Flow cytometry as a rapid analytical tool to determine physiological responses to changing O2 and iron concentration by Magnetospirillum gryphiswaldense strain MSR-1

Magnetotactic bacteria (MTB) are a diverse group of bacteria that synthesise magnetosomes, magnetic membrane-bound nanoparticles that have a variety of diagnostic, clinical and biotechnological applications. We present the development of rapid methods using flow cytometry to characterize several aspects of the physiology of the commonly-used MTB Magnetospirillum gryphiswaldense MSR-1. Flow cytometry is an optical technique that rapidly measures characteristics of individual bacteria within a culture, thereby allowing determination of population heterogeneity and also permitting direct analysis of bacteria. Scatter measurements were used to measure and compare bacterial size, shape and morphology. Membrane permeability and polarization were measured using the dyes propidium iodide and bis-(1,3-dibutylbarbituric acid) trimethine oxonol to determine the viability and ‘health’ of bacteria. Dyes were also used to determine changes in concentration of intracellular free iron and polyhydroxylakanoate (PHA), a bacterial energy storage polymer. These tools were then used to characterize the responses of MTB to different O2 concentrations and iron-sufficient or iron-limited growth. Rapid analysis of MTB physiology will allow development of bioprocesses for the production of magnetosomes, and will increase understanding of this fascinating and useful group of bacteria

RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

BACKGROUND: The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. RESULTS: The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences < ~200 bases) were sequenced, 52 million reads were mapped, and 24,616 known transcripts were quantified according to the bovine reference genome. A comparison of the high- and low-RFI groups revealed 70 and 19 significantly DEGs in Holstein and Jersey cows, respectively. The interaction analysis (high vs. low RFI x control vs. high concentrate diet) showed no interaction effects in the Holstein cows, while two genes showed interaction effects in the Jersey cows. The analyses showed that DEGs act through certain pathways to affect or regulate FE, including steroid hormone biosynthesis, retinol metabolism, starch and sucrose metabolism, ether lipid metabolism, arachidonic acid metabolism and drug metabolism cytochrome P450. CONCLUSION: We used RNA-Seq-based liver transcriptomic profiling of high- and low-RFI dairy cows in two breeds and identified significantly DEGs, their molecular mechanisms, their interactions with other genes and functional enrichments of different molecular pathways. The DEGs that were identified were the CYP’s and GIMAP genes for the Holstein and Jersey cows, respectively, which are related to the primary immunodeficiency pathway and play a major role in feed utilization and the metabolism of lipids, sugars and proteins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3622-9) contains supplementary material, which is available to authorized users

Search for pair production of heavy particles decaying to a top quark and a gluon in the lepton+jets final state in proton–proton collisions at s=13TeV

A search is presented for the pair production of new heavy resonances, each decaying into a top quark (t) or antiquark and a gluon (g). The analysis uses data recorded with the CMS detector from proton-proton collisions at a center-of-mass energy of 13 TeV at the LHC, corresponding to an integrated luminosity of 138 fb-1 . Events with one muon or electron, multiple jets, and missing transverse momentum are selected. After using a deep neural network to enrich the data sample with signal-like events, distributions in the scalar sum of the transverse momenta of all reconstructed objects are analyzed in the search for a signal. No significant deviations from the standard model prediction are found. Upper limits at 95% confidence level are set on the product of cross section and branching fraction squared for the pair production of excited top quarks in the t∗→tg decay channel. The upper limits range from 120 to 0.8 fb for a t∗ with spin-1/2 and from 15 to 1.0 fb for a t∗ with spin-3/2. These correspond to mass exclusion limits up to 1050 and 1700 GeV for spin-1/2 and spin-3/2 t∗ particles, respectively. These are the most stringent limits to date on the existence of t∗→tg resonances

Search for bottom quark associated production of the standard model Higgs boson in final states with leptons in proton-proton collisions at s = 13 TeV

This Letter presents the first search for bottom quark associated production of the standard model Higgs boson, in final states with leptons. Higgs boson decays to pairs of tau leptons and pairs of leptonically decaying W bosons are considered. The search is performed using data collected from 2016 to 2018 by the CMS experiment in proton-proton collisions at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 138fb−1. Upper limits at the 95% confidence level are placed on the signal strength for Higgs boson production in association with bottom quarks; the observed (expected) upper limit is 3.7 (6.1) times the standard model prediction

Measurements of polarization and spin correlation and observation of entanglement in top quark pairs using lepton+jets events from proton-proton collisions at s=13 TeV

Measurements of the polarization and spin correlation in top quark pairs ((Formula presented)) are presented using events with a single electron or muon and jets in the final state. The measurements are based on proton-proton collision data from the LHC at (Formula presented) collected by the CMS experiment, corresponding to an integrated luminosity of (Formula presented). All coefficients of the polarization vectors and the spin correlation matrix are extracted simultaneously by performing a binned likelihood fit to the data. The measurement is performed inclusively and in bins of additional observables, such as the mass of the (Formula presented) system and the top quark scattering angle in the (Formula presented) rest frame. The measured polarization and spin correlation are in agreement with the standard model. From the measured spin correlation, conclusions on the (Formula presented) spin entanglement are drawn by applying the Peres-Horodecki criterion. The standard model predicts entangled spins for (Formula presented) states at the production threshold and at high masses of the (Formula presented) system. Entanglement is observed for the first time in events at high (Formula presented) mass, where a large fraction of the (Formula presented) decays are spacelike separated, with an expected and observed significance of above 5 standard deviations

Measurement of the Higgs boson mass and width using the four-lepton final state in proton-proton collisions at √s =13 TeV

A measurement of the Higgs boson mass and width via its decay to two (Formula presented) bosons is presented. Proton-proton collision data collected by the CMS experiment, corresponding to an integrated luminosity of (Formula presented) at a center-of-mass energy of 13 TeV, is used. The invariant mass distribution of four leptons in the on-shell Higgs boson decay is used to measure its mass and constrain its width. This yields the most precise single measurement of the Higgs boson mass to date, (Formula presented), and an upper limit on the width (Formula presented) at 95% confidence level. A combination of the on- and off-shell Higgs boson production decaying to four leptons is used to determine the Higgs boson width, assuming that no new virtual particles affect the production, a premise that is tested by adding new heavy particles in the gluon fusion loop model. This result is combined with a previous CMS analysis of the off-shell Higgs boson production with decay to two leptons and two neutrinos, giving a measured Higgs boson width of (Formula presented), in agreement with the standard model prediction of 4.1 MeV. The strength of the off-shell Higgs boson production is also reported. The scenario of no off-shell Higgs boson production is excluded at a confidence level corresponding to 3.8 standard deviations

Search for new physics in high-mass diphoton events from proton-proton collisions at √s = 13 TeV

Results are presented from a search for new physics in high-mass diphoton events from proton-proton collisions at √s = 13 TeV. The data set was collected in 2016–2018 with the CMS detector at the LHC and corresponds to an integrated luminosity of 138 fb−1. Events with a diphoton invariant mass greater than 500 GeV are considered. Two different techniques are used to predict the standard model backgrounds: parametric fits to the smoothly-falling background and a first-principles calculation of the standard model diphoton spectrum at next-to-next-to-leading order in perturbative quantum chromodynamics calculations. The first technique is sensitive to resonant excesses while the second technique can identify broad differences in the invariant mass shape. The data are used to constrain the production of heavy Higgs bosons, Randall-Sundrum gravitons, the large extra dimensions model of Arkani-Hamed, Dimopoulos, and Dvali (ADD), and the continuum clockwork mechanism. No statistically significant excess is observed. The present results are the strongest limits to date on ADD extra dimensions and RS gravitons with a coupling parameter greater than 0.1

Observation of Λ Hyperon Local Polarization in p-Pb Collisions at sNN\sqrt{s_{NN}}=8.16 TeV

The polarization of the Λ and ¯Λ hyperons along the beam direction has been measured in proton-lead (p-Pb) collisions at a center-of-mass energy per nucleon pair of 8.16 TeV. The data were obtained with the CMS detector at the LHC and correspond to an integrated luminosity of 186.0 $\pm$ 6.5 nb$^{−1}$. A significant azimuthal dependence of the hyperon polarization, characterized by the second-order Fourier sine coefficient P$_{z;s2}$, is observed. The P$_{z;s2}$ values decrease as a function of charged particle multiplicity, but increase with transverse momentum. A hydrodynamic model that describes the observed P$_{z;s2}$ values in nucleus-nucleus collisions by introducing vorticity effects does not reproduce either the sign or the magnitude of the p-Pb results. These observations pose a challenge to the current theoretical implementation of spin polarization in heavy ion collisions and offer new insights into the origin of spin polarization in hadronic collisions at LHC energies

Determination of the strong coupling and its running from measurements of inclusive jet production

The value of the strong coupling S is determined in a comprehensive analysis at next-to-next-to-leading order accuracy in quantum chromodynamics. The analysis uses double-differential cross section measurements from the CMS Collaboration at the CERN LHC of inclusive jet production in proton-proton collisions at centre-of- mass energies of 2.76, 7, 8, and 13 TeV, combined with inclusive deep-inelastic data from HERA. The value $_S$($_Z$ ) = 0.1176 $^{+0.0014}_{-0.0016}$ is obtained at the scale of the Z boson mass. By using the measurements in different intervals of jet transverse momentum, the running of $_S$ is probed for energies between 100 and 1600 GeV

Search for pair production of heavy particles decaying to a top quark and a gluon in the lepton+jets final state in proton–proton collisions at s=13 TeV\sqrt{s}=13\,\text {Te}\hspace{-.08em}\text {V}

A search is presented for the pair production of new heavy resonances, each decaying into a top quark (t) or antiquark and a gluon (g). The analysis uses data recorded with the CMS detector from proton-proton collisions at a center-of-mass energy of 13 TeV at the LHC, corresponding to an integrated luminosity of 138 fb$^{-1}$. Events with one muon or electron, multiple jets, and missing transverse momentum are selected. After using a deep neural network to enrich the data sample with signal-like events, distributions in the scalar sum of the transverse momenta of all reconstructed objects are analyzed in the search for a signal. No significant deviations from the standard model prediction are found. Upper limits at 95% confidence level are set on the product of cross section and branching fraction squared for the pair production of excited top quarks in the t$^∗$ → tg decay channel. The upper limits range from 120 to 0.8 fb for a t$^∗$ with spin-1/2 and from 15 to 1.0 fb for a t∗ with spin-3/2. These correspond to mass exclusion limits up to 1050 and 1700 GeV for spin-1/2 and spin-3/2 t$^∗$ particles, respectively. These are the most stringent limits to date on the existence of t$^∗$ → tg resonances