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Search Results: 1 - 10 of 19359 matches for " Richard Christen "
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Querying the public databases for sequences using complex keywords contained in the feature lines
Olivier Croce, Micha?l Lamarre, Richard Christen
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-45
Abstract: We show that Entrez has severe limitations with respect to retrieving subsequences. SRS works well with simple keywords but not with keywords composed of several terms, and has problems with complex queries. ACNUC works well, but does not allow precise queries in the Feature qualifiers. We developed specific Perl scripts to precisely retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries. We improved parts of the bioPerl library to allow parsing of large data files, and we embedded these scripts in a user friendly interface (OS independent) for easy use.Although not as fast as the public tools that use prebuilt indexes, parsing the complete entries using a script is often necessary in order to retrieve the exact data searched for. Embedding in a user friendly interface allows biologists to use the scripts, which can easily be modified, if necessary, by bioinformaticians for unforeseen needs.The quantity of biological information available in the public databases is now very large and doubling nearly every year [1]. Projects involving high throughput data from approaches such as the new transcriptomic or genomic technologies require large quantities of data to be dealt with. For example, in order to design a DNA chip for bacterial identification, one may want to retrieve every available sequence for a universal gene such as the 16S rRNA gene (nearly 200,000 sequences expected by the end of year 2005).Retrieval of such sequences is not trivial. Retrieval by sequence similarity is not feasible, since some of these genes are very variable (ITS regions for example). Also it is difficult, if not impossible, to determine a cutoff level in order to exclude non homologous gene sequences. Blast [2] for example allows a cutoff according to the "E value", while Exonerate [3] also allows a cutoff on percentage of similarity. The "E value" cutoff depends on the database size that changes every day. The percentage of similarity is be
Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences
Dipankar Bachar,Laure Guillou,Richard Christen
Dataset Papers in Science , 2013, DOI: 10.7167/2013/854869
Abstract: The gene encoding SSU-rRNA sequences is the tool of choice for phylogenetic analyses and environmental biodiversity analyses of bacteria, Archaea but also unicellular Eukaryota. In Eukaryota, gene sequences may often be interrupted by long or several introns. Searching in GenBank release 188, we found descriptions of 3638 such sequences. Using a database of 180?000 SSU-rRNA sequences well annotated for taxonomy and a C++ program written for that purpose, we computed the presence of 18?691 introns (among which the 3638 described introns). Filtering on length and sequence quality, 3646 sequences were retained. These introns were clustered; clusters were analyzed for the presence of single or multiple clades at various levels of taxonomic depth, allowing future analyses of horizontal transfers. Various analyses of the results are provided as tabulated files as well as FASTA files of described or computed introns. Each sequence is annotated for cellular location (nuclear, chloroplast, and mitochondria), positions at which they were found in the SSU-rRNA sequences and taxonomy as provided by GenBank. 1. Introduction The gene that microbiologists use to determine the taxonomic affiliations of microbes using molecular methods needs to meet a number of requirements. It has to be conservative in its function and present in every organism analyzed. Often the presence of conserved domains is required, allowing the design and use of universal PCR primers. Finally, sequences of most known organisms must be available in the public databases (i.e., International Nucleotide Sequence Database Collaboration (INSDC) between Japanese, European, and American nucleotide databases, resp., DDBJ, ENA, and GenBank, http://www.insdc.org/). A gene meets these requirements to a high degree: the gene for one of the RNA subunits that together form the ribosome, also known as the small subunit ribosomal RNA (SSU-rRNA) gene. For that reason, the gene encoding the SSU-rRNA serves as a prominent tool for phylogenetic and environmental biodiversity analyses of bacteria, Archaea but also unicellular Eukaryota [1–3]. SSU-rRNA gene sequences may contain numerous self-splicing introns of variable lengths [4–23]. The SSU-rRNA genes can thus be enlarged to up to 3.5?kb. Introns have rarely been identified in bacterial SSU-rRNA gene sequences (see one example in Thiomargarita namibiensis [5]), but they are often present in SSU-rRNA gene sequences of Eukaryota (see the aforementioned part). Such length heterogeneity of SSU-rRNA gene sequences has so far seldomly been considered when constructing
THEA: ontology-driven analysis of microarray data
Claude Pasquier,Fabrice Girardot,Karim Jevardat De Fombelle,Richard Christen
Quantitative Biology , 2007, DOI: 10.1093/bioinformatics/bth295
Abstract: MOTIVATION: Microarray technology makes it possible to measure thousands of variables and to compare their values under hundreds of conditions. Once microarray data are quantified, normalized and classified, the analysis phase is essentially a manual and subjective task based on visual inspection of classes in the light of the vast amount of information available. Currently, data interpretation clearly constitutes the bottleneck of such analyses and there is an obvious need for tools able to fill the gap between data processed with mathematical methods and existing biological knowledge. RESULTS: THEA (Tools for High-throughput Experiments Analysis) is an integrated information processing system allowing convenient handling of data. It allows to automatically annotate data issued from classification systems with selected biological information coming from a knowledge base and to either manually search and browse through these annotations or automatically generate meaningful generalizations according to statistical criteria (data mining). AVAILABILITY: The software is available on the website http://thea.unice.fr/
Early Gene Expression in Wounded Human Keratinocytes Revealed by DNA Microarray Analysis
Manal A. Dayem,Chimène Moreilhon,Laurent Turchi,Virginie Magnone,Richard Christen,Gilles Ponzio,Pascal Barbry
Comparative and Functional Genomics , 2003, DOI: 10.1002/cfg.239
Abstract: Wound healing involves several steps: spreading of the cells, migration and proliferation. We have profiled gene expression during the early events of wound healing in normal human keratinocytes with a home-made DNA microarray containing about 1000 relevant human probes. An original wounding machine was used, that allows the wounding of up to 40% of the surface of a confluent monolayer of cultured cells grown on a Petri dish (compared with 5% with a classical ‘scratch’ method). The two aims of the present study were: (a) to validate a limited number of genes by comparing the expression levels obtained with this technique with those found in the literature; (b) to combine the use of the wounding machine with DNA microarray analysis for large-scale detection of the molecular events triggered during the early stages of the wound-healing process. The time-courses of RNA expression observed at 0.5, 1.5, 3, 6 and 15 h after wounding for genes such as c-Fos, c-Jun, Egr1, the plasminogen activator PLAU (uPA) and the signal transducer and transcription activator STAT3, were consistent with previously published data. This suggests that our methodologies are able to perform quantitative measurement of gene expression. Transcripts encoding two zinc finger proteins, ZFP36 and ZNF161, and the tumour necrosis factor α-induced protein TNFAIP3, were also overexpressed after wounding. The role of the p38 mitogen-activated protein kinase (p38MAPK) in wound healing was shown after the inhibition of p38 by SB203580, but our results also suggest the existence of surrogate activating pathways.
Defining Reference Sequences for Nocardia Species by Similarity and Clustering Analyses of 16S rRNA Gene Sequence Data
Manal Helal,Fanrong Kong,Sharon C. A. Chen,Michael Bain,Richard Christen,Vitali Sintchenko
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019517
Abstract: The intra- and inter-species genetic diversity of bacteria and the absence of ‘reference’, or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia.
TreeDyn: towards dynamic graphics and annotations for analyses of trees
Fran?ois Chevenet, Christine Brun, Anne-Laure Ba?uls, Bernard Jacq, Richard Christen
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-439
Abstract: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees.TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.Graphical management of trees requires processing and information visualization methods allowing the user to deal with single large trees or multiple connected trees. Although solutions have been proposed for the management of single and large trees [1-5], comparisons among trees [6,7], and annotations of trees [8-10], an integrated tool for the graphical management of annotations and comparisons of multiple trees is not yet available (see Discussion). Presently, there are real needs to explore, compare, display and interpret trees using information not directly contained in these trees, such as taxonomy, geography, life history traits or even ontologies [11-14]. TreeDyn aims at filling these needs. Tree
Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci
Maha Bouzid, Kevin M Tyler, Richard Christen, Rachel M Chalmers, Kristin Elwin, Paul R Hunter
BMC Microbiology , 2010, DOI: 10.1186/1471-2180-10-213
Abstract: The majority of the putative species-specific genes examined were in fact common to C. parvum and C. hominis. PCR product sequence analysis revealed interesting SNPs, the majority of which were species-specific. These genetic loci allowed us to construct a robust and multi-locus analysis. The Neighbour-Joining phylogenetic tree constructed clearly discriminated the previously described lineages of Cryptosporidium species and subtypes.Most of the genes identified as being species specific during bioinformatics in Cryptosporidium sp. are in fact present in multiple species and only appear species specific because of gaps in published genome sequences. Nevertheless SNPs may offer a promising approach to studying the taxonomy of closely related species of Cryptosporidia.At least eight Cryptosporidium species infect humans [1]; however, only two species are of major significance to public health by causing the majority of human cases both sporadic and outbreak related cases, C. hominis and C. parvum [2-5]. Cryptosporidium parvum is zoonotic and infects a wide range of animal hosts including humans, whereas C. hominis is generally restricted to humans [6]. Therefore, the main phenotypic difference between C. hominis and C. parvum is the host range [1-3]. In addition, these two Cryptosporidium species differ in geographical and temporal distribution and pathogenicity [7,8]. Differential risk factors and transmission routes have also been identified [3,7,9]. However human infections are not solely linked to these two species and other species and genotypes have been associated with illness [10]. These additional species and genotypes are therefore considered emergent. This was the case of the rabbit genotype, the aetiological agent in an outbreak of waterborne human cryptosporidiosis in Northamptonshire, East Midlands, England [11,12]. Subsequent characterization studies revealed that the rabbit genotype, which caused this outbreak, corresponds to Cryptosporidium cuniculus
Biochemical, Transcriptional and Translational Evidences of the Phenol-meta-Degradation Pathway by the Hyperthermophilic Sulfolobus solfataricus 98/2
Alexia Comte, Pierre Christen, Sylvain Davidson, Matthieu Pophillat, Jean Lorquin, Richard Auria, Gwenola Simon, Laurence Casalot
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0082397
Abstract: Phenol is a widespread pollutant and a model molecule to study the biodegradation of monoaromatic compounds. After a first oxidation step leading to catechol in mesophilic and thermophilic microorganisms, two main routes have been identified depending on the cleavage of the aromatic ring: ortho involving a catechol 1,2 dioxygenase (C12D) and meta involving a catechol 2,3 dioxygenase (C23D). Our work aimed at elucidating the phenol-degradation pathway in the hyperthermophilic archaea Sulfolobus solfataricus 98/2. For this purpose, the strain was cultivated in a fermentor under different substrate and oxygenation conditions. Indeed, reducing dissolved-oxygen concentration allowed slowing down phenol catabolism (specific growth and phenol-consumption rates dropped 55% and 39%, respectively) and thus, evidencing intermediate accumulations in the broth. HPLC/Diode Array Detector and LC-MS analyses on culture samples at low dissolved-oxygen concentration (DOC = 0.06 mg.L?1) suggested, apart for catechol, the presence of 2-hydroxymuconic acid, 4-oxalocrotonate and 4-hydroxy-2-oxovalerate, three intermediates of the meta route. RT-PCR analysis on oxygenase-coding genes of S. solfataricus 98/2 showed that the gene coding for the C23D was expressed only on phenol. In 2D-DIGE/MALDI-TOF analysis, the C23D was found and identified only on phenol. This set of results allowed us concluding that S. solfataricus 98/2 degrade phenol through the meta route.
Modeling Electric Discharges with Entropy Production Rate Principles
Thomas Christen
Entropy , 2009, DOI: 10.3390/e11041042
Abstract: Under which circumstances are variational principles based on entropy production rate useful tools for modeling steady states of electric (gas) discharge systems far from equilibrium? It is first shown how various different approaches, as Steenbeck’s minimum voltage and Prigogine’s minimum entropy production rate principles are related to the maximum entropy production rate principle (MEPP). Secondly, three typical examples are discussed, which provide a certain insight in the structure of the models that are candidates for MEPP application. It is then thirdly argued that MEPP, although not being an exact physical law, may provide reasonable model parameter estimates, provided the constraints contain the relevant (nonlinear) physical effects and the parameters to be determined are related to disregarded weak constraints that affect mainly global entropy production. Finally, it is additionally conjectured that a further reason for the success of MEPP in certain far from equilibrium systems might be based on a hidden linearity of the underlying kinetic equation(s).
Dialekt/ologie an der Jahrtausendwende - Die neuen dialektologischen Wenden
Christen, Helen
Linguistik Online , 2005,
Abstract:
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