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Correction to: The model structure of the copper-dependent ammonia Monooxygenase (JBIC Journal of Biological Inorganic Chemistry, (2020), 25, 7, (995-1007), 10.1007/s00775-020-01820-0)
No full textIn the original article published, the authors missed to acknowledging an article published by Liew et al. (Mutagenesis of the hydrocarbon monooxygenase indicates a metal centre in subunit-C, and not subunit-B, is essential for copper- containing membrane monooxygenase activity, Microbiology 2014, 160, 1267–1277). “Thus far, however, the crystal structures have not fully established the location and composition of the pMMO active site [48], but all evidence points to either the CuB or the CuC site for this role. It is the opinion of the authors of the present study that the latter, with its labile water-bound position, should more logically constitute the enzyme active metal site. This conclusion is strongly supported by site-directed mutagenesis studies on the copper-dependent hydrocarbon monooxygenase (HMO) from Mycobacterium NBB4 which provided the first evidence that the C site was essential for activity, whereas mutations in the B site impaired, but did not eliminate, activity (E. F. Liew, D. Tong, N. V. Coleman, A. J. Holmes, Microbiology 2014, 160, 1267–1277)”
The model structure of the copper-dependent ammonia monooxygenase
Full text linkAbstract: Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. Graphic abstract: [Figure not available: see fulltext.
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
Facilitating Nitrification Inhibition through Green, Mechanochemical Synthesis of a Novel Nitrapyrin Complex
Full text linkNitrapyrin (NP) is applied to cultivated soils to inhibit the enzymatic activity of ammonia monooxygenase (AMO), but its poor aqueous solubility and high volatility severely limit its application. β-Cyclodextrin (β-CD) is commonly used to form inclusion complexes with hydrophobic molecules, improving water solubility and stability upon complexation. Here we report on the mechanochemical synthesis of the inclusion complex β-CD·NP, characterized via a combination of solid-state techniques, including ex-situ and in situ X-ray diffraction, Raman and NMR spectroscopies, transmission electron microscopy, and energy dispersive X-ray spectroscopy. The pure inhibitor NP was also structurally characterized. The β-CD·NP complex presents improved solubility and thermal stability, and still inhibits the enzymatic activity of AMO with high efficacy. All results indicate that the inclusion of NP into β-CD represents a viable route for the preparation of a novel class of inhibitors, with improved properties related to stability, water solubility, and good inhibition activity
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
Multifunctional urea cocrystal with combined ureolysis and nitrification inhibiting capabilities for enhanced nitrogen management
No full textThe novel ternary Zn(II)-thiourea-urea ionic cocrystal [Zn(thiourea)(urea)Cl2], (ZnTU) has been prepared by both solution and mechanochemical processes and structurally characterized by solid-state methods. ZnTU exhibited improved response properties to water as relative humidity as inherited from thiourea. The results of enzymatic activity measurements provide evidence that ZnTU is effective in modulating urea hydrolysis both in vitro (negatively impacting on the activity of isolated urease) and in vivo (decreasing the ureolytic activity of Sporosarcina pasteurii, a widespread soil bacterium), and that Zn(II) is the component of the cocrystal acting as the actual urease inhibitor. Concomitantly, the analysis of the ammonia monooxygenase (AMO) enzymatic activity in Nitrosomonas europaea, taken as a representative of soil ammonia-oxidizing bacteria, in the presence of ZnTU reveals that thiourea is the only component of ZnTU able to inhibit ammonia conversion to nitrite. It has also been shown that ZnTU maintains these capabilities when applied to bacterial cultures containing both S. pasteurii and N. europaea working in tandem. The compound can thus act both as a fertilizer via urea and via the Zn(II) and thiourea components, as a dual action inhibitor of the activities of the enzymes urease and AMO, which are responsible for the negative environmental and economic impact of the agricultural use of urea as soil fertilizer. These results indicate that ZnTU should be considered a novel material to improve N fertilization efficiency, toward a more environment-friendly agricultural practice
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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