Browsing by Issue Date, starting with "2010-06"
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- Actividades económicas de pequena escalaPublication . Dias, Nelson; Soares, Priscila; Sousa, Vanessa Duarte deEste estudo pretende identificar as principais fragilidades e potencialidade dos empreendedores de pequena escala económica. O objetivo mais amplo deste livro é o de situar a emergência de problemas sociais não cobertos pelas políticas sociais existentes, procurando identificar grupos sociais que escapam a essas mesmas políticas e propor medidas para proteção social específicas para grupos distintos.
- Fertilization capacity with rainbow trout DNA-damaged sperm and embryo developmental successPublication . Perez-Cerezales, S.; Martinez-Paramo, S.; Beirao, J.; Herraez, M. P.Mammalian spermatozoa undergo a strong selection process along the female tract to guarantee fertilization by good quality cells, but risks of fertilization with DNA-damaged spermatozoa have been reported. In contrast, most external fertilizers such as fish seem to have weaker selection procedures. This fact, together with their high prolificacy and external embryo development, indicates that fish could be useful for the study of the effects of sperm DNA damage on embryo development. We cryopreserved sperm from rainbow trout using egg yolk and low-density lipoprotein as additives to promote different rates of DNA damage. DNA fragmentation and oxidization were analyzed using comet assay with and without digestion with restriction enzymes, and fertilization trials were performed. Some embryo batches were treated with 3-aminobenzamide (3AB) to inhibit DNA repair by the poly (ADP-ribose) polymerase, which is an enzyme of the base excision repair pathway. Results showed that all the spermatozoa cryopreserved with egg yolk carried more than 10% fragmented DNA, maintaining fertilization rates of 61.1+/-2.3 but a high rate of abortions, especially during gastrulation, and only 14.5+/-4.4 hatching success. Furthermore, after 3AB treatment, hatching dropped to 3.2+/-2.2, showing that at least 10% DNA fragmentation was repaired. We conclude that trout sperm maintains its ability to fertilize in spite of having DNA damage, but that embryo survival is affected. Damage is partially repaired by the oocyte during the first cleavage. Important advantages of using rainbow trout for the study of processes related to DNA damage and repair during development have been reported. Reproduction (2010) 139 989-997
- Efficiency analysis of Portuguese courts using DEAPublication . Santos, Sérgio Pereira dos; Amado, CarlaThe Portuguese judicial system has attracted considerable criticism in recent years and demands for better performance and accountability have gained prominence. By using the Data Envelopment Analysis technique, this research has found evidence that supports some of this criticism. In particular, our analysis suggests that the average efficiency in the sector for the year 2008 was around 67%, and that the sector experienced productivity gains of only 2% in recent years. These results indicate considerable scope for improvement and that the reforms initiated in 2009 are timely and well targeted.
- Arenas Simbólicas VirtuaisPublication . Silva, BrunoEste trabalho propõe uma reflexão sobre o videojogo enquanto espaço simbólico onde a simulação transfigura a realidade em hiper-realidade, possibilitando, assim, a vivência controlada de perigos ficcionados. As facetas virtuais dos jogadores de consola transcendem os limites da vida quotidiana abrindo-lhe portas de mundos paralelos onde pode praticar aptidões fálicas e agressivas.
- Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformityPublication . Ferraresso, Serena; Milan, Massimo; Pellizzari, Caterina; Vitulo, Nicola; Reinhardt, Richard; Canario, Adelino V. M.; Patarnello, T.; Bargelloni, LucaAbstract Background The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for D. labrax. Results A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant. Conclusions The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon.
- Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyroseqeuencingPublication . Clark, M. S.; Thorne, Michael A. S.; Vieira, Florbela A.; Cardoso, João CR; Power, Deborah; Peck, Lloyd S.Abstract Background The Antarctic clam, Laternula elliptica, is an infaunal stenothermal bivalve mollusc with a circumpolar distribution. It plays a significant role in bentho-pelagic coupling and hence has been proposed as a sentinel species for climate change monitoring. Previous studies have shown that this mollusc displays a high level of plasticity with regard to shell deposition and damage repair against a background of genetic homogeneity. The Southern Ocean has amongst the lowest present-day CaCO3 saturation rate of any ocean region, and is predicted to be among the first to become undersaturated under current ocean acidification scenarios. Hence, this species presents as an ideal candidate for studies into the processes of calcium regulation and shell deposition in our changing ocean environments. Results 454 sequencing of L. elliptica mantle tissue generated 18,290 contigs with an average size of 535 bp (ranging between 142 bp-5.591 kb). BLAST sequence similarity searching assigned putative function to 17% of the data set, with a significant proportion of these transcripts being involved in binding and potentially of a secretory nature, as defined by GO molecular function and biological process classifications. These results indicated that the mantle is a transcriptionally active tissue which is actively proliferating. All transcripts were screened against an in-house database of genes shown to be involved in extracellular matrix formation and calcium homeostasis in metazoans. Putative identifications were made for a number of classical shell deposition genes, such as tyrosinase, carbonic anhydrase and metalloprotease 1, along with novel members of the family 2 G-Protein Coupled Receptors (GPCRs). A membrane transport protein (SEC61) was also characterised and this demonstrated the utility of the clam sequence data as a resource for examining cold adapted amino acid substitutions. The sequence data contained 46,235 microsatellites and 13,084 Single Nucleotide Polymorphisms(SNPs/INDELS), providing a resource for population and also gene function studies. Conclusions This is the first 454 data from an Antarctic marine invertebrate. Sequencing of mantle tissue from this non-model species has considerably increased resources for the investigation of the processes of shell deposition and repair in molluscs in a changing environment. A number of promising candidate genes were identified for functional analyses, which will be the subject of further investigation in this species and also used in model-hopping experiments in more tractable and economically important model aquaculture species, such as Crassostrea gigas and Mytilus edulis.
- Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breedPublication . Ginja, Catarina; Penedo, Maria; Sobral, M.; Matos, José; Borges, Carla; Neves, D.; Rangel-Figueiredo, Teresa; Cravador, A.Abstract Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P < 0.001). The four Algarvia bulls had Y-haplotypes H6Y2 and H11Y2, common in Portuguese cattle. The mtDNA composition showed prevalence of T3 matrilines and presence of the African-derived T1a haplogroup. This analysis confirmed the genetic proximity of Algarvia and Garvonesa breeds (Fst = 0.028, P > 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the Algarvia breed. Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed.
- MARINE-EXPRESS: taking advantage of high throughput cloning and expression strategies for the post-genomic analysis of marine organismsPublication . Groisillier, Agnes; Herve, Cecile; Jeudy, Alexandra; Rebuffet, Etienne; Pluchon, Pierre F.; Chevolot, Yann; Flament, Didier; Geslin, Claire; Morgado, Isabel; Power, Deborah; Branno, Margherita; Moreau, Herve; Michel, Gurvan; Boyen, Catherine; Czjzek, MirjamAbstract Background The production of stable and soluble proteins is one of the most important steps prior to structural and functional studies of biological importance. We investigated the parallel production in a medium throughput strategy of genes coding for proteins from various marine organisms, using protocols that involved recombinatorial cloning, protein expression screening and batch purification. This strategy was applied in order to respond to the need for post-genomic validation of the recent success of a large number of marine genomic projects. Indeed, the upcoming challenge is to go beyond the bioinformatic data, since the bias introduced through the genomes of the so called model organisms leads to numerous proteins of unknown function in the still unexplored world of the oceanic organisms. Results We present here the results of expression tests for 192 targets using a 96-well plate format. Genes were PCR amplified and cloned in parallel into expression vectors pFO4 and pGEX-4T-1, in order to express proteins N-terminally fused to a six-histidine-tag and to a GST-tag, respectively. Small-scale expression and purification permitted isolation of 84 soluble proteins and 34 insoluble proteins, which could also be used in refolding assays. Selected examples of proteins expressed and purified to a larger scale are presented. Conclusions The objective of this program was to get around the bottlenecks of soluble, active protein expression and crystallization for post-genomic validation of a number of proteins that come from various marine organisms. Multiplying the constructions, vectors and targets treated in parallel is important for the success of a medium throughput strategy and considerably increases the chances to get rapid access to pure and soluble protein samples, needed for the subsequent biochemical characterizations. Our set up of a medium throughput strategy applied to genes from marine organisms had a mean success rate of 44% soluble protein expression from marine bacteria, archaea as well as eukaryotic organisms. This success rate compares favorably with other protein screening projects, particularly for eukaryotic proteins. Several purified targets have already formed the base for experiments aimed at post-genomic validation.
- A noninvasive monitoring device for anesthetics in fishPublication . Power, Deborah; Fuentes, J.; Harrison, Adrian P.A noninvasive device capable of recording both gill and lateral fin movements was assembled and used to analyze initial and post-treatment activity frequency (Hz) in fish exposed to anesthetics. Exposure of platy fish (Xiphosphorus maculatus) to saponins from quillaja bark (0.185 mM and 0.555 mM) initially caused hyperactivity, but within five minutes all activity ceased and the fish failed to recover. In contrast, clove oil (67 μg/L) added to water at 22oC reduced activity by 22.8% ± 8.9% (P = 0.038) after 125 ± 19 sec, a sedative effect that was totally reversible. Cinnamon oil compared with clove oil had a significantly longer time to sedation (125 ± 19 versus 235 ± 24 sec, P = 0.02), although no significant difference in the decline in activity was noted.
- Descrição e análise fonética do dialeto de Belém do Pará orientadas à incorporação de conhecimento fonético à conversão de texto em falaPublication . Correa, Carla Patrícia Valenzuela; Baptista, JorgeEste trabalho descreve as características fonéticas do português falado na cidade de Belém do Pará, norte do Brasil, e pretende ser uma contribuição linguistica para o desenvolvimento de tecnologias de conversão de texto em fala para esta variedade do português.