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  • 1
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    Relevance of silicate surface morphology in interstellar H2 formation. Insights from quantum chemical calculations (2015)
    Oxford University Press
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    Publication Date: 2015-08-24
    Description: The adsorption of H atoms and their recombination to form an H 2 molecule on slab models of the crystalline Mg 2 SiO 4 forsterite (001) and (110) surfaces was studied by means of quantum mechanical calculations based on periodic density functional theory (DFT). Present results are compared with those previously reported for the most stable (010) surface, showing the relevance of the surface morphology and their stability on the H 2 formation. Different H chemisorption states were identified, mostly on the outermost O atoms of the surfaces. In agreement with the higher instability of the (001) and (110) surfaces, the calculated adsorption energies are larger than those for the (010) surface. Computed energy barriers for the H hopping on these surfaces are exceedingly high to occur at the very low temperatures of deep space. For the adsorption of two H atoms, the most stable complexes are those in which the H atoms form Mg-H and SiOH surface groups. From these complexes, we did not identify energetically feasible paths for H 2 formation through a Langmuir–Hinshelwood mechanism on the (001) surface because the initial states are more stable than the final products. However, on the (110) surface one path was found to be exoergic with very low energy barriers. This differs to that observed for the (010) surface, for which two feasible Langmuir–Hinshelwood-based channels were identified. H 2 formation through the Eley–Rideal mechanism was also simulated, in which an incoming H atom impinges on a pre-adsorbed H atom at the (001) and (110) surfaces in a barrierless way.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Structure and tectonics of the central Chilean margin (31{degrees}-33{degrees}S): implications for subduction erosion and shallow crustal seismicity (2015)
    Oxford University Press
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    Publication Date: 2015-09-11
    Description: The pre- and current collision of the Juan Fernández Ridge with the central Chilean margin at 31°–33°S is characterized by large-scale crustal thinning and long-term subsidence of the submarine forearc caused by subduction erosion processes. Here, we study the structure of the central Chilean margin in the ridge–trench collision zone by using wide-angle and multichannel seismic data. The transition from the upper to middle continental slope is defined by a trenchward dipping normal scarp with variable offsets of 500–2000 m height. Beneath the scarp, the 2-D velocity–depth models show a prominent lateral velocity contrast of 〉1 s –1 that propagates deep into the continental crust defining a major lateral seismic discontinuity. The discontinuity is interpreted as the lithological contact between the subsided/collapsed outermost forearc (composed of eroded and highly fractured volcanic rocks) and the seaward part of the uplifted Coastal Cordillera (made of less fractured metamorphic/igneous rocks). Extensional faults are abundant in the collapsed outermost forearc, however, landward of the continental slope scarp, both extensional and compressional structures are observed along the uplifted continental shelf that forms part of the Coastal Cordillera. Particularly, at the landward flank of the Valparaíso Forearc Basin (32°–33.5°S), shallow crustal seismicity has been recorded in 2008–2009 forming a dense cluster of thrust events of M w 4–5. The estimated hypocentres spatially correlate with the location of the fault scarp, and they highlight the upper part of the seismic crustal discontinuity.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 3
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    Electronic monitoring trials on in the tropical tuna purse-seine fishery (2015)
    Oxford University Press
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    Publication Date: 2015-05-30
    Description: The difficulty of ensuring adequate statistical coverage of whole fleets is a challenge for the implementation of observer programmes and may reduce the usefulness of the data they obtain for management purposes. This makes it necessary to find cost-effective alternatives. Electronic monitoring (EM) systems are being used in some fisheries as an alternative or a complement to human observers. The objective of this study was to test the use and reliability of EM on the tropical tuna purse-seine fishery. To achieve this objective, seven trips of tuna purse seiners operating in the three Oceans were closely monitored to compare the information provided by EM and on-board observers to determine if EM can reliably document fishing effort, set type, tuna catch, and bycatch. Total tuna catch per set was not significantly different between EM and observer datasets; however, regarding species composition, only main species matched between EM and observers. Success on set-type identification using EM varied between 98.3 and 56.3%, depending on the camera placement. Overall, bycatch species were underestimated by EM, but large bodied species, such as billfishes, were well documented. The analyses in this study showed that EM can be used to determine the fishing effort (number of sets) and total tuna catch as reliably as observers can. Set-type identification also had very promising results, but indicated that refinement of the methods is still needed. To be fully comparable with observer data, improvements for accurately estimating the bycatch will need to be developed in the application and use of the EM system. Operational aspects that need to be improved for an EM programme to be implemented include standardizing installation and on-board catch handling methodology as well as improvements in video technology deployment.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 4
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    pic gene of enteroaggregative Escherichia coli and its association with diarrhea in Peruvian children (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: Enteroaggregative Escherichia coli (EAEC) causes acute and persistent diarrhea among children, HIV-infected patients, and travelers to developing countries. We have searched for 18 genes-encoding virulence factors associated with aggregative adherence, dispersion, biofilm, toxins, serine protease autotransporters of Enterobacteriaceae (SPATEs) and siderophores, analyzed in 172 well-characterized EAEC strains ( aggR + ) isolated from stool samples of 97 children with diarrhea and 75 healthy controls from a passive surveillance diarrhea cohort study in Peru. Eighty-one different genetic profiles were identified, 37 were found only associated with diarrhea and 25 with control samples. The most frequent genetic profile was aggC + aatA + aap + shf + fyuA + , present in 19 strains, including diarrhea and controls. The profile set1A + set1B + pic + was associated with diarrhea ( P 〈 0.05). Of all genes evaluated, the most frequent were aatA (CVD 342) present in 159 strains (92.4%) and fyuA in 157 (91.3%). When EAEC strains were analyzed as a single pathogen (excluding co-infections), only pic was associated with diarrhea ( P 〈 0.05) and with prolonged diarrhea (diarrhea ≥ 7 days) ( P 〈 0.05). In summary, this is the first report on the prevalence of a large set of EAEC virulence genes and its association with diarrhea in Peruvian children. More studies are needed to elucidate the exact role of each virulence factor.
    Print ISSN: 0928-8244
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Role of hydraulic and chemical signals in leaves, stems and roots in the stomatal behaviour of olive trees under water stress and recovery conditions (2015)
    Oxford University Press
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    Publication Date: 2015-04-30
    Description: The control of plant transpiration by stomata under water stress and recovery conditions is of paramount importance for plant performance and survival. Although both chemical and hydraulic signals emitted within a plant are considered to play a major role in controlling stomatal dynamics, they have rarely been assessed together. The aims of this study were to evaluate (i) the dynamics of chemical and hydraulic signals at leaf, stem and root level, and (ii) their effect on the regulation of stomatal conductance ( g s ) during water stress and recovery. Measurements of g s , water potential, abscisic acid (ABA) content and loss of hydraulic functioning at leaf, stem and root level were conducted during a water stress and recovery period imposed on 1-year-old olive plants ( Olea europaea L.). Results showed a strong hydraulic segmentation in olive plants, with higher hydraulic functioning losses in roots and leaves than in stems. The dynamics of hydraulic conductance of roots and leaves observed as water stress developed could explain both a protection of the hydraulic functionality of larger organs of the plant (i.e., branches, etc.) and a role in the down-regulation of g s . On the other hand, ABA also increased, showing a similar pattern to g s dynamics, and thus its effect on g s in response to water stress cannot be ruled out. However, neither hydraulic nor non-hydraulic factors were able to explain the delay in the full recovery of g s after soil water availability was restored.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 6
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    The economic value of environmental data: a notional insurance scheme for the European anchovy (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: Anchovy population dynamics in the Gulf of Cádiz are governed by environmental processes. Sea surface temperature, intense easterly winds, and discharges from the Guadalquivir River have been identified as key factors determining early life stage mortality in this anchovy stock. We have constructed an environment-based recruitment model that simulates the abundance of juveniles under alternative parameters representing plausible biological hypotheses. We are able to evaluate how modelling environment-based recruitment can affect stock assessment and how responding to environmental information can benefit fishery management to allow greater average catch levels through the application of harvest control rules (HCRs) based on environmental conditions. While the environment-based rules generally increase allowable catch levels the variance in catch levels also increases, detracting from the improved value based only on average yield. In addition to changes in revenue, the probability of stock collapse is also reduced by using environmental factors in HCRs. To assess the value of these management systems we simulate a notional insurance scheme, which applies a value to both average yields and uncertainty. The value of the information-driven rules can be determined by comparing the relevant premiums payable for equal levels of insurance cover on revenue within each specific management regime. We demonstrate the net value of incorporating environmental factors in the management of anchovies in the Gulf of Cádiz despite the increased variability in revenue. This could be an effective method to describe outcomes for both commercial fisheries and ecosystem management policies, and as a guide to management of other species whose dynamics are predictable based on in-season observations.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 7
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    Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History (2015)
    Oxford University Press
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    Publication Date: 2015-01-20
    Description: Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Genomics of Ecological Adaptation in Cactophilic Drosophila (2015)
    Oxford University Press
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    Publication Date: 2015-02-02
    Description: Cactophilic Drosophila species provide a valuable model to study gene–environment interactions and ecological adaptation. Drosophila buzzatii and Drosophila mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, we sequenced the genome and developmental transcriptome of D. buzzatii and compared its gene content with that of D. mojavensis and two other noncactophilic Drosophila species in the same subgenus. The newly sequenced D. buzzatii genome (161.5 Mb) comprises 826 scaffolds (〉3 kb) and contains 13,657 annotated protein-coding genes. Using RNA sequencing data of five life-stages we found expression of 15,026 genes, 80% protein-coding genes, and 20% noncoding RNA genes. In total, we detected 1,294 genes putatively under positive selection. Interestingly, among genes under positive selection in the D. mojavensis lineage, there is an excess of genes involved in metabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. We found 117 orphan genes in the shared D. buzzatii–D. mojavensis lineage. In addition, gene duplication analysis identified lineage-specific expanded families with functional annotations associated with proteolysis, zinc ion binding, chitin binding, sensory perception, ethanol tolerance, immunity, physiology, and reproduction. In summary, we identified genetic signatures of adaptation in the shared D. buzzatii–D. mojavensis lineage, and in the two separate D. buzzatii and D. mojavensis lineages. Many of the novel lineage-specific genomic features are promising candidates for explaining the adaptation of these species to their distinct ecological niches.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Riemann problem for the Born-Infeld system without differential constraints (2013)
    Oxford University Press
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    Publication Date: 2013-01-18
    Description: We consider the Born–Infeld system without differential constraints, which occurs as soon as the differential constraints are not satisfied at the initial time. In such a case, the Poynting vector is not a conservative variable and the technique of enlargement of systems cannot be applied. In one space dimension, the resulting system consists of five conservative equations for which only one Riemann invariant exists. It is fully linearly degenerate but neither strictly hyperbolic nor rich. Under a smallness condition on the initial datum of only one variable, we prove that the Riemann problem has a unique entropy solution having discontinuities with three separated speeds. It is surprising that the result holds even for initial data lying in non-hyperbolic regions.
    Print ISSN: 0272-4960
    Electronic ISSN: 1464-3634
    Topics: Mathematics
    Published by Oxford University Press
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  • 10
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    Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features (2012)
    Oxford University Press
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    Publication Date: 2012-09-30
    Description: Motivation: The prediction of a protein’s contact map has become in recent years, a crucial stepping stone for the prediction of the complete 3D structure of a protein. In this article, we describe a methodology for this problem that was shown to be successful in CASP8 and CASP9. The methodology is based on (i) the fusion of the prediction of a variety of structural aspects of protein residues, (ii) an ensemble strategy used to facilitate the training process and (iii) a rule-based machine learning system from which we can extract human-readable explanations of the predictor and derive useful information about the contact map representation. Results: The main part of the evaluation is the comparison against the sequence-based contact prediction methods from CASP9, where our method presented the best rank in five out of the six evaluated metrics. We also assess the impact of the size of the ensemble used in our predictor to show the trade-off between performance and training time of our method. Finally, we also study the rule sets generated by our machine learning system. From this analysis, we are able to estimate the contribution of the attributes in our representation and how these interact to derive contact predictions. Availability: http://icos.cs.nott.ac.uk/servers/psp.html . Contact: natalio.krasnogor@nottingham.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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