphasized. To improve annotation results, all multimodular proteins in an organism should be detected and when known each function should be connected with its location in the sequence of the protein. When transferring functions by sequence similarity, alignment locations must be noted, particularly when alignments cover only part of the sequences, in order to enable transfer of the correct function. Separating multimodular proteins into module units makes it possible to generate protein groups related by both sequence and function, avoiding mixing of unrelated sequences. Organisms differ in sizes of groups of sequence-related proteins. A sample comparison of orthologs to selected E. coli paralogous groups correlates with known physiological and taxonomic relationships between the organisms

Inclusive and differential cross section measurements of single top quark production in association with a Z boson in proton-proton collisions at √s = 13 TeV

Copyright © CERN, for the benefit of the CMS Collaboration. Inclusive and differential cross sections of single top quark production in association with a Z boson are measured in proton-proton collisions at a center-of-mass energy of 13 TeV with a data sample corresponding to an integrated luminosity of 138 fb−1 recorded by the CMS experiment. Events are selected based on the presence of three leptons, electrons or muons, associated with leptonic Z boson and top quark decays. The measurement yields an inclusive cross section of 87.9+7.5−7.3(stat)+7.3−6.0(syst) fb for a dilepton invariant mass greater than 30 GeV, in agreement with standard model (SM) calculations and represents the most precise determination to date. The ratio between the cross sections for the top quark and the top antiquark production in association with a Z boson is measured as 2.37+0.56−0.42(stat)+0.27−0.13(syst). Differential measurements at parton and particle levels are performed for the first time. Several kinematic observables are considered to study the modeling of the process. Results are compared to theoretical predictions with different assumptions on the source of the initial-state b quark and found to be in agreement, within the uncertainties. Additionally, the spin asymmetry, which is sensitive to the top quark polarization, is determined from the differential distribution of the polarization angle at parton level to be 0.54 ± 0.16 (stat) ± 0.06 (syst), in agreement with SM predictions.SCOAP3

Precision measurement of the W boson decay branching fractions in proton-proton collisions at √s=13 TeV

The leptonic and inclusive hadronic decay branching fractions of the W boson are measured using proton-proton collision data collected at ffiffi s p ¼ 13 TeV by the CMS experiment at the CERN LHC, corresponding to an integrated luminosity of 35.9 fb−1. Events characterized by the production of one or two W bosons are selected and categorized based on the multiplicity and flavor of reconstructed leptons, the number of jets, and the number of jets identified as originating from the hadronization of b quarks. A binned maximum likelihood estimate of the W boson branching fractions is performed simultaneously in each event category. The measured branching fractions of the W boson decaying into electron, muon, and tau lepton final states are ð10.83 0.10Þ%, ð10.94 0.08Þ%, and ð10.77 0.21Þ%, respectively, consistent with lepton flavor universality for the weak interaction. The average leptonic and inclusive hadronic decay branching fractions are estimated to be ð10.89 0.08Þ% and ð67.32 0.23Þ%, respec tively. Based on the hadronic branching fraction, three standard model quantities are subsequently derived: the sum of squared elements in the first two rows of the Cabibbo–Kobayashi–Maskawa (CKM) matrix P ij jVijj 2 ¼ 1.984 0.021, the CKM element jVcsj ¼ 0.967 0.011, and the strong coupling constant at the W boson mass scale, αSðm2 WÞ ¼ 0.095 0.033

Search for a W' boson decaying to a vector-like quark and a top or bottom quark in the all-jets final state at root s=13 TeV

A search is presented for a heavy W′ boson resonance decaying to a B or T vector-like quark and a t or a b quark, respectively. The analysis is performed using proton-proton collisions collected with the CMS detector at the LHC. The data correspond to an integrated luminosity of 138 fb−1 at a center-of-mass energy of 13 TeV. Both decay channels result in a signature with a t quark, a Higgs or Z boson, and a b quark, each produced with a significant Lorentz boost. The all-hadronic decays of the Higgs or Z boson and of the t quark are selected using jet substructure techniques to reduce standard model backgrounds, resulting in a distinct three-jet W′ boson decay signature. No significant deviation in data with respect to the standard model background prediction is observed. Upper limits are set at 95% confidence level on the product of the W′ boson cross section and the final state branching fraction. A W′ boson with a mass below 3.1 TeV is excluded, given the benchmark model assumption of democratic branching fractions. In addition, limits are set based on generalizations of these assumptions. These are the most sensitive limits to date for this final state

Search for long-lived particles decaying to leptons with large impact parameter in proton-proton collisions at root s=13 TeV

Copyright © CERN for the benefit of the CMS collaboration 2022. A search for new long-lived particles decaying to leptons using proton–proton collision data produced by the CERN LHC at s√=13TeV is presented. Events are selected with two leptons (an electron and a muon, two electrons, or two muons) that both have transverse impact parameter values between 0.01 and 10cm and are not required to form a common vertex. Data used for the analysis were collected with the CMS detector in 2016, 2017, and 2018, and correspond to an integrated luminosity of 118 (113)fb−1 in the ee channel (eμ and μμ channels). The search is designed to be sensitive to a wide range of models with displaced eμ, ee, and μμ final states. The results constrain several well-motivated models involving new long-lived particles that decay to displaced leptons. For some areas of the available phase space, these are the most stringent constraints to date.SCOAP3

Observation of triple J/ψ meson production in proton-proton collisions

Data availability: Tabulated results are provided in the HEPData record for this analysis71. Release and preservation of data used by the CMS Collaboration as the basis for publications is guided by the CMS policy as stated in CMS data preservation, re-use and open access policy.Code availability: The CMS core software is publically available at https://github.com/cms-sw/cmssw.Copyright . Protons consist of three valence quarks, two up-quarks and one down-quark, held together by gluons and a sea of quark-antiquark pairs. Collectively, quarks and gluons are referred to as partons. In a proton-proton collision, typically only one parton of each proton undergoes a hard scattering – referred to as single-parton scattering – leaving the remainder of each proton only slightly disturbed. Here, we report the study of double- and triple-parton scatterings through the simultaneous production of three J/ψ mesons, which consist of a charm quark-antiquark pair, in proton-proton collisions recorded with the CMS experiment at the Large Hadron Collider. We observed this process – reconstructed through the decays of J/ψ mesons into pairs of oppositely charged muons – with a statistical significance above five standard deviations. We measured the inclusive fiducial cross-section to be 272+141−104(stat)±17(syst)fb, and compared it to theoretical expectations for triple-J/ψ meson production in single-, double- and triple-parton scattering scenarios. Assuming factorization of multiple hard-scattering probabilities in terms of single-parton scattering cross-sections, double- and triple-parton scattering are the dominant contributions for the measured process.SCOAP3.Change history: 27 February 2023A Correction to this paper has been published: https://doi.org/10.1038/s41567-023-01992-

Search for long-lived particles decaying into muon pairs in proton-proton collisions at √s = 13 TeV collected with a dedicated high-rate data stream

ArXiv ePrint: 2112.13769, https://arxiv.org/abs/2112.13769.Copyright © CERN, for the benefit of the CMS Collaboration 2022. A search for long-lived particles decaying into muon pairs is performed using proton-proton collisions at a center-of-mass energy of 13 TeV, collected by the CMS experiment at the LHC in 2017 and 2018, corresponding to an integrated luminosity of 101 fb−1. The data sets used in this search were collected with a dedicated dimuon trigger stream with low transverse momentum thresholds, recorded at high rate by retaining a reduced amount of information, in order to explore otherwise inaccessible phase space at low dimuon mass and nonzero displacement from the primary interaction vertex. No significant excess of events beyond the standard model expectation is found. Upper limits on branching fractions at 95% confidence level are set on a wide range of mass and lifetime hypotheses in beyond the standard model frameworks with the Higgs boson decaying into a pair of long-lived dark photons, or with a long-lived scalar resonance arising from a decay of a b hadron. The limits are the most stringent to date for substantial regions of the parameter space. These results can be also used to constrain models of displaced dimuons that are not explicitly considered in this paper.SCOAP3