BYKdb: the Bacterial protein tYrosine Kinase database

Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. These enzymes have been shown to control several biological functions in the bacterial cells. In recent years biochemical studies, sequence analyses and structure resolutions allowed the deciphering of a common signature. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences: the Bacterial protein tyrosine-kinase database (BYKdb). BY-kinase sequences are first identified, thanks to a workflow developed in a previous work. A second workflow annotates the UniProtKB entries in order to provide the BYKdb entries. The database can be accessed through a web interface that allows static and dynamic queries and offers integrated sequence analysis tools. BYKdb can be found at http://bykdb.ibcp.fr

Effect of β-glucan and black tea in a functional bread on short chain fatty acid production by the gut microbiota in a gut digestion/fermentation model

β-Glucan and black tea are fermented by the colonic microbiota producing short chain fatty acids (SCFA) and phenolic acids (PA). We hypothesized that the addition of β-glucan, a dietary fiber, and tea polyphenols to a food matrix like bread will also affect starch digestion in the upper gut and thus further influence colonic fermentation and SCFA production. This study investigated SCFA and PA production from locally developed breads: white bread (WB), black tea bread (BT), β-glucan bread (βG), β-glucan plus black tea bread (βGBT). Each bread was incubated in an in vitro system mimicking human digestion and colonic fermentation. Digestion with α-amylase significantly (p = 0.0001) increased total polyphenol and polyphenolic metabolites from BT bread compared with WB, βG, and βGBT. Total polyphenols in βGBT remained higher (p = 0.016; 1.3-fold) after digestion with pepsin and pancreatin compared with WB. Fermentations containing βG and βGBT produced similar propionate concentrations ranging from 17.5 to 18.6 mmol/L and total SCFA from 46.0 to 48.9 mmol/L compared with control WB (14.0 and 37.4 mmol/L, respectively). This study suggests that combination of black tea with β-glucan in this functional bread did not impact on SCFA production. A higher dose of black tea and β-glucan or in combination with other fibers may be needed to increase SCFA production

Spallation dominated propagation of Heavy Cosmic Rays and the Local Interstellar Medium (LISM)

Measurements of ultra heavy nuclei at GeV/n energies in the galactic cosmic radiation address the question of the sources (nucleosynthetic s- and r-processes). As such, the determination of CR source abundances is a promising way to discriminate between existing nucleosynthesis models. For primary species (nuclei present and accelerated at sources), it is generally assumed that the relative propagated abundances, if they are close in mass, are not too different from their relative source abundances. Besides, the range of the correction factor associated to propagation has been estimated in weighted slab models only. Heavy CRs that are detected near Earth were accelerated from regions that are closer to us than were the light nuclei. Hence, the geometry of sources in the Solar neighbourhood, and as equally important, the geometry of gas in the same region, must be taken into account. In this paper, a two zone diffusion model is used, and as was previously investigated for radioactive species, we report here on the impact of the local interstellar medium (LISM) feature (under-dense medium over a scale ~100 pc) on primary and secondary stable nuclei propagated abundances. Going down to Fe nuclei, the connection between heavy and light abundances is also inspected. A general trend is found that decreases the UHCR source abundances relative to the HCR ones. This could have an impact on the level of r-process required to reproduce the data.Comment: 12 pages, 9 figures, accepted by A&A. Comparison with truncated weighted slab and discussion added. Figure 8 modified. New appendix on truncated weighted slab techniqu

Identification of the Beutler-Fano formula in eigenphase shifts and eigentime delays near a resonance

Eigenphase shifts and eigentime delays near a resonance for a system of one discrete state and two continua are shown to be functionals of the Beutler- Fano formulas using appropriate dimensionless energy units and line profile indices. Parameters responsible for the avoided crossing of eigenphase shifts and eigentime delays are identified. Similarly, parameters responsible for the eigentime delays due to a frame change are identified. With the help of new parameters, an analogy with the spin model is pursued for the S matrix and time delay matrix. The time delay matrix is shown to comprise three terms, one due to resonance, one due to a avoided crossing interaction, and one due to a frame change. It is found that the squared sum of time delays due to the avoided crossing interaction and frame change is unity.Comment: 17 pages, 3 figures, RevTe

Coincidence measurement of residues and light particles in the reaction 56Fe+p at 1 GeV per nucleon with SPALADIN

The spallation of $^{56}$Fe in collisions with hydrogen at 1 A GeV has been studied in inverse kinematics with the large-aperture setup SPALADIN at GSI. Coincidences of residues with low-center-of-mass kinetic energy light particles and fragments have been measured allowing the decomposition of the total reaction cross-section into the different possible de-excitation channels. Detailed information on the evolution of these de-excitation channels with excitation energy has also been obtained. The comparison of the data with predictions of several de-excitation models coupled to the INCL4 intra-nuclear cascade model shows that only GEMINI can reasonably account for the bulk of collected results, indicating that in a light system with no compression and little angular momentum, multifragmentation might not be necessary to explain the data.Comment: 4 pages, 5 figures, revised version accepted in Phys. Rev. Let

Hexameric oligomerization of mitochondrial peroxiredoxin PrxIIF and formation of an ultrahigh affinity complex with its electron donor thioredoxin Trx-o

Mitochondria from plants, yeast, and animals each contain at least one peroxiredoxin (Prx) that is involved in peroxide detoxification and redox signalling. The supramolecular dynamics of atypical type II Prx targeted to the mitochondrion was addressed in pea. Microcalorimetric (ITC) titrations identified an extremely high-affinity binding between the mitochondrial PsPrxIIF and Trx-o with a KD of 126±14 pM. Binding was driven by a favourable enthalpy change (ΔH= –60.6 kcal mol−1) which was counterbalanced by unfavourable entropy changes (TΔS= –47.1 kcal mol−1). This is consistent with the occurrence of large conformational changes during binding which was abolished upon site-directed mutaganesis of the catalytic C59S and C84S. The redox-dependent interaction was confirmed by gel filtration of mitochondrial extracts and co-immunoprecipitation from extracts. The heterocomplex of PsPrxIIF and Trx-o reduced peroxide substrates more efficiently than free PsPrxIIF suggesting that Trx-o serves as an efficient and specific electron donor to PsPrxIIF in vivo. Other Trx-s tested by ITC analysis failed to interact with PsPrxIIF indicating a specific recognition of PsPrxIIF by Trx-o. PsPrxIIF exists primarily as a dimer or a hexamer depending on the redox state. In addition to the well-characterized oligomerization of classical 2-Cys Prx the results also show that atypical Prx undergo large structural reorganization with implications for protein–protein interaction and function

Planck intermediate results. XLI. A map of lensing-induced B-modes

The secondary cosmic microwave background (CMB) $B$-modes stem from the post-decoupling distortion of the polarization $E$-modes due to the gravitational lensing effect of large-scale structures. These lensing-induced $B$-modes constitute both a valuable probe of the dark matter distribution and an important contaminant for the extraction of the primary CMB $B$-modes from inflation. Planck provides accurate nearly all-sky measurements of both the polarization $E$-modes and the integrated mass distribution via the reconstruction of the CMB lensing potential. By combining these two data products, we have produced an all-sky template map of the lensing-induced $B$-modes using a real-space algorithm that minimizes the impact of sky masks. The cross-correlation of this template with an observed (primordial and secondary) $B$-mode map can be used to measure the lensing $B$-mode power spectrum at multipoles up to $2000$. In particular, when cross-correlating with the $B$-mode contribution directly derived from the Planck polarization maps, we obtain lensing-induced $B$-mode power spectrum measurement at a significance level of $12\,\sigma$, which agrees with the theoretical expectation derived from the Planck best-fit $\Lambda$CDM model. This unique nearly all-sky secondary $B$-mode template, which includes the lensing-induced information from intermediate to small ($10\lesssim \ell\lesssim 1000$) angular scales, is delivered as part of the Planck 2015 public data release. It will be particularly useful for experiments searching for primordial $B$-modes, such as BICEP2/Keck Array or LiteBIRD, since it will enable an estimate to be made of the lensing-induced contribution to the measured total CMB $B$-modes.Comment: 20 pages, 12 figures; Accepted for publication in A&A; The B-mode map is part of the PR2-2015 Cosmology Products; available as Lensing Products in the Planck Legacy Archive http://pla.esac.esa.int/pla/#cosmology; and described in the 'Explanatory Supplement' https://wiki.cosmos.esa.int/planckpla2015/index.php/Specially_processed_maps#2015_Lensing-induced_B-mode_ma

Planck 2015 results. XXIII. The thermal Sunyaev-Zeldovich effect--cosmic infrared background correlation

We use Planck data to detect the cross-correlation between the thermal Sunyaev-Zeldovich (tSZ) effect and the infrared emission from the galaxies that make up the the cosmic infrared background (CIB). We first perform a stacking analysis towards Planck-confirmed galaxy clusters. We detect infrared emission produced by dusty galaxies inside these clusters and demonstrate that the infrared emission is about 50% more extended than the tSZ effect. Modelling the emission with a Navarro--Frenk--White profile, we find that the radial profile concentration parameter is $c_{500} = 1.00^{+0.18}_{-0.15}$. This indicates that infrared galaxies in the outskirts of clusters have higher infrared flux than cluster-core galaxies. We also study the cross-correlation between tSZ and CIB anisotropies, following three alternative approaches based on power spectrum analyses: (i) using a catalogue of confirmed clusters detected in Planck data; (ii) using an all-sky tSZ map built from Planck frequency maps; and (iii) using cross-spectra between Planck frequency maps. With the three different methods, we detect the tSZ-CIB cross-power spectrum at significance levels of (i) 6 $\sigma$, (ii) 3 $\sigma$, and (iii) 4 $\sigma$. We model the tSZ-CIB cross-correlation signature and compare predictions with the measurements. The amplitude of the cross-correlation relative to the fiducial model is $A_{\rm tSZ-CIB}= 1.2\pm0.3$. This result is consistent with predictions for the tSZ-CIB cross-correlation assuming the best-fit cosmological model from Planck 2015 results along with the tSZ and CIB scaling relations.Comment: 18 pages, 16 figure

Planck 2015 results. XXVII. The Second Planck Catalogue of Sunyaev-Zeldovich Sources

We present the all-sky Planck catalogue of Sunyaev-Zeldovich (SZ) sources detected from the 29 month full-mission data. The catalogue (PSZ2) is the largest SZ-selected sample of galaxy clusters yet produced and the deepest all-sky catalogue of galaxy clusters. It contains 1653 detections, of which 1203 are confirmed clusters with identified counterparts in external data-sets, and is the first SZ-selected cluster survey containing > $10^3$ confirmed clusters. We present a detailed analysis of the survey selection function in terms of its completeness and statistical reliability, placing a lower limit of 83% on the purity. Using simulations, we find that the Y5R500 estimates are robust to pressure-profile variation and beam systematics, but accurate conversion to Y500 requires. the use of prior information on the cluster extent. We describe the multi-wavelength search for counterparts in ancillary data, which makes use of radio, microwave, infra-red, optical and X-ray data-sets, and which places emphasis on the robustness of the counterpart match. We discuss the physical properties of the new sample and identify a population of low-redshift X-ray under- luminous clusters revealed by SZ selection. These objects appear in optical and SZ surveys with consistent properties for their mass, but are almost absent from ROSAT X-ray selected samples

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

The majority of previously deposited X-ray structures can be improved by applying current refinement methods