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  • 1
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    R-type bacteriocins in related strains of Xenorhabdus bovienii: Xenorhabdicin tail fiber modularity and contribution to competitiveness (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-19
    Description: R-type bacteriocins are contractile phage tail-like structures that are bactericidal towards related bacterial species. The C-terminal region of the phage tail fiber protein determines target-binding specificity. The mutualistic bacteria Xenorhabdus nematophila and X. bovienii produce R-type bacteriocins (xenorhabdicins) that are selectively active against different Xenorhabdus species. We analyzed the P2-type remnant prophage clusters in draft sequences of nine strains of X. bovienii . The C-terminal tail fiber region in each of the respective strains was unique and consisted of mosaics of modular units. The region between the main tail fiber gene ( xbpH1 ) and the sheath gene ( xbpS1 ) contained a variable number of modules encoding tail fiber fragments. DNA inversion and module exchange between strains was involved in generating tail fiber diversity. Xenorhabdicin-enriched fractions from three different X. bovienii strains isolated from the same nematode species displayed distinct activities against each other. In one set of strains, the strain that produced highly active xenorhabdicin was able to eliminate a sensitive strain. In contrast, xenorhabdicin activity was not a determining factor in the competitive fitness of a second set of strains. These findings suggest that related strains of X. bovienii use xenorhabdicin and additional antagonistic molecules to compete against each other.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Comparative analysis of MazEF and HicAB toxin-antitoxin systems of the cyanobacterium, Anabaena sp. PCC7120 (2017)
    Oxford University Press
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    Publication Date: 2017-01-19
    Description: Anabaena PCC7120 has two annotated toxin–antitoxin systems: MazEF and HicAB. Overexpression of either of the toxins severely inhibited the growth of Escherichia coli BL21(p lysS )(DE3). Of the two Anabaena toxins, MazF exhibited higher toxicity than HicA as evidenced by (i) 100-fold lower viability upon overexpression of MazF compared to HicA; (ii) complete loss of cell viability within 1 h of induction of MazF expression, as against 〉10 3 colony forming units mL –1 in case of HicA; (iii) inability to maintain the MazF overexpressing plasmid in E. coli cells; and (iv) neutralisation of the toxin was effective at the molar ratio of 1:1.9 for MazF:MazE and 13:1 for HicA:HicB, indicating higher antitoxin requirement for neutralisation of MazF. The growth inhibitory effect of MazF was found to be higher in lag phase cultures compared to mid-logarithmic phase cultures of E. coli , while the reverse was true for HicA. The results suggest possible distinct roles for MazEF and HicAB systems of Anabaena .
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    The excreted microbiota of bats: evidence of niche specialisation based on multiple body habitats (2017)
    Oxford University Press
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    Publication Date: 2017-01-13
    Description: Animal-associated microbiotas form complex communities, which play crucial functions for their host, including susceptibility to infections. Despite increasing attention to bats as reservoirs of zoonotic pathogens, their microbiota is poorly documented, especially for samples potentially implicated in pathogen transmission such as urine and saliva. Here, using low-biomass individual samples, we examined the composition and structure of bacterial communities excreted by insectivorous bats, focusing on three body habitats (saliva, urine and faeces). We show that niche specialisation occurs as bacterial community composition was distinct across body habitats with the majority of phylotypes being body habitat specific. Our results suggest that urine harbours more diverse bacterial communities than saliva and faeces and reveal potentially zoonotic bacteria such as Leptospira , Rickettsia , Bartonella and Coxiella in all body habitats. Our study emphasised that, in addition to the traditional use of gut-associated samples such as faeces, both urine and saliva are also of interest because of their diverse microbiota and the potential transmission of pathogenic bacteria. Our results represent a critical baseline for future studies investigating the interactions between microbiota and infection dynamics in bats.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Preserved history of global mean spreading rate: 83 Ma to present (2017)
    Oxford University Press
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    Publication Date: 2017-01-07
    Description: Using an up-to-date global plate rotation model, applied to the endpoints of preserved major spreading ridge isochrons, we have calculated the explicitly reconstructable length-weighted mean global half-spreading rate (HSR), ridge length and area production as a function of time since the end of the Cretaceous Normal Superchron at 83.0 Ma. Our calculations integrate uncertainties in rotation parameters and chron boundary ages with the partial sampling uncertainties arising from progressive subduction of older oceanic lithosphere and its preserved spreading record. This record of directly reconstructable oceanic ridge production provides a well-constrained baseline that can be compared to reconstructions that include the largely unconstrained extrapolated histories of entirely subducted oceanic plates. The directly reconstructable global mean HSR has not varied by more than ±15 per cent about an average rate of 28.4 ± 4.6 mm a –1 since 83 Ma. No long-term secular trend is evident: a maximum global mean half-rate of 32 ± 6 mm a –1 occurred from 33.1 Ma to about 25.8 Ma, with minima of 26 ± 5 mm a –1 between about 56 and 40.2 Ma, and 24 ± 1 mm a –1 since 3.2 Ma. Only this most recent interval has a rate that differs significantly (at ±2) from the long-term mean. The global, reconstructable ridge length at 56 Ma decreases by less than 15 per cent relative to the modern ridge system; by 83 Ma it has decreased by 38 per cent. These relatively high preserved ridge fractions mean that the estimated uncertainty due to partial sampling stays roughly equivalent to the estimated rotation model uncertainties, allowing long-term spreading rate variations of 〉20 per cent since the Late Cretaceous to be ruled out. In contrast, prior to 83 Ma too little oceanic lithosphere is preserved to reliably reconstruct global spreading rates.
    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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  • 5
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    The Value of Heterogeneous Property Rights and the Costs of Water Volatility (2017)
    Oxford University Press
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    Publication Date: 2017-01-05
    Description: The system of prior appropriation in the Western Unites States prioritizes property rights for water based on the establishment of beneficial use, creating a hierarchy where rights initiated first are more secure. I estimate the demand for security in water rights through their capitalization in agricultural property markets in the Yakima River Basin, a major watershed in Washington State. All water rights are satisfied in an average year, so the relative value of secure property rights is a function of water supply volatility and the costs of droughts are predominantly born by those with weak rights. In aggregate, security in water rights does not capitalize into property values at the irrigation district level; however, there is heterogeneity in the premium for secure water rights. The lack of a premium for district-level water security is robust to a variety of econometric methods to account for correlated district unobservables, and the null result produces an economically significant upper bound on the value to water security for the district. The ability for farmers to adapt to water supply volatility, as well as expectations about water markets and government infrastructure investment, are leading explanations for the lack of an aggregate premium. These explanations are supported by the pattern of heterogeneity in the water security premium.
    Keywords: Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q21 - Demand and Supply, Q24 - Land, Q25 - Water, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 6
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    Present-day velocity field and block kinematics of Tibetan Plateau from GPS measurements (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: In this study, we present a new synthesis of GPS velocities for tectonic deformation within the Tibetan Plateau and its surrounding areas, a combined data set of ~1854 GPS-derived horizontal velocity vectors. Assuming that crustal deformation is localized along major faults, a block modelling approach is employed to interpret the GPS velocity field. We construct a 30-element block model to describe present-day deformation in western China, with half of them located within the Tibetan Plateau, and the remainder located in its surrounding areas. We model the GPS velocities simultaneously for the effects of block rotations and elastic strain induced by the bounding faults. Our model yields a good fit to the GPS data with a mean residual of 1.08 mm a –1 compared to the mean uncertainty of 1.36 mm a –1 for each velocity component, indicating a good agreement between the predicted and observed velocities. The major strike-slip faults such as the Altyn Tagh, Xianshuihe, Kunlun and Haiyuan faults have relatively uniform slip rates in a range of 5–12 mm a –1 along most of their segments, and the estimated fault slip rates agree well with previous geologic and geodetic results. Blocks having significant residuals are located at the southern and southeastern Tibetan Plateau, suggesting complex tectonic settings and further refinement of accurate definition of block geometry in these regions.
    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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  • 7
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    New and highly active microbial phosphotriesterase sources (2016)
    Oxford University Press
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    Publication Date: 2016-12-29
    Description: Many toxic insecticides used worldwide as well as some chemical warfare agents are phosphotriester derivatives. Therefore, detoxification of organophosphorus compounds has become the subject of many studies and in particular bioremediation, based on the phosphotriesterase catalysed hydrolysis of these compounds, has shown to be an effective and ecological methodology. In order to identify new bacterial phosphotriesterases, a simple and sensitive fluorimetric screening method on solid media was employed that allowed the selection of six strains with phosphotriesterase activity. Since pH and temperature are important parameters for bioremediation of contaminated soils and waters, the influence of these variables on the rate of the enzymatic hydrolysis was assessed. This study afforded notable results, being the most remarkable one the increased activity exhibited by Nocardia asteroides and Streptomyces setonii strains at 50°C, 7 and 30 times higher than at 30°C, respectively. Compared with the results obtained with Brevundimonas diminuta , whose activity is usually considered as reference, an increase of 26 and 75 times is observed, respectively.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Bacterial biodegradation of neonicotinoid pesticides in soil and water systems (2016)
    Oxford University Press
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    Publication Date: 2016-12-23
    Description: Neonicotinoids are neurotoxic systemic insecticides used in plant protection worldwide. Unfortunately, application of neonicotinoids affects both beneficial and target insects indiscriminately. Being water soluble and persistent, these pesticides are capable of disrupting both food chains and biogeochemical cycles. This review focuses on the biodegradation of neonicotinoids in soil and water systems by the bacterial community. Several bacterial strains have been isolated and identified as capable of transforming neonicotinoids in the presence of an additional carbon source. Environmental parameters have been established for accelerated transformation in some of these strains. Studies have also indicated that enhanced biotransformation of these pesticides can be accomplished by mixed microbial populations under optimised environmental conditions. Substantial research into the identification of neonicotinoid-mineralising bacterial strains and identification of the genes and enzymes responsible for neonicotinoid degradation is still required to complete the understanding of microbial biodegradation pathways, and advance bioremediation efforts.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Current deformation in Central Afar and triple junction kinematics deduced from GPS and InSAR measurements (2016)
    Oxford University Press
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    Publication Date: 2016-12-22
    Description: Kinematics of divergent boundaries and Rift-Rift-Rift junctions are classically studied using long-term geodetic observations. Since significant magma-related displacements are expected, short-term deformation provides important constraints on the crustal mechanisms involved both in active rifting and in transfer of extensional deformation between spreading axes. Using InSAR and GPS data, we analyse the surface deformation in the whole Central Afar region in detail, focusing on both the extensional deformation across the Quaternary magmato-tectonic rift segments, and on the zones of deformation transfer between active segments and spreading axes. The largest deformation occurs across the two recently activated Asal-Ghoubbet (AG) and Manda Hararo-Dabbahu (MH-D) magmato-tectonic segments with very high strain rates, whereas the other Quaternary active segments do not concentrate any large strain, suggesting that these rifts are either sealed during interdyking periods or not mature enough to remain a plate boundary. Outside of these segments, the GPS horizontal velocity field shows a regular gradient following a clockwise rotation of the displacements from the Southeast to the East of Afar, with respect to Nubia. Very few shallow creeping structures can be identified as well in the InSAR data. However, using these data together with the strain rate tensor and the rotations rates deduced from GPS baselines, the present-day strain field over Central Afar is consistent with the main tectonic structures, and therefore with the long-term deformation. We investigate the current kinematics of the triple junction included in our GPS data set by building simple block models. The deformation in Central Afar can be described by adding a central microblock evolving separately from the three surrounding plates. In this model, the northern block boundary corresponds to a deep EW-trending trans-tensional dislocation, locked from the surface to 10–13 km and joining at depth the active spreading axes of the Red Sea and the Aden Ridge, from AG to MH-D rift segments. Over the long-term, this plate configuration could explain the presence of the en-échelon magmatic basins and subrifts. However, the transient behaviour of the spreading axes implies that the deformation in Central Afar evolves depending on the availability of magma supply within the well-established segments.
    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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  • 10
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    Compound dislocation models (CDMs) for volcano deformation analyses (2016)
    Oxford University Press
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    Publication Date: 2016-12-22
    Description: Volcanic crises are often preceded and accompanied by volcano deformation caused by magmatic and hydrothermal processes. Fast and efficient model identification and parameter estimation techniques for various sources of deformation are crucial for process understanding, volcano hazard assessment and early warning purposes. As a simple model that can be a basis for rapid inversion techniques, we present a compound dislocation model (CDM) that is composed of three mutually orthogonal rectangular dislocations (RDs). We present new RD solutions, which are free of artefact singularities and that also possess full rotational degrees of freedom. The CDM can represent both planar intrusions in the near field and volumetric sources of inflation and deflation in the far field. Therefore, this source model can be applied to shallow dikes and sills, as well as to deep planar and equidimensional sources of any geometry, including oblate, prolate and other triaxial ellipsoidal shapes. In either case the sources may possess any arbitrary orientation in space. After systematically evaluating the CDM, we apply it to the co-eruptive displacements of the 2015 Calbuco eruption observed by the Sentinel-1A satellite in both ascending and descending orbits. The results show that the deformation source is a deflating vertical lens-shaped source at an approximate depth of 8 km centred beneath Calbuco volcano. The parameters of the optimal source model clearly show that it is significantly different from an isotropic point source or a single dislocation model. The Calbuco example reflects the convenience of using the CDM for a rapid interpretation of deformation data.
    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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