1,721,017 research outputs found
Peculiar substrate specificity of δ1-pyrroline-5-carboxylate reductase in the obligately fermentative bacterium Zymomonas mobilis
No full textBackground: The enzyme that catalyzes the last step in proline synthesis, δ1-pyrroline-5-carboxylate reductase, showed in most cases a distinct preference in vitro for NADPH as the electron donor. Methods and results: A Zymomonas mobilis gene coding for a δ1-pyrroline-5-carboxylate reductase was cloned and heterologously expressed, and the recombinant protein was purified and characterized. The enzyme showed higher affinity to, and higher catalytic rate with NADH, with a specific activity of about 600 nkat (mg protein)−1. The molecular basis of this feature was investigated by analysis of the dinucleotide binding domain in silico. Conclusions: We postulate that the main determinants of coenzyme preference for P5C reductases are the length and the sequence of the motif A, whereas the overall sequence identity is insufficient to predict it a priori. Results are discussed in view of the obligately fermentative metabolism of this bacterium. Graphic abstract: [Figure not available: see fulltext.
Chaotic cold accretion on to black holes
No full textBondi theory is often assumed to adequately describe the mode of accretion in astrophysical environments. However, the Bondi flow must be adiabatic, spherically symmetric, steady, unperturbed, with constant boundary conditions. Using 3D adaptive mesh refinement simulations, linking the 50 kpc to the sub-parsec (sub-pc) scales over the course of 40 Myr, we systematically relax the classic assumptions in a typical galaxy hosting a supermassive black hole. In the more realistic scenario, where the hot gas is cooling, while heated and stirred on large scales, the accretion rate is boosted up to two orders of magnitude compared with the Bondi prediction. The cause is the non-linear growth of thermal instabilities, leading to the condensation of cold clouds and filaments when t_cool/t_ff ≲ 10. The clouds decouple from the hot gas, `raining' on to the centre. Subsonic turbulence of just over 100 km s^-1 (M > 0.2) induces the formation of thermal instabilities, even in the absence of heating, while in the transonic regime turbulent dissipation inhibits their growth (t_turb/t_cool ≲ 1). When heating restores global thermodynamic balance, the formation of the multiphase medium is violent, and the mode of accretion is fully cold and chaotic. The recurrent collisions and tidal forces between clouds, filaments and the central clumpy torus promote angular momentum cancellation, hence boosting accretion. On sub-pc scales the clouds are channelled to the very centre via a funnel. In this study, we do not inject a fixed initial angular momentum, though vorticity is later seeded by turbulence. A good approximation to the accretion rate is the cooling rate, which can be used as subgrid model, physically reproducing the boost factor of 100 required by cosmological simulations, while accounting for the frequent fluctuations. Since our modelling is fairly general (turbulence/heating due to AGN feedback, galaxy motions, mergers, stellar evolution), chaotic cold accretion may be common in many systems, such as hot galactic haloes, groups and clusters. In this mode, the black hole can quickly react to the state of the entire host galaxy, leading to efficient self-regulated AGN feedback and the symbiotic Magorrian relation. Chaotic accretion can generate high-velocity clouds, likely leading to strong variations in the AGN luminosity, and the deflection or mass-loading of jets. During phases of overheating, the hot mode becomes the single channel of accretion, though strongly suppressed by turbulence. High-resolution data could determine the current mode of accretion: assuming quiescent feedback, the cold mode results in a quasi-flat-temperature core as opposed to the cuspy profile of the hot mode
Cause and Effect of Feedback: Multiphase Gas in Cluster Cores Heated by AGN Jets
Full text linkMultiwavelength data indicate that the X-ray-emitting plasma in the cores of galaxy clusters is not cooling catastrophically. To a large extent, cooling is offset by heating due to active galactic nuclei (AGNs) via jets. The cool-core clusters, with cooler/denser plasmas, show multiphase gas and signs of some cooling in their cores. These observations suggest that the cool core is locally thermally unstable while maintaining global thermal equilibrium. Using high-resolution, three-dimensional simulations we study the formation of multiphase gas in cluster cores heated by collimated bipolar AGN jets. Our key conclusion is that spatially extended multiphase filaments form only when the instantaneous ratio of the thermal instability and free-fall timescales (t(TI)/t(ff)) falls below a critical threshold of approximate to 10. When this happens, dense cold gas decouples from the hot intracluster medium (ICM) phase and generates inhomogeneous and spatially extended Ha filaments. These cold gas clumps and filaments ``rain'' down onto the central regions of the core, forming a cold rotating torus and in part feeding the supermassive black hole. Consequently, the self-regulated feedback enhances AGN heating and the core returns to a higher entropy level with t(TI)/t(ff) > 10. Eventually, the core reaches quasi-stable global thermal equilibrium, and cold filaments condense out of the hot ICM whenever t(TI)/t(ff) less than or similar to 10. This occurs despite the fact that the energy from AGN jets is supplied to the core in a highly anisotropic fashion. The effective spatial redistribution of heat is enabled in part by the turbulent motions in the wake of freely falling cold filaments. Increased AGN activity can locally reverse the cold gas flow, launching cold filamentary gas away from the cluster center. Our criterion for the condensation of spatially extended cold gas is in agreement with observations and previous idealized simulations
Functional Characterization of Saccharomyces cerevisiae P5C Reductase, the Enzyme at the Converging Point of Proline and Arginine Metabolism
No full textThe enzyme that, in Saccharomyces cerevisiae, catalyzes the last step in both proline synthesis and arginine catabolism, δ1-pyrroline-5-carboxylate (P5C) reductase, was purified to near homogeneity and characterized thoroughly. Retention patterns upon gel permeation chromatography were consistent with a homodecameric composition of the holomer. High lability of the purified preparations and stabilization by reducing compounds suggested susceptibility to reactive-oxygen-species-mediated damage. Both NADH and NADPH were used as the electron donor, the latter resulting in a 3-fold higher Vmax. However, a higher affinity toward NADH was evident, and the NADPH-dependent activity was inhibited by NAD+, proline, arginine, and a variety of anions. With proline and arginine, the inhibition was of the competitive type with respect to the specific substrate, and of the uncompetitive- or mixed-type with respect to NADPH, respectively. The results suggest that, contrary to the enzyme from higher plants, yeast P5C reductase may preferentially use NADH in vivo. An in silico analysis was also performed to investigate the structural basis of such enzyme features. Superposition of the protein model with the experimental structure of P5C reductase from Medicago truncatula allowed us to hypothesize on the possible allosteric sites for arginine and anion binding, and the cysteine pairs that may be involved in disulfide formation
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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