1,720,958 research outputs found
Allosteric control of the c-di-GMP metabolism: insights from RmcA hybrid protein
Full text linkBiofilm is a microbial community whose formation is regulated by the dinucleotide cyclic-di GMP. The GGDEF diguanylate cyclases and EAL or HD-GYP phosphodiesterases control the balance of c-di-GMP. Most of these proteins have N-terminal sensing domains indicating that their activities are modulated by cellular and environmental stimuli. Moreover there are proteins bearing both the GGDEF and EAL or HD-GYP domains named hybrid proteins. The cross-talk between these two domains and with other regulatory domains is crucial to understand the output and the regulation of hybrid proteins. Given that nutrients are among the major driving forces guiding the change of c-diGMP levels, the characterization of the mechanistic details linking nutrients sensing to c-di-GMP homeostasis is very interesting and up to now poorly characterized. The aim of study was to identify a putative protein in P. aeruginosa able to link the nutrient state to c-di-GMP signalling. In particular my project has been focused on the characterization of the Hybrid Protein RmcA (Redox modulator of c-di-GMP A) from Pseudomonas aeruginosa. RmcA is a multidomain transmembrane protein carrying a periplasmic Venus Fly Trap (VFT) sensory domain, a transmembrane helix, three Per-Arnt-Sim (PAS) domain and one light, oxygen, or voltage domain (LOV) and finally the GGDEF-EAL domains.Few structural data are available on Hybrid Protein family of enzymes and these data indicate that the output of these proteins is regulated by a reciprocal allosteric control between the two GGDEF and EAL domains occuring via inter-domain interactions and ligand-induced conformationals changes. In addition, the final output is difficult to predict since it depends also on the interaction between the two domains and the upstream sensing/regulatory ones.
During the enzymatic characterization of RmcA, we observed alternative and novel reactivity of the GGDEF domain which has been analysed more deeply, also in comparison with other GGDEFcontaining enzymes. We found that DUAL protein showed an unusual catalytic activity converting GTP to GMP. We therefore investigated whether this unexpected feature is a common feature of different GGDEF containing proteins, including both DGCs and hybrid proteins. This side project has been useful for the overall study presented in this PhD thesis, since it allowed us to establish the best experimental conditions to study this domain
Beyond nitrogen metabolism: nitric oxide, cyclic-di-GMP and bacterial biofilms
No full textThe nitrogen cycle pathways are responsible for the circulation of inorganic and organic N-containing molecules in nature. Among these pathways, those involving amino acids, N-oxides and in particular nitric oxide (NO) play strategic roles in the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond their role in the N-cycle, amino acids and NO are also signalling molecules able to influence group behaviour in microorganisms and cell-cell communication in multicellular organisms, including humans.In this mini-review, we summarize the role of these compounds in the homeostasis of the bacterial communities called biofilms, commonly found in environmental, industrial and medical settings. Biofilms are difficult to eradicate since they are highly resistant to antimicrobials and to the host immune system. We highlight the effect of amino acids such as glutamate, glutamine and arginine and of NO on the signalling pathways involved in the metabolism of 3', 5'-cyclic diguanylic acid (c-di-GMP), a master regulator of motility, attachment and group behaviour in bacteria. The study of the metabolic routes involving these N-containing compounds represents an attractive topic to identify targets for biofilm control in both natural and medical settings
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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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