17 research outputs found
Modular Neural Networks and Their Application in Exon Prediction
Rapid progress in genome research has produced a huge amount of nucleotide sequence data, including hundreds of complete genomes (Entrez Genomes). There is therefore a need to automate the gene prediction process to ensure that the amount of information does not in itself become a problem. Many prediction engines are available to facilitate such identification, but their application scope and prediction capability vary. This paper investigates the potential to improve gene prediction by integrating three available engines, GrailEXP, Genscan, and MZEF by means of a modular mixture of expert (MoE) neural network, where the utilization of a modular architecture is able to directly support the partitioned nature of the original data sources. The three selected engines represent three different categories of the prediction software. We were able to demonstrate that the integration system has markedly better recovery (proportion of actual exons that are predicted) than any of the individual prediction engines alone. After integration, we were able to achieve a higher correlation coefficient of exon prediction and thus a higher accuracy of the results. <!-- The program is available on line at <a href="http://cbr-rbc.nrc-cnrc.gc.ca/pany/integ.html ">http://cbr-rbc.nrc-cnrc.gc.ca/pany/integ.html</a> with links to the data used for this research. -->Les avanc\ue9es rapides r\ue9alis\ue9es dans la recherche g\ue9nomique ont produit une vaste quantit\ue9 de donn\ue9es sur la s\ue9quence des nucl\ue9otides, et notamment des centaines de g\ue9nomes complets (Entrez Genome). Il s'av\ue8re par cons\ue9quent n\ue9cessaire d'automatiser le processus de pr\ue9diction des g\ue8nes, pour que la quantit\ue9 d'information disponible ne devienne pas un probl\ue8me par elle-m\ueame. Il existe de nombreux moteurs de pr\ue9diction qui permettent de faciliter cette identification, mais leur champ d'application et leurs capacit\ue9s de pr\ue9diction varient. Cet article \ue9tudie la possibilit\ue9 d'am\ue9liorer la pr\ue9diction des g\ue8nes, en int\ue9grant trois moteurs existants, GrailEXP, Genscan et MZEF, au moyen d'une combinaison modulaire de r\ue9seaux neuronaux experts, dans laquelle l'utilisation d'une architecture modulaire est en mesure de prendre en charge directement la nature partitionn\ue9e des sources de donn\ue9es originales. Les trois moteurs choisis repr\ue9sentent trois cat\ue9gories diff\ue9rentes de logiciels de pr\ue9diction. Nous avons pu d\ue9montrer que le syst\ue8me d'int\ue9gration comportait des capacit\ue9s de r\ue9cup\ue9ration significativement meilleures (proportion des exons pr\ue9dits) que celles de n'importe quel des moteurs de pr\ue9diction individuels. Apr\ue8s int\ue9gration, nous avons \ue9t\ue9 en mesure d'obtenir un coefficient de corr\ue9lation sup\ue9rieur dans la pr\ue9diction des exons, et par cons\ue9quent une plus grande exactitude dans les r\ue9sultats. <!-- Le programme est disponible en ligne \ue0 l'adresse <a href="http://cbr-rbc.nrc-cnrc.gc.ca/pany/integ.html ">http://cbr-rbc.nrc-cnrc.gc.ca/pany/integ.html</a>, avec des liens vers les donn\ue9es utilis\ue9es pour ce travail de recherche. -->NRC publication: Ye
Two different and highly organized mechanisms of translation initiation in the archaeon <i>Sulfolobus solfataricus</i>
Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: The thermoalkaliphile Anaerobranca gottschalkii.
Anaerobranca gottschalkii strain LBS3 T is an extremophile living at high temperature (up to 65 degrees C) and in alkaline environments (up to pH 10.5). An assembly of 696 DNA contigs representing about 96% of the 2.26-Mbp genome of A. gottschalkii has been generated with a low-sequence-coverage shotgun-sequencing strategy. The chosen sequencing strategy provided rapid and economical access to genes encoding key enzymes of the mono- and polysaccharide metabolism, without dilution of spare resources for extensive sequencing of genes lacking potential economical value. Five of these amylolytic enzymes of considerable commercial interest for biotechnological applications have been expressed and characterized in more detail after identification of their genes in the partial genome sequence: type I pullulanase, cyclodextrin glycosyltransferase (CGTase), two alpha-amylases (AmyA and AmyB), and an alpha-1,4-glucan-branching enzyme
Identification and molecular characterization of the first a-xylosidase from an Archaeon
We here report the first molecular characterization of an -xylosidase (XylS) from an Archaeon. Sulfolobus solfataricus is able to grow at temperatures higher than 80 °C on several carbohydrates at acidic pH. The isolated xylS gene encodes a monomeric enzyme homologous to -glucosidases, -xylosidases, glucoamylases and sucrase-isomaltases of the glycosyl hydrolase family 31. xylS belongs to a cluster of four genes in the S. solfataricus genome, including a -glycosidase, an hypothetical membrane protein homologous to the major facilitator superfamily of transporters, and an open reading frame of unknown function. The -xylosidase was overexpressed in Escherichia coli showing optimal activity at 90 °C and a half-life at this temperature of 38 h. The purified enzyme follows a retaining mechanism of substrate hydrolysis, showing high hydrolytic activity on the disaccharide isoprimeverose and catalyzing the release of xylose from xyloglucan oligosaccharides. Synergy is observed in the concerted in vitro hydrolysis of xyloglucan oligosaccharides by the -xylosidase and the -glycosidase from S. solfataricus. The analysis of the total S. solfataricus RNA revealed that all the genes of the cluster are actively transcribed and that xylS and orf3 genes are cotranscribed
Properties of the recombinant a-glucosidase from Sulfolobus solfataricus in relation to starch processing
An -glucosidase activity (EC 3.2.1.20) isolated from Sulfolobus solfataricus strain MT-4 was characterised and found of interest at industrial level in the saccharification step of hydrolysis process of starch. The gene encoding for the enzyme was expressed in Escherichia coli BL21 (DE3) with a yield of 87.5 U/g of wet biomass. The recombinant cytosolic enzyme was purified to homogeneity with a rapid purification procedure employing only steps of selective and progressive thermal precipitations with a final yield of 75.4nd a purification of 14.5-fold. The properties of this thermophilic -glucosidase were compared with those of the -glucosidase of a commercial preparation from Aspergillus niger used in the starch processing
Addressing proteolytic efficiency in enzymatic degradation therapy for celiac disease.
Celiac disease is triggered by partially digested gluten proteins. Enzyme therapies that complete protein digestion in vivo could support a gluten-free diet, but the barrier to completeness is high. Current options require enzyme amounts on the same order as the protein meal itself. In this study, we evaluated proteolytic components of the carnivorous pitcher plant (Nepenthes spp.) for use in this context. Remarkably low doses enhance gliadin solubilization rates, and degrade gliadin slurries within the pH and temporal constraints of human gastric digestion. Potencies in excess of 1200:1 (substrate-to-enzyme) are achieved. Digestion generates small peptides through nepenthesin and neprosin, the latter a novel enzyme defining a previously-unknown class of prolyl endoprotease. The digests also exhibit reduced TG2 conversion rates in the immunogenic regions of gliadin, providing a twin mechanism for evading T-cell recognition. When sensitized and dosed with enzyme-treated gliadin, NOD/DQ8 mice did not show intestinal inflammation, when compared to mice challenged with only pepsin-treated gliadin. The low enzyme load needed for effective digestion suggests that gluten detoxification can be achieved in a meal setting, using metered dosing based on meal size. We demonstrate this by showing efficient antigen processing at total substrate-to-enzyme ratios exceeding 12,000:1.YesThis work was supported by the University of Calgary and by a grant to DCS from the Canadian Celiac Association. EFV holds a Canada Research Chair and is funded by CIHR MOP#142773. PM, HM and PH were supported by MEYS (LO1509) and EU (CZ.1.05/1.1.00/02.0109). We thank Drs. Chella David and Joseph Murray of the Mayo Clinic for kindly providing the original breeding pairs of SPF NOD AB?DQ8 (NOD/DQ8) mice. We thank Luppo Edens of DSM Food Specialties (Netherlands) for the gift of AN-PEP. We thank Brent Schriemer, Laurent Brechenmacher and the Urban Bog for technical support
Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2
We have initiated a project to sequence the 3 Mbp genome of the thermoacidophilic archaebacterium Sulfolobus solfataricus P2. Cosmids were selected from a provisional set of minimally overlapping clones, subcloned in pUC18, and sequenced using a hybrid (random plus directed) strategy to give two blocks of contiguous unique sequence, respectively, 100 389 and 56 105bp. These two contigs contain a total of 163 open reading frames (ORFs) in 26-29 putative operons; 56 ORFs could be identified with reasonable certainty. Clusters of ORFs potentially encode proteins of glycogen biosynthesis, oxidative decarboxylation of pyruvate, ATP-dependent transport across membranes, isoprenoid biosynthesis, protein synthesis, and ribosomes. Putative promoters occur upstream of most ORFs. Thirty per cent of the predicted strong and medium-strength promoters can initiate transcription at the start codon or within 10 nucleotides upstream, indicating a process of initial mRNA-ribosome contact unlike that of most eubacterial genes. A novel termination motif is proposed to account for 15 additional terminations. The two contigs differ in densities of ORFs, insertion elements and repeated sequences; together they contain two copies of the previously reported insertion sequence ISC1217, five additional IS elements representing four novel types, four classes of long non-IS repeated sequences, and numerous short, perfect repeats