Teoria asintotica de vigas elasticas lineales anisotropas y no homogeneas

Available from Centro de Informacion y Documentacion Cientifica CINDOC. Joaquin Costa, 22. 28002 Madrid. SPAIN / CINDOC - Centro de Informaciòn y Documentaciòn CientìficaSIGLEESSpai

De novo assembly of Manila clam (<i>Ruditapes philippinarum</i>) and protozoan parasite (<i>Perkinsus olseni</i>) transcriptome from RNA-Seq data

Manila clam (Ruditapes philippinarum) with its high commercial value has become a major contributor to the world´s clam production from both bivalve fishery and aquaculture ventures. But, the production of manila clam is at greater risk from diseases, especially caused by Perkinsus olseni. Considering the limited genomic resources of R. philippinarum and P. olseni as well as the increasing interest in immune-genes response in the host, the present work was conducted to analyze the transcriptome profile of R. philippinarum and of P. olseni using RNA-Seq technology. Data obtained will be used to construct transcriptome databases and to design oligo-microarrays both in the host and the parasite for understanding their transcriptional expressions through host-pathogen interactions. cDNA libraries were synthesized using RNA aliquots of clam haemocytes and perkinsus trophozoites collected from different experimental conditions (in vitro, in vivo and natural environment) for further sequencing carried out on Illumina HiSeq 2000 (Oxford Genomics Center, UK). A total of 131,037,742 pair-end reads for R. philippinarum and 67,840,472 for P. olseni were produced. De novo assembly was evaluated using different parameters of Trinity and Abyss assembler programs. De novo transcriptome of clam was further undergone through filtering steps by expression (> 5 FPKM), and length (500 bp) for improving transcriptome quality. CAP3 software was executed to cluster final de novo transcriptomes. Trinity+CAP3 assembly was the best approach after manual evaluation of 30 annotated contigs randomly sampled from each strategy and was chosen finally to assemble transcriptomes. 33,182 unique transcripts (3,031 contigs and 30,151 singletons) from de novo clam transcriptome, and 47,590 unique transcripts (7,251 contigs and 40,339 singletons) from perkinsus transcriptome were obtained. Among them; 3,031 (9.13%) unigenes of R. philippinarum, and 7,251 (15.24%) of P. olseni were annotated with NCBI nucleotide (nt) databases based on e-value P. olseni, and also the first one from RNA-Seq for R. philippinarum. Using these de novo transcriptome resources, microarrays will be designed for all the unique sequences and their splice variants identified in each database. The comparative analysis will provide new insights into understanding molecular mechanisms of gene expressions through clam-perkinsus interactions

Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping

Abstract: The turbot (Scophthalmus maximus) is a commercially valuable flatfish and one of the most promising aquaculture species in Europe. Two transcriptome 454-pyrosequencing runs were used in order to detect Single Nucleotide Polymorphisms (SNPs) in genes related to immune response and gonad differentiation. A total of 866 true SNPs were detected in 140 different contigs representing 262,093 bp as a whole. Only one true SNP was analyzed in each contig. One hundred and thirteen SNPs out of the 140 analyzed were feasible (genotyped), while Ш were polymorphic in a wild population. Transition/transversion ratio (1.354) was similar to that observed in other fish studies. Unbiased gene diversity (He) estimates ranged from 0.060 to 0.510 (mean = 0.351), minimum allele frequency (MAF) from 0.030 to 0.500 (mean = 0.259) and all loci were in Hardy-Weinberg equilibrium after Bonferroni correction. A large number of SNPs (49) were located in the coding region, 33 representing synonymous and 16 non-synonymous changes. Most SNP-containing genes were related to immune response and gona

Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping

The turbot (Scophthalmus maximus) is a commercially valuable flatfish and one of the most promising aquaculture species in Europe. Two transcriptome 454-pyrosequencing runs were used in order to detect Single Nucleotide Polymorphisms (SNPs) in genesrelated to immune response and gonad differentiation. A total of 866 true SNPs were detected in 140 different contigs representing 262,093 bp as a whole. Only one true SNP was analyzed in each contig. One hundred and thirteen SNPs out of the 140 analyzed were feasible (genotyped), while Ш were polymorphic in a wild population. Transition/transversion ratio (1.354) was similar to that observed in other fish studies. Unbiased gene diversity (He) estimates ranged from 0.060 to 0.510 (mean = 0.351), minimum allele frequency (MAF) from 0.030 to 0.500 (mean = 0.259) and all loci were in Hardy-Weinberg equilibrium after Bonferroni correction. A large number of SNPs (49) were located in the coding region, 33 representing synonymous and 16 non-synonymous changes. Most SNP-containing genes were related to immune response and gonad differentiation processes, and could be candidates for functional changes leading to phenotypic changes. These markers will be useful for population screening to look for adaptive variation in wild and domestic turbo

Identification of Bacillus and Yersinia species and hoax agents by protein profiling using microfluidic capillary electrophoresis with peak detection algorithms

Bacillus anthracis and Yersinia pestis are biological agents that pose an increasing concern to national security if deliberately disseminated. Hoax agents, including suspicious white powders and environmental bacterial species, can also cause disruption. In either scenario it is of high importance to rapidly and accurately identify any suspicious powder as hazardous or hoax. Protein profiling, using microfluidic capillary electrophoresis, provides a rapid (less than 40 minutes), reliable and field-based screening method.This work was supported by the Australian Commonwealth Government [Endeavour Fellowship