On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome

Phytochromes are photoreceptors in plants, fungi, and various microorganisms and cycle between metastable red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Their light responses are thought to follow a conserved structural mechanism that is triggered by isomerization of the chromophore. Downstream structural changes involve refolding of the so-called tongue extension of the phytochrome-specific GAF-related (PHY) domain of the photoreceptor. The tongue is connected to the chromophore by conserved DIP and PRXSF motifs and a conserved tyrosine, but the role of these residues in signal transduction is not clear. Here, we examine the tongue interactions and their interplay with the chromophore by substituting the conserved tyrosine (Tyr(263)) in the phytochrome from the extremophile bacterium Deinococcus radiodurans with phenylalanine. Using optical and FTIR spectroscopy, X-ray solution scattering, and crystallography of chromophore-binding domain (CBD) and CBD-PHY fragments, we show that the absence of the Tyr(263) hydroxyl destabilizes the -sheet conformation of the tongue. This allowed the phytochrome to adopt an -helical tongue conformation regardless of the chromophore state, hence distorting the activity state of the protein. Our crystal structures further revealed that water interactions are missing in the Y263F mutant, correlating with a decrease of the photoconversion yield and underpinning the functional role of Tyr(263) in phytochrome conformational changes. We propose a model in which isomerization of the chromophore, refolding of the tongue, and globular conformational changes are represented as weakly coupled equilibria. The results also suggest that the phytochromes have several redundant signaling routes.Peer reviewe

Measurement of Neutrino-Electron Scattering Cross-Section with a CsI(Tl) Scintillating Crystal Array at the Kuo-Sheng Nuclear Power Reactor

The $\bar{\nu}_{e}-e^{-}$ elastic scattering cross-section was measured with a CsI(Tl) scintillating crystal array having a total mass of 187kg. The detector was exposed to an average reactor $\bar{\nu}_{e}$ flux of $\rm{6.4\times 10^{12} ~ cm^{-2}s^{-1}}$ at the Kuo-Sheng Nuclear Power Station. The experimental design, conceptual merits, detector hardware, data analysis and background understanding of the experiment are presented. Using 29882/7369 kg-days of Reactor ON/OFF data, the Standard Model(SM) electroweak interaction was probed at the squared 4-momentum transfer range of $\rm{Q^2 \sim 3 \times 10^{-6} ~ GeV^2}$. The ratio of experimental to SM cross-sections of $\xi =[ 1.08 \pm 0.21(stat)\pm 0.16(sys)]$ was measured. Constraints on the electroweak parameters $(g_V , g_A)$ were placed, corresponding to a weak mixing angle measurement of \s2tw = 0.251 \pm 0.031({\it stat}) \pm 0.024({\it sys}) . Destructive interference in the SM \nuebar -e process was verified. Bounds on anomalous neutrino electromagnetic properties were placed: neutrino magnetic moment at \mu_{\nuebar}< 2.2 \times 10^{-10} \mu_{\rm B} and the neutrino charge radius at -2.1 \times 10^{-32} ~{\rm cm^{2}} < \nuchrad < 3.3 \times 10^{-32} ~{\rm cm^{2}}, both at 90% confidence level.Comment: 18 Figures, 7 Tables; published version as V2 with minor revision from V

Associated Charm Production in Neutrino-Nucleus Interactions

In this paper a search for associated charm production both in neutral and charged current $\nu$-nucleus interactions is presented. The improvement of automatic scanning systems in the {CHORUS} experiment allows an efficient search to be performed in emulsion for short-lived particles. Hence a search for rare processes, like the associated charm production, becomes possible through the observation of the double charm-decay topology with a very low background. About 130,000 $\nu$ interactions located in the emulsion target have been analysed. Three events with two charm decays have been observed in the neutral-current sample with an estimated background of 0.18$\pm$0.05. The relative rate of the associated charm cross-section in deep inelastic $\nu$ interactions, $\sigma(c\bar{c}\nu)/\sigma_\mathrm{NC}^\mathrm{DIS}= (3.62^{+2.95}_{-2.42}({stat})\pm 0.54({syst}))\times 10^{-3}$ has been measured. One event with two charm decays has been observed in charged-current $\nu_\mu$ interactions with an estimated background of 0.18$\pm$0.06 and the upper limit on associated charm production in charged-current interactions at 90% C.L. has been found to be $\sigma (c\bar{c} \mu^-)/\sigma_\mathrm{CC} < 9.69 \times 10^{-4}$.Comment: 10 pages, 4 figure

Leading order analysis of neutrino induced dimuon events in the CHORUS experiment

We present a leading order QCD analysis of a sample of neutrino induced charged-current events with two muons in the final state originating in the lead-scintillating fibre calorimeter of the CHORUS detector. The results are based on a sample of 8910 neutrino and 430 antineutrino induced opposite-sign dimuon events collected during the exposure of the detector to the CERN Wide Band Neutrino Beam between 1995 and 1998. % with $E_{\mu 1},E_{\mu 2} > 5$ GeV and $Q^2 > 3$ GeV$^2$ collected %between 1995 and 1998. The analysis yields a value of the charm quark mass of \mc = (1.26\pm 0.16 \pm 0.09) \GeVcc and a value of the ratio of the strange to non-strange sea in the nucleon of $\kappa = 0.33 \pm 0.05 \pm 0.05$, improving the results obtained in similar analyses by previous experiments.Comment: Submitted to Nuclear Physics

Charged-Particle Multiplicities in Charged-Current Neutrino-- and Anti-Neutrino--Nucleus Interactions

The CHORUS experiment, designed to search for $\nu_{\mu}\to\nu_{\tau}$ oscillations, consists of a nuclear emulsion target and electronic detectors. In this paper, results on the production of charged particles in a small sample of charged-current neutrino-- and anti-neutrino--nucleus interactions at high energy are presented. For each event, the emission angle and the ionization features of the charged particles produced in the interaction are recorded, while the standard kinematic variables are reconstructed using the electronic detectors. The average multiplicities for charged tracks, the pseudo-rapidity distributions, the dispersion in the multiplicity of charged particles and the KNO scaling are studied in different kinematical regions. A study of quasi-elastic topologies performed for the first time in nuclear emulsions is also reported. The results are presented in a form suitable for use in the validation of Monte Carlo generators of neutrino--nucleus interactions.Comment: 17 pages, 5 figure

Large-angle production of charged pions by 3 GeV/c - 12 GeV/c protons on carbon, copper and tin targets

A measurement of the double-differential $\pi^{\pm}$ production cross-section in proton--carbon, proton--copper and proton--tin collisions in the range of pion momentum 100 \MeVc \leq p < 800 \MeVc and angle 0.35 \rad \le \theta <2.15 \rad is presented. The data were taken with the HARP detector in the T9 beam line of the CERN PS. The pions were produced by proton beams in a momentum range from 3 \GeVc to 12 \GeVc hitting a target with a thickness of 5% of a nuclear interaction length. The tracking and identification of the produced particles was done using a small-radius cylindrical time projection chamber (TPC) placed in a solenoidal magnet. An elaborate system of detectors in the beam line ensured the identification of the incident particles. Results are shown for the double-differential cross-sections at four incident proton beam momenta (3 \GeVc, 5 \GeVc, 8 \GeVc and 12 \GeVc)

Measurement of the production of charged pions by protons on a tantalum target

A measurement of the double-differential cross-section for the production of charged pions in proton--tantalum collisions emitted at large angles from the incoming beam direction is presented. The data were taken in 2002 with the HARP detector in the T9 beam line of the CERN PS. The pions were produced by proton beams in a momentum range from 3 \GeVc to 12 \GeVc hitting a tantalum target with a thickness of 5% of a nuclear interaction length. The angular and momentum range covered by the experiment (100 \MeVc \le p < 800 \MeVc and 0.35 \rad \le \theta <2.15 \rad) is of particular importance for the design of a neutrino factory. The produced particles were detected using a small-radius cylindrical time projection chamber (TPC) placed in a solenoidal magnet. Track recognition, momentum determination and particle identification were all performed based on the measurements made with the TPC. An elaborate system of detectors in the beam line ensured the identification of the incident particles. Results are shown for the double-differential cross-sections ${{\mathrm{d}^2 \sigma}} / {{\mathrm{d}p\mathrm{d}\theta}}$ at four incident proton beam momenta (3 \GeVc, 5 \GeVc, 8 \GeVc and 12 \GeVc). In addition, the pion yields within the acceptance of typical neutrino factory designs are shown as a function of beam momentum. The measurement of these yields within a single experiment eliminates most systematic errors in the comparison between rates at different beam momenta and between positive and negative pion production.Comment: 49 pages, 31 figures. Version accepted for publication on Eur. Phys. J.

Large-angle production of charged pions by 3 GeV/c - 12.9 GeV/c protons on beryllium, aluminium and lead targets

Measurements of the double-differential $\pi^{\pm}$ production cross-section in the range of momentum 100 \MeVc \leq p < 800 \MeVc and angle 0.35 \rad \leq \theta < 2.15 \rad in proton--beryllium, proton--aluminium and proton--lead collisions are presented. The data were taken with the HARP detector in the T9 beam line of the CERN PS. The pions were produced by proton beams in a momentum range from 3 \GeVc to 12.9 \GeVc hitting a target with a thickness of 5% of a nuclear interaction length. The tracking and identification of the produced particles was performed using a small-radius cylindrical time projection chamber (TPC) placed inside a solenoidal magnet. Incident particles were identified by an elaborate system of beam detectors. Results are obtained for the double-differential cross-sections at six incident proton beam momenta (3 \GeVc, 5 \GeVc, 8 \GeVc, 8.9 \GeVc (Be only), 12 \GeVc and 12.9 \GeVc (Al only)) and compared to previously available data

Performance and calibration of the CHORUS scintillating fiber tracker and opto-electronics readout system

An essential component of the CERN WA95/CHORUS experiment is a scintillating fiber tracker system for precise track reconstruction of particles. The tracker design, its opto-electronics readout and calibration system are discussed. Performances of the detector are presented

Measurement of the production cross-section of positive pions in the collision of 8.9 GeV/c protons on beryllium

The double-differential production cross-section of positive pions, $d^2\sigma^{\pi^{+}}/dpd\Omega$, measured in the HARP experiment is presented. The incident particles are 8.9 GeV/c protons directed onto a beryllium target with a nominal thickness of 5% of a nuclear interaction length. The measured cross-section has a direct impact on the prediction of neutrino fluxes for the MiniBooNE and SciBooNE experiments at Fermilab. After cuts, 13 million protons on target produced about 96,000 reconstructed secondary tracks which were used in this analysis. Cross-section results are presented in the kinematic range 0.75 GeV/c < $p_{\pi}$ < 6.5 GeV/c and 30 mrad < $\theta_{\pi}$ < 210 mrad in the laboratory frame.Comment: 39 pages, 21 figures. Version accepted for publication by Eur. Phys. J.