FE - Contribuições em Revistas Científicas / Contribution to Journals
Permanent URI for this collection
Browse
Recent Submissions
- Genome sequencing reveals a phage in Helicobacter pyloriPublication . Lehours, Philippe; Vale, Filipa F.; Bjursell, Magnus K.; Melefors, Ojar; Advani, Reza; Glavas, Steve; Guegueniat, Julia; Gontier, Etienne; Lacomme, Sabrina; Matos, António Alves; Menard, Armelle; Mégraud, Francis; Engstrand, Lars; Andersson, Anders F.Helicobacter pylori chronically infects the gastric mucosa in more than half of the human population; in a subset of this population, its presence is associated with development of severe disease, such as gastric cancer. Genomic analysis of several strains has revealed an extensive H pylori pan-genome, likely to grow as more genomes are sampled. Here we describe the draft genome sequence (63 contigs; 26× mean coverage) of H pylori strain B45, isolated from a patient with gastric mucosa-associated lymphoid tissue (MALT) lymphoma. The major finding was a 24.6-kb prophage integrated in the bacterial genome. The prophage shares most of its genes (22/27) with prophage region II of Helicobacter acinonychis strain Sheeba. After UV treatment of liquid cultures, circular DNA carrying the prophage integrase gene could be detected, and intracellular tailed phage-like particles were observed in H pylori cells by transmission electron microscopy, indicating that phage production can be induced from the prophage. PCR amplification and sequencing of the integrase gene from 341 H pylori strains from different geographic regions revealed a high prevalence of the prophage (21.4%). Phylogenetic reconstruction showed four distinct clusters in the integrase gene, three of which tended to be specific for geographic regions. Our study implies that phages may play important roles in the ecology and evolution of H pylori.
- Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptomePublication . Mollet, I. G.; Ben-Dov, Claudia; Felício-Silva, Daniel; Grosso, A. R.; Eleutério, Pedro; Alves, Ruben; Staller, Ray; Silva, Tito Santos; Carmo-Fonseca, MariaMining massive amounts of transcript data for alternative splicing information is paramount to help understand how the maturation of RNA regulates gene expression. We developed an algorithm to cluster transcript data to annotated genes to detect unannotated splice variants. A higher number of alternatively spliced genes and isoforms were found compared to other alternative splicing databases. Comparison of human and mouse data revealed a marked increase, in human, of splice variants incorporating novel exons and retained introns. Previously unannotated exons were validated by tiling array expression data and shown to correspond preferentially to novel first exons. Retained introns were validated by tiling array and deep sequencing data. The majority of retained introns were shorter than 500 nt and had weak polypyrimidine tracts. A subset of retained introns matching small RNAs and displaying a high GC content suggests a possible coordination between splicing regulation and production of noncoding RNAs. Conservation of unannotated exons and retained introns was higher in horse, dog and cow than in rodents, and 64% of exon sequences were only found in primates. This analysis highlights previously bypassed alternative splice variants, which may be crucial to deciphering more complex pathways of gene regulation in human.
- Prediction of dynamic plasmid production by recombinant escherichia coli fed-batch cultivations with a generalized regression neural networkPublication . Silva, T.; Lima, P.; Roxo-Rosa, M.; Hageman, S.; Fonseca, L. P.; Calado, C. R. C.A generalized regression neural network with external feedback was used to predict plasmid production in a fed-batch cultivation of recombinant Escherichia coli. The neu ral network was built out of the experimental data obtained on a few cultivations, of which the general strategy was based on an initial batch phase followed by an exponen tial feeding phase. The different cultivation conditions used resulted in significant differ ences in bacterial growth and plasmid production. The obtained model allows estimation of the experimental outputs (biomass, glucose, acetate and plasmid) based on the bioreactor starting conditions and the following on-line inputs: feeding rate, dissolved oxygen concentration and bioreactor stirring speed. Therefore, the proposed methodol ogy presents a quick, simple and reliable way to perform on-line feedback prediction of the dynamic behaviour of the complex plasmid production process, based on simple on-line input data obtained directly from the bioreactor control unit and with few cultiva tion experiments for neural network learning.
- Geographic distribution of methyltransferases of Helicobacter pylori: evidence of human host population isolation and migrationPublication . Vale, Filipa F.; Mégraud, Francis; Vítor, Jorge M.Background. Helicobacter pylori colonizes the human stomach and is associated with gastritis, peptic ulcer, and gastric cancer. This ubiquitous association between H. pylori and humans is thought to be present since the origin of modern humans. The H. pylori genome encodes for an exceptional number of restriction and modifications (R-M) systems. To evaluate if R-M systems are an adequate tool to determine the geographic distribution of H. pylori strains, we typed 221 strains from Africa, America, Asia, and Europe, and evaluated the expression of different 29 methyltransferases. Results. Independence tests and logistic regression models revealed that ten R-M systems correlate with geographical localization. The distribution pattern of these methyltransferases may have been originated by co-divergence of regional H. pylori after its human host migrated out of Africa. The expression of specific methyltransferases in the H. pylori population may also reflect the genetic and cultural background of its human host. Methyltransferases common to all strains, M. HhaI and M. NaeI, are likely conserved in H. pylori, and may have been present in the bacteria genome since the human diaspora out of Africa. Conclusion. This study indicates that some methyltransferases are useful geomarkers, which allow discrimination of bacterial populations, and that can be added to our tools to investigate human migrations.
- Ulcerogenic helicobacter pylori strains isolated from children: a contribution to get insight into the virulence of the bacteriaPublication . Vitoriano, Inês; Saraiva-Pava, Kathy D.; Rocha-Gonçalves, Alexandra; Santo, Andrea; Lopes, Ana I.; Oleastro, Mónica; Roxo-Rosa, MónicaInfection with Helicobacter pylori is the major cause for the development of peptic ulcer disease (PUD). In children, with no other etiology for the disease, this rare event occurs shortly after infection. In these young patients, habits of smoking, diet, consumption of alcohol and non-steroid anti-inflammatory drugs and stress, in addition to the genetic susceptibility of the patient, represent a minor influence. Accordingly, the virulence of the implicated H. pylori strain should play a crucial role in the development of PUD. Corroborating this, our in vitro infection assays comparing a pool of five H. pylori strains isolated from children with PUD to a pool of five other pediatric clinical isolates associated with non-ulcer dyspepsia (NUD) showed the greater ability of PUD strains to induce a marked decrease in the viability of gastric cells and to cause severe damage in the cells cytoskeleton as well as an impairment in the production/secretion of mucins. To uncover virulence features, we compared the proteome of these two groups of H. pylori strains. Two-dimensional gel electrophoresis followed by mass-spectrometry allowed us to detect 27 differentially expressed proteins between them. In addition to the presence of genes encoding well established virulence factors, namely cagA, vacAs1, oipA "on" status, homB and jhp562 genes, the pediatric ulcerogenic strains shared a proteome profile characterized by changes in the abundance of: motility-associated proteins, accounting for higher motility; antioxidant proteins, which may confer increased resistance to inflammation; and enzymes involved in key steps in the metabolism of glucose, amino acids and urea, which may be advantageous to face fluctuations of nutrients. In conclusion, the enhanced virulence of the pediatric ulcerogenic H. pylori strains may result from a synergy between their natural ability to better adapt to the hostile human stomach and the expression of the established virulence factors.
- The effects of cryogenic cooling on surface integrity in hard machiningPublication . Umbrello, D.; Pu, Z.; Caruso, S.; Outeiro, J. C.; Jayal, A. D.; Dillon, O. W.; Jawahir, I. S.This paper presents the results of an experimental investigation to determine the effects of cryogenic coolant on surface integrity in orthogonal machining of hardened AISI 52100 bearing steel. Experiments were performed under dry and cryogenic conditions using chamfered CBN tool inserts. Several experimental techniques were used in the analyzing of the machined surface and subsurface: optical and scanning electron microscopes (SEM) were utilized for the surface topography characterization; chemical characterization (phase study) was carried out by means of Energydispersive spectroscopy (EDS) techniques; and X-ray diffraction (XRD) technique was used to determine residual stresses and phase changes induced by dry and cryogenic machining. The results show the benefits and the future potential of cryogenic cooling for surface integrity enhancement to achieve improved product's functional performance in hard machining.
- Surface integrity in dry and cryogenic machining of AZ31B Mg alloy with varying cutting edge radius toolsPublication . Pu, Z.; Outeiro, J. C.; Batista, A. C.; Dillon, O. W.; Puleo, D. A.; Jawahir, I. S.Surface integrity of machined products has a critical impact on their functional performance. Magnesium alloys are lightweight materials for transportation industry and are also emerging as a potential material for temporary biomedical implants. However, their unsatisfactory corrosion resistance limits their application to a great extent. Surface integrity factors, such as grain size, crystallographic orientation and residual stresses, were reported to have significant influence on corrosion resistance of AZ31 Mg alloys. In this study, AZ31B Mg discs were orthogonally turned using cutting tools with two edge radii under both dry and cryogenic conditions. The influence of cutting edge radius and cooling method on surface integrity was investigated. Cryogenic machining using a large edge radius tool led to a thicker grain refinement layer, larger compressive residual stresses and stronger intensity of basal texture, which may remarkably enhance the corrosion performance of magnesium alloys.
- Formal extension of the Whitney functor and dualityPublication . Martins, Ana Rita; Fernandes, Teresa MonteiroOn a complex manifold we introduce the formal extension of the Whitney functor and the algebraic extension of the tempered cohomology functor, and prove a natural topological duality between them.
- Robot skills and cognitive performance of preschool childrenPublication . Poletz, Linda; Encarnação, Pedro; Adams, Kim; Cook, AlSeveral studies have demonstrated the potential of robots as assistive tools for play activities. Through the use of robots, children with motor impairments may be able to manipulate objects and engage in play activities as their typically developing peers, thus having the same opportunities to learn cognitive, social, motor and linguistic skills. Robot use can also provide a proxy measure of disabled children's cognitive abilities by comparing their performance with that of typically developing children. This paper reports a study with eighteen typically developing children aged three, four and five years to assess at which ages the cognitive concepts of causality, negation, binary logic, and sequencing are demonstrated during Lego robot use.
- An experimental investigation of residual stresses in hard machining of AISI 52100 steelPublication . Caruso, S.; Umbrello, D.; Outeiro, J. C.; Filice, L.; Micari, F.In this paper an experimental investigation was conducted to determine the effects of the tool cutting-edge geometry, workpiece hardness, cutting speed, and microstructural changes (white and dark layers) on the residual stresses in dry orthogonal hard machining of AISI 52100 steel. X-ray diffraction technique was used to obtain in-depth residual stresses profiles in both axial and circumferential directions. The results show that tool geometry, workpiece hardness and cutting parameters significantly affect the surface residual stress, maximum compressive residual stress below the machined surface and its location. Moreover, microstructural analysis shows that thermally-induced phase transformations have a significant impact on the magnitude and location of this maximum compressive residual stress peak.