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Rodriguez-Ezpeleta N.,Northumbria University | Embley T.M.,Tecnalia
PLoS ONE | Year: 2012

Although free living, members of the successful SAR11 group of marine alpha-proteobacteria contain a very small and A+T rich genome, two features that are typical of mitochondria and related obligate intracellular parasites such as the Rickettsiales. Previous phylogenetic analyses have suggested that Candidatus Pelagibacter ubique, the first cultured member of this group, is related to the Rickettsiales+mitochondria clade whereas others disagree with this conclusion. In order to determine the evolutionary position of the SAR11 group and its relationship to the origin of mitochondria, we have performed phylogenetic analyses on the concatenation of 24 proteins from 5 mitochondria and 71 proteobacteria. Our results support that SAR11 group is not the sistergroup of the Rickettsiales+mitochondria clade and confirm that the position of this group in the alpha-proteobacterial tree is strongly affected by tree reconstruction artefacts due to compositional bias. As a consequence, genome reduction and bias toward a high A+T content may have evolved independently in the SAR11 species, which points to a different direction in the quest for the closest relatives to mitochondria and Rickettsiales. In addition, our analyses raise doubts about the monophyly of the newly proposed Pelagibacteraceae family. © 2012 Rodríguez-Ezpeleta. Source

Sporadic Creutzfeldt-Jakob disease (sCJD) is a rare neurodegenerative disorder in humans included in the group of Transmissible Spongiform Encephalopathies or prion diseases. The vast majority of sCJD cases are molecularly classified according to the abnormal prion protein (PrPSc) conformations along with polymorphism of codon 129 of the PRNP gene. Recently, a novel human disease, termed "protease-sensitive prionopathy", has been described. This disease shows a distinct clinical and neuropathological phenotype and it is associated to an abnormal prion protein more sensitive to protease digestion. We report the case of a 75-year-old-man who developed a clinical course and presented pathologic lesions compatible with sporadic Creutzfeldt-Jakob disease, and biochemical findings reminiscent of "protease-sensitive prionopathy". Neuropathological examinations revealed spongiform change mainly affecting the cerebral cortex, putamen/globus pallidus and thalamus, accompanied by mild astrocytosis and microgliosis, with slight involvement of the cerebellum. Confluent vacuoles were absent. Diffuse synaptic PrP deposits in these regions were largely removed following proteinase treatment. PrP deposition, as revealed with 3F4 and 1E4 antibodies, was markedly sensitive to pre-treatment with proteinase K. Molecular analysis of PrPSc showed an abnormal prion protein more sensitive to proteinase K digestion, with a five-band pattern of 28, 24, 21, 19, and 16 kDa, and three aglycosylated isoforms of 19, 16 and 6 kDa. This PrPSc was estimated to be 80% susceptible to digestion while the pathogenic prion protein associated with classical forms of sporadic Creutzfeldt-Jakob disease were only 2% (type VV2) and 23% (type MM1) susceptible. No mutations in the PRNP gene were found and genotype for codon 129 was heterozygous methionine/valine. A novel form of human disease with abnormal prion protein sensitive to protease and MV at codon 129 was described. Although clinical signs were compatible with sporadic Creutzfeldt-Jakob disease, the molecular subtype with the abnormal prion protein isoforms showing enhanced protease sensitivity was reminiscent of the "protease-sensitive prionopathy". It remains to be established whether the differences found between the latter and this case are due to the polymorphism at codon 129. Different degrees of proteinase K susceptibility were easily determined with the chemical polymer detection system which could help to detect proteinase-susceptible pathologic prion protein in diseases other than the classical ones. Source

Tedeschi E.,Tecnalia | Molinas M.,Norwegian University of Science and Technology
IEEE Transactions on Industrial Electronics | Year: 2012

In wave energy converters (WECs), the maximum power extraction would be achievable at the expense of a very high rating of the electric and power electronics equipment. The goal of this paper is to show how a convenient tradeoff between high-power extraction and viable electrical device rating can be achieved by a proper choice of the WEC control strategy. Referring to a direct coupled point absorber in heave operating in regular waves, it will be analytically shown how most common control techniques impact on both the power performance and the power takeoff (PTO) rating. Thus, a tool that can assist in the preliminary PTO sizing by taking into account the main constraints imposed by the application is obtained. Following, an adaptive control strategy including a reactive component is proposed, whose goal is to improve the overall system performance when the WEC is already operative in the sea. Its effectiveness in increasing the average power extraction while respecting the PTO peak power constraint is proved by computer simulations in both regular and irregular waves, and specific analyses also including the PTO force/torque limitation are finally developed. © 2012 IEEE. Source

The time-series of daily catch, fishing effort, and mean body mass of the summer fishing seasons of the squid, Loligo gahi, in the Falkland Islands from 1990 to 2009 are investigated with generalizations of depletion models that account for in-season pulses of recruitment (i.e. open populations) and non-linear relationships between catch as the response variable, and effort and abundance as the predictor variables. Two main results were found. First, stock dynamics are more complex than assumed by LeslieDavis or De Lury depletion models, because in most years, there are several major in-season recruitment pulses, sometimes even larger than the pre-season pulse, contradicting the basic assumption of a decline in catch rates over the fishing season. Second, the fishery operates under a regime of hyperstabilitycatch rates decline slower than abundanceat low stock abundance and hyperdepletioncatch rates decline faster than abundanceat intermediate and high stock abundance. The hyperdepleted regime is far more prevalent, a result attributed to the availability of refuges from fishing operations, which may lower the abundance threshold to pass from the low-abundance hyperstable regime to the higher-abundance hyperdepleted regime. © 2012 International Council for the Exploration of the Sea. Published by Oxford University Press. All rights reserved. Source

Borja A.,Tecnalia | Tunberg B.G.,Smithsonian Marine Station
Ecological Indicators | Year: 2011

The Indian River Lagoon (IRL) and the St. Lucie Estuary (SLE), both located in Florida, USA, are affected by a variety of anthropogenic pressures. Benthic macroinvertebrates have been monitored quarterly since February 2005, at 15 stations, in order to assess benthic health. Since the SLE and IRL are situated in a subtropical area, it is affected by two major climatic seasons, dry (winter) and wet (summer). This contribution investigates the application of the AZTI's Marine Biotic Index (AMBI) and multivariate-AMBI (M-AMBI), to assess the ecological status of these estuaries. AMBI was firstly calculated after assigning most of the previously unassigned species to each of the five ecological groups (from sensitive to first order opportunistic species). Three main benthic assemblages, associated tooligohaline, meso-polyhaline and euhaline stretches, have been identified within the area. Reference conditions of richness, Shannon's diversity and AMBI have been derived for these assemblages; M-AMBI has then been calculated. Both methods show that the inner part of the SLE is affected by anthropogenic pressures (increased freshwater inflow, with elevated nutrient input, and sedimentation), whilst the IRL is less affected. We have demonstrated that AMBI and M-AMBI are insensitive to the dramatic seasonal changes occurring in the SLE/IRL. At some of the stations a significant positive trend in benthic quality has been identified, linked to the polluted freshwater discharges decrease. The use of both tools seems adequate in assessing benthic health in this subtropical area. © 2010 Elsevier Ltd. All rights reserved. Source

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