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De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum
Samuel E. Fox, Matthew Geniza, Mamatha Hanumappa, Sushma Naithani, Chris Sullivan, Justin Preece, Vijay K. Tiwari, Justin Elser, Jeffrey M. Leonard, Abigail Sage, Cathy Gresham, Arnaud Kerhornou, Dan Bolser, Fiona McCarthy, Paul Kersey, Gerard R. Lazo, Pankaj Jaiswal
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0096855
Abstract: Background Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Principal Findings The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ~500,000 single nucleotide polymorphism (SNP) and ~22,000 simple sequence repeat (SSR) sites. Conclusions De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers.
The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants
Lisa C Crossman, Virginia C Gould, J Maxwell Dow, Georgios S Vernikos, Aki Okazaki, Mohammed Sebaihia, David Saunders, Claire Arrowsmith, Tim Carver, Nicholas Peters, Ellen Adlem, Arnaud Kerhornou, Angela Lord, Lee Murphy, Katharine Seeger, Robert Squares, Simon Rutter, Michael A Quail, Mari-Adele Rajandream, David Harris, Carol Churcher, Stephen D Bentley, Julian Parkhill, Nicholas R Thomson, Matthew B Avison
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-4-r74
Abstract: The genome of the bacteremia-associated isolate S. maltophilia K279a is 4,851,126 bp and of high G+C content. The sequence reveals an organism with a remarkable capacity for drug and heavy metal resistance. In addition to a number of genes conferring resistance to antimicrobial drugs of different classes via alternative mechanisms, nine resistance-nodulation-division (RND)-type putative antimicrobial efflux systems are present. Functional genomic analysis confirms a role in drug resistance for several of the novel RND efflux pumps. S. maltophilia possesses potentially mobile regions of DNA and encodes a number of pili and fimbriae likely to be involved in adhesion and biofilm formation that may also contribute to increased antimicrobial drug resistance.The panoply of antimicrobial drug resistance genes and mobile genetic elements found suggests that the organism can act as a reservoir of antimicrobial drug resistance determinants in a clinical environment, which is an issue of considerable concern.The rise of antimicrobial drug resistance in bacteria is one of the biggest threats to healthcare provision in the developed world. Few new antimicrobial drugs are undergoing clinical trials, and almost none are effective against Gram-negative multi-drug resistant (MDR) pathogens [1]. A return to the pre-antibiotic era is a possibility, and for some infections is the current reality [2].Antimicrobial resistance in historically common pathogens is usually either acquired on a mobile genetic element or results from a mutation [3]. However, some opportunistic pathogens are intrinsically resistant to the actions of a number of antimicrobial classes. These tend to be of environmental origin, and their intrinsic drug resistance determinants either provide resistance to antibiotics produced by competitors, or represent broad-spectrum methods for removing toxic compounds or waste products that, by chance, protect against antimicrobials [3,4]. It is known that established opportuni
Arts and Scholastic Performance  [PDF]
Arnaud Cabanac
Creative Education (CE) , 2017, DOI: 10.4236/ce.2017.815163
Abstract: Pleasant environmental music during an academic test helped students to overcome stress. As a result the grades they obtained were higher. It was also demonstrated that students selecting music as optional course performed better, than music-less control students over three consecutive years. Yet, there remained ambiguities as for the causes of the higher test performance of these students. Our study confirmed a Mozart effect, and further showed a latency of two to three years for such a positive influence to take place, suggesting that it is the practice of music itself that helps cognition. We showed also that other art courses, when freely chosen, have similar positiveinfluences on students’ performances, illustrating that the principles of learning are linked to hedonism and to will effort in a more general manner.
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.
Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord Barboza, Raoul JP Bonnal, Richard Bruskiewich, Jan C Bryne, José M Fernández, Akira Funahashi, Paul MK Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho
Journal of Biomedical Semantics , 2010, DOI: 10.1186/2041-1480-1-8
Abstract: Web services are software systems designed to be manipulated remotely over a network, often through web-based application programming interfaces (APIs). Through web services, users can take advantage of the latest maintained data and computational resources of remote service providers via a thin client. Web services are increasingly being adopted in the field of bioinformatics as an effective means for data and software access, especially in light of the rapid accumulation of large amounts of information for the life sciences [1]. Most of the major bioinformatics centers, including the National Center for Biotechnology Information (NCBI) in the US [2], the European Bioinformatics Institute (EBI) in the UK [3], and the DNA Data Bank of Japan (DDBJ) [4]/Kyoto Encyclopedia of Genes and Genomes (KEGG) [5]/Protein Data Bank Japan (PDBj) [6] in Japan, provide web service interfaces to their databases and computational resources. Since the web service model is based on open standards, these services are designed and expected to be interoperable [7]. However, many of the services currently available use their own data type definitions and naming conventions, resulting in a lack of interoperability that makes it harder for end users and developers to utilize these services for the creation of biological analysis workflows [8]. Moreover, these services are often not easily usable from programs written in specific computer languages, despite the language-independent specification of web services themselves. Some of the main reasons for that are the use of functionality not supported in a particular web service software implementation, and the lack of compliance with the SOAP/WSDL specification in a programming language's web service libraries.To overcome this situation and to assure interoperability between web services for biology, standardization of exchangeable data types and adoption of compatible interfaces to each service are essential. As a pilot study, the BioMoby proj
Dissociation between Performances in Water Maze and Spontaneous Alternation in BALB/C versus A/J Mice  [PDF]
Julien Celestine, Arnaud Tanti, Arnaud Aubert
Journal of Behavioral and Brain Science (JBBS) , 2012, DOI: 10.4236/jbbs.2012.22018
Abstract: Learning processes are extensively studied in behavioral neuroscience. As experimental models, Morris Water Maze (MWM) and Spontaneous Alternation (SA) represent two of the most frequently used laboratory tests to respectively address spatial vs non-spatial tasks. Several factors have been shown to impact on those learning, including strain, gender, apparatus, conditioning, vision, lighting conditions and stress level. In order to focus on the later, we compared the acquisition of two learning tasks (MWM and SA) in BALB/c and A/J mice, which are known as fearful and stress-sensitive strains. Here, we report that BALB/c mice exhibited higher performances than A/J mice in the MWM (i.e. spatial reference memory task), whereas A/J mice performed better in the SA (i.e. spatial working memory task). These results indicate dissociated processes in the acquisition of spatial vs non-spatial tasks, and emphasize a varying influence of emotional reactivity on different forms of cognition.
Criatividade, comunica??o e produ??o do saber
Sales, Arnaud;
Sociologias , 2008, DOI: 10.1590/S1517-45222008000100003
Abstract: knowledge production is a key element of the dynamics of contemporary societies that until now have been based on uneven levels of scientific and professional knowledge. the aim of this work is to understand, from a sociological point of view, the various aspects of the relationship between creativity, communication and knowledge production, starting from the following questions: what is the role of communication in the elaboration of discoveries or intellectual advances? what is the role of individuals and networks in these advances? and finally, what are the characteristics, especially the communicational ones, of the more creative institutions? the text is based on the works of philippe breton (communication and the status of knowledge), randal collins (network creativity), rogers hollingsworth (cognitive complexity, institutional diversity, quality of the research environment in terms of scientific exchange and discussion). these questions are not restricted to a strictly academic debate. they are also directly related to the practices of research environments, professors-researchers and students of master’s and doctor’s degree.
Um candomblé na Bélgica: tra?os etnográficos de tentativa de instala??o e suas dificuldades
Halloy, Arnaud;
Revista de Antropologia , 2004, DOI: 10.1590/S0034-77012004000200004
Abstract: in this article, i propose to go through some difficulties encountered in a setting up attempt of a candomblé (afro-brasilian cult) in belgium. my analysis will propose three main categories of problems: situations undermining the legitimation of the cult's chief and the respect of some ritual constraints; various "adaptation" attempts to human and material resources available; difficulties of learning some categories of knowledge that are not based on a linguistic formulation. to focus in this study on problematic situations does not aim to drow a chaotic picture of a "disrooted" cult but to account ethnographicaly for the dynamic and the multi-facial and builded characteristics of religious experience.
Les réseaux négociants de trois maisons huguenotes de Cadix, à la fin du xviiie siècle : des réseaux languedociens, protestants ou fran ais ?
Arnaud Bartolomei
Liame : Histoire et Histoire de l’Art des époques Moderne et Contemporaine de l’Europe Méditerranéenne et de ses Périphéries , 2012,
Abstract: Dans le dernier tiers du xviiie siècle, pour faire leur commerce, les négociants fran ais de Cadix – le port qui servait de tête de pont au commerce colonial espagnol – s’appuyaient sur deux types de réseaux marchands : d’une part, des correspondants résidant en Europe, qui leur fournissaient les biens manufacturés recherchés sur les marchés américains et qui recevaient, en échange, les piastres et autres denrées coloniales que les cargadores leur rapportaient en retour ; d’autre part, de...
Le multilinguisme, un atout pour le fran ais au Danemark
Arnaud Sgambato
Synergies Pays Scandinaves , 2011,
L'affectivité et le comportement non verbal en classe de langue étrangère
Christine Arnaud
Synergies Espagne , 2008,
Abstract: Nous abordons dans cet article les aspects affectifs dansl’enseignement/apprentissage des langues étrangères et nous nous intéressonsplus précisément aux comportements non verbaux des apprenants et desenseignants. Nos réflexions sont basées sur la thèse de doctorat (Arnaud,1999) intitulée : Les enseignants et les apprenants en classe de langueétrangère. étude des aspects affectifs , et sur une étude postérieureconcernant les interactions en classe de langue. Des marqueurs non verbauxliés à des paramètres tels que l’implication, l’extraversion, le fait de sesentir à l’aise en classe, la cohésion de groupe et l’adhésion au professeur,sont décrits sur la base de nombreuses heures de classe filmées. Le r lenotamment du regard, du silence, du rire, de l’expression faciale, de certainsgestes, certaines postures est décrit et analysé, parallèlement aux jugementsémis par les apprenants au début et à l’issue du cours.
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