1,721,049 research outputs found
Research and caracterization of new enzymes from marine bacteria active on algal polysaccharides
No full textLes polysaccharides algaux sont une ressource marine dont la valorisation est limitée par le manque d’outils adéquats à leur modification chimique. Grâce aux enzymes qu’elles synthétisent, les bactéries marines, qui vivent au contact des algues, représentent un enjeu majeur pour le développement des biotechnologies bleues. Cette thèse a permis de cloner et d’obtenir sous forme soluble plusieurs dizaines de nouvelles enzymes bactériennes marines actives sur des polysaccharides algaux. Quatre d’entre elles ont fait l’objet d’une étude plus spécifique. Les deux premières sont impliquées dans les voies de dégradation des carraghénanes. La première, ZgCgkA, est une κ-carraghénase de la famille 16 des glycosides hydrolases (GH), synthétisée par la bactérie Zobellia galactanivorans. Son étude biochimique et structurale, par cristallographie des rayons X, a permis de corréler certaines différences structurales à des modes d’interaction différents avec le substrat, au sein de cette sous-famille des GH16. La seconde enzyme étudiée, une β-carrabiose hydrolase de Pseudoalteromonas carrageenovora, agit sur des oligosaccharides hybrides β/κ. Son étude biochimique et phylogénétique a permis de proposer la création d’une nouvelle famille de GH apparentée aux GH42. Enfin, les deux dernières enzymes étudiées, une GH29 et une GH non-classée, sont codées dans un locus de Z. galactanivorans qui semble impliqué dans la dégradation de substrats enrichis en fucose sulfaté. La GH29 a fait l’objet d’une caractérisation biochimique sur substrat synthétique, et son analyse structurale est en cours. Ces différents résultats permettent d’envisager l’utilisation de ces enzymes comme outils de valorisation des polysaccharides algaux, en particulier des carraghénanes.Algal polysaccharides are marine resources valorization of which is hindered by the lack of proper tools to modify their structure. Marine bacteria living associated to macroalgae synthesize enzymes acting on these polysaccharides. They represent a great opportunity for the development of bleu biotechnology. This thesis project resulted in the successful cloning and soluble protein production of several dozen new bacterial enzymes active on algal polysaccharides. Four of them have been studied in detail. The first two are involved in carrageenan degradation pathways. The first one, ZgCgkA, is a κ-carrageenase from family 16 of glycoside hydrolases (GH), synthesized by Zobellia galactanivorans. Its biochemical and structural study, by X-ray crystallography, provided a link between structural features and different interaction modes with the substrate in this GH16 sub-family. The second enzyme, a β-carrabiose hydrolase from Pseudoalteromonas carrageenovora, is active on hybrid oligosaccharides of β/κ-carrageenan. Its biochemical and phylogenetic study suggests the creation of a new GH family, distantly related to the GH42 family. The last two enzymes, a GH29 and a non-classified GH, are encoded in a locus of Z. galactanivorans probably dedicated to the degradation of sulfated fucans. GH29 was biochemically characterized on synthetic substrate, and its structural study is ongoing. These results raise the possibility to use these enzymes as tools for the valorization of algal polysaccharides, particularly carrageenans
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
The Agarolytic System of Microbulbifer elongatus PORT2, Isolated from Batu Karas, Pangandaran West Java Indonesia
Get PDFAgar is a marine heteropolysaccharide with repeating units consisting of 3,6-α-anhydro-L-galactopyranose and D-galactopyranose linked by α-(1,3) and β-(1,4) linkages. It has been promoted as a prospective replacement for petroleum-based feedstocks and other applications. Enzymatic biotransformation of agar generates high specific products: It is also more environmentally friendly than chemical hydrolysis. In particular, agarolytic bacteria and their agarases are preferred for the processing of agar into sugar derivatives.
Agar-producing macroalgae are one of Indonesia's national commodities. However, agar-based products and technology are rarely developed in Indonesia. This research is aimed to explore the potential of an Indonesian marine bacterium and its agarases as bioagents for agar bioprocessing. The research objectives are to identify the novelty of the isolate among known agarolytic bacteria using microbiology and molecular biology approaches, to elucidate the agarolytic system of the bacterium using in silico genome analysis, to express and characterize the recombinant agarases, and to elucidate their potential for producing agar-derived saccharides from Indonesian natural agar.
Microbulbifer elongatus PORT2 is a gram-negative marine bacterium that had been isolated from Batu Karas seawater, Pangandaran, West Java Indonesia. PORT2 shows potential as biocatalysts for agar saccharides conversion by showing remarkable agar liquefaction. The annotation of the draft genome identifies six putative β-agarases consist of three GH50, two GH86, and one GH16 in M. elongatus PORT2. Those agarases are clustered at two different contigs. Besides agarases, other genes for D-galactose and 3,6 anhydro-L galactose metabolism, sugar transports and regulatory system are found in the vicinity of the agarases clusters. Despite the ability to utilize agar as a sole carbon sole, PORT2 lacks any putative α-agarase GH117 or GH96. Both are responsible for the cleavage of α-glycosidic bonds in agar. Indeed, several hypothetical proteins are in the neighborhood of the agarase gene clusters in M. elongatus PORT2. They probably could have a function as the alternative machinery or pathway for agar monomerization that needs clarification in future research work.
Four recombinant β-agarases from PORT2; AgaA50, AgaB50, AgaC50, and AgaF16A have been successfully overexpressed in E.coli and characterized. The AgaA50 and AgaC50 exhibit metal-dependent activity. They perform exo-agarolytic modes and generates neoagarobiose (NA2). The AgaB50 can act as endo-and exo-β-agarase without any additional activator and produces neoagarohexaose (NA6), neoagarotetraose (NA4), and NA2. AgaF16 produces NA6 and NA4. The enzyme shows pure endo-catalytic action which thiol agents positively affect its activity. The synergetic reaction of AgaF16A and AgaA50 converts Indonesian Gelidium agar into NA2 and Gracilaria agar into modified NA2. The modified NA2 from Gracilaria agar could promise new potential bioactivity that is different from agarose-derived NA2 due to the presence of additional side chains on the saccharide backbone. The NA6, NA4, and NA2 products from agarose have shown potential pharmaceutical applications such as immunomodulator, anti-tumor, antioxidant, anti-diabetic, and moisturizer.
Despite being isolated from a mesophilic marine bacterium, the recombinant agarases from M. elongatus PORT2 are active at 50 °C and pH between 6.5 to 8. They maintain more than 75% of their activities even after 1 h preincubation at 50 °C, except for AgaC50. Their thermostability gives advantages for the effective biocatalytic conversion of agar because the substrate is more accessible at mild pH and the temperature above the sol-gel condition (> 40 °C).:Contents
1. Introduction 1
1.1. Motivation and Scientific Goals 1
1.2. Literature Review 3
2. Materials and Methods 12
2.1. Materials 12
2.2. Methods 13
3. Agarolytic Bacterium Microbulbifer elongatus PORT2 22
3.1. Results 22
3.2. Discussion 28
4. Genome Profiling for In Silico Elucidation of the Agarolytic System 32
4.1. Results 32
4.2. Discussion 41
5. Recombinant Agarases from Microbulbifer elongatus PORT2 44
5.1. Results 44
5.2. Discussion 71
6. Conclusions and Outlooks 78
References 81
Appendices 97
Acknowledgements 11
Functions and specificity of bacterial carbohydrate sulfatases targeting host glycans
Get PDFSulfated host glycans (mucin O-glycans and glycosaminoglycans [GAGs]) are critical nutrient sources and colonisation factors for Bacteroidetes of the human gut microbiota (HGM); a complex ecosystem comprising essential microorganisms that coevolved with humans to serve important roles in pathogen protection, immune signalling, and host nutrition. Carbohydrate sulfatases are essential enzymes to access sulfated host glycans and are capable of exquisite regio- and stereo-selective substrate recognition. In these enzymes, the common recognition features of each subfamily are correlated with their genomic and environmental context. The exo-acting carbohydrate sulfatases are attractive drug targets amenable to small-molecule screening and subsequent engineering, and their high specificity will help elucidate the role of glycan sulfation in health and disease. Inhibition of carbohydrate sulfatases provides potential routes to control Bacteroidetes growth and to explore the influence of host glycan metabolism by Bacteroidetes on the HGM ecosystem. The roles of carbohydrate sulfatases from the HGM organism Bacteroides thetaiotaomicron and the soil isolated Pedobacter heparinus (P. heparinus) in sulfated host glycan metabolism are examined and contrasted, and the structural features underpinning glycan recognition and specificity explored
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe 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
Get PDFWe 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
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