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  • Geodynamics and Tectonics  (182)
  • Synthetic Biology and Assembly Cloning  (70)
  • Pathogens & Pathogenicity  (51)
  • Natural Disasters  (42)
  • Oxford University Press  (345)
  • 1
    Publication Date: 2017-01-13
    Description: As a leading pathogen, Edwardsiella piscicida can cause hemorrhagic septicemia in fish and gastro-intestinal infections in humans. The two-component regulatory system EsrA-EsrB plays essential roles in pathogenesis through the type III and type VI secretion systems, and hemolysin production in E. piscicida . It is unclear whether other virulence- or stress response-associated genes are regulated by EsrA-EsrB. In this study, the proteomes of wild-type E. piscicida EIB202 and esrB mutant strains were compared to reveal EsrB regulon components after growth in Luria–Bertani broth (LB). Overall, the expression levels of nine genes exhibited significant changes, and five of them required the presence of EsrB, while others exhibited higher levels in the esrB mutant. The diverse functions of these proteins were identified, including amino acid metabolism, oxidative stress defense and energy production. Interestingly, superoxidase dismutase and thiol peroxidase were the most significantly down-regulated by EsrB. Furthermore, other reported reactive oxygen species (ROS) resistance-related genes were also down-regulated by EsrB as revealed by quantitative real-time. Compared with the wild-type and the complement strain esrB + , esrB displayed a significantly enhanced ROS resistance. These results demonstrated that EsrB plays important roles in the ROS resistance pathway in E. piscicida grown in LB conditions.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 2
    Publication Date: 2017-01-13
    Description: The sepsis caused by Vibrio vulnificus is characterized by an average incubation period of 26 h and a high mortality rate exceeding 50%. The fast growth and dissemination of V. vulnificus in vivo lead to poor clinical outcomes in patients. Therefore, elucidation of the proliferation mechanisms of this organism in vivo may lead to the development of an effective therapeutic strategy. In this study, we focused on the low oxygen concentration in the intestinal milieu because of its drastic difference from that in air. Fumarate and nitrate reduction regulatory protein (FNR) is known to be a global transcriptional regulator for adaptation to anaerobic conditions in various bacteria. We generated a strain of V. vulnificus in which the fnr gene was replaced with an erythromycin resistance gene ( fnr :: erm mutant). When the fnr :: erm mutant was tested in a growth competition assay against the wild-type (WT) in vivo , the competitive index of fnr :: erm mutant to WT in the intestinal loop and liver was 0.378 ± 0.192 (mean ± SD) and 0.243 ± 0.123, respectively. These data suggested that FNR is important for the proliferation of V. vulnificus in the intestine to achieve a critical mass to be able to invade the systemic circulation.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 3
    Publication Date: 2017-01-10
    Description: Despite the extensive use of  Saccharomyces cerevisiae  as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locus and promoter selection, as well as protein localization and solubility. The toolkit includes 23 Cas9-sgRNA plasmids, 37 promoters of various strengths and temporal expression profiles, and 10 protein-localization, degradation and solubility tags. We facilitated the use of these parts via a web-based tool, that automates the generation of DNA fragments for integration. Our system builds upon existing gene editing methods in the thoroughness with which the parts are standardized and characterized, the types and number of parts available and the ease with which our methodology can be used to perform genetic edits in yeast. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important enzyme, taxadiene synthase (TXS). This approach enabled us to diagnose an issue with TXS solubility, the resolution of which yielded a 25-fold improvement in taxadiene production.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2017-01-08
    Description: Helicobacter pylori is an important cause of gastric pathologies and persistent infection can lead to stomach cancer. Virulent H. pylori strains encode a type IV secretion system responsible for translocation of the oncogenic CagA protein into cells of the gastric mucosa. Gene HP0522 encodes the essential component Cag (Cag3), and we show by gel filtration and cross-linking that purified Cag forms high molecular mass complexes. In contrast, its interaction partner CagT is mostly monomeric, but co-fractionates after gel filtration. Analysis by transmission electron microscopy revealed that purified Cag complexes can self-assemble ring-like structures. Cag-overexpressing Escherichia coli exhibits membrane-associated circular profiles in regions of the cell envelope with intense immunogold labelling with a Cag-specific antiserum. Our results suggest that Cag has the capacity to form macromolecular structures contributing to the assembly of the type IV secretion system.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 5
    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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  • 6
    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
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  • 7
    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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  • 8
    Publication Date: 2016-12-29
    Description: Helicobacter pylori commonly infects the epithelial layer of the human stomach and in some individuals causes peptic ulcers, gastric adenocarcinoma or gastric lymphoma. Helicobacter pylori is a genetically diverse species, and the most important bacterial virulence factor that increases the risk of developing disease, versus asymptomatic colonization, is the cytotoxin associated gene pathogenicity island ( cag PAI). Socially housed rhesus macaques are often naturally infected with H. pylori similar to that which colonizes humans, but little is known about the cag PAI. Here we show that H. pylori strains isolated from naturally infected rhesus macaques have a cag PAI very similar to that found in human clinical isolates, and like human isolates, it encodes a functional type IV secretion system. These results provide further support for the relevance of rhesus macaques as a valid experimental model for H. pylori infection in humans.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 9
    Publication Date: 2016-12-29
    Description: Sporisorium scitamineum is the fungus that causes sugarcane smut disease. Despite of the importance of sugarcane for Brazilian agribusiness and the persistence of the pathogen in most cropping areas, genetic variation studies are still missing for Brazilian isolates. In this study, sets of isolates were analyzed using two molecular markers (AFLP and telRFLP) and ITS sequencing. Twenty-two whips were collected from symptomatic plants in cultivated sugarcane fields of Brazil. A total of 41 haploid strains of compatible mating types were selected from individual teliospores and used for molecular genetic analyses. telRFLP and ITS analyses were expanded to six Argentine isolates, where the sugarcane smut was first recorded in America. Genetic relationship among strains suggests the human-mediated dispersal of S. scitamineum within the Brazilian territory and between the two neighboring countries. Two genetically distinct groups were defined by the combined analysis of AFLP and telRFLP. The opposite mating-type strains derived from single teliospores were clustered together into these main groups, but had not always identical haplotypes. telRFLP markers analyzed over two generations of selfing and controlled outcrossing confirmed the potential for emergence of new variants and occurrence of recombination, which are relevant events for evolution of virulence and environmental adaptation.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 10
    Publication Date: 2016-12-23
    Description: Burkholderia pseudomallei causes melioidosis, a potentially fatal infectious disease in tropical and subtropical countries worldwide. The intracellular behaviour of this pathogen in host cells has been reported to impact the severity of melioidosis, including the development of septicaemia, a consequence of pneumonia melioidosis. We previously identified a predicted cation transporter protein, BPSS1228, that participates in the transitional stage of this intracellular pathogen. For further analysis, in this study B. pseudomallei bpss1228 mutant and complemented strains were constructed and bacterial infectivity on human lung epithelial cells, A549, investigated in vitro . Burkholderia pseudomallei bpss1228 mutant showed impaired bacterial adhesion and invasion into A549 cells compared with wild-type strain, while the deficient phenotypes were restored to wild-type levels by the complemented strain. Additionally, the inactivation of bpss1228 in the mutant strain affected flagella-based swimming on a semi-solid surface and resistance to acid stresses simulating intracellular environments. These observations of BPSS1228 relating to B. pseudomallei infection strategies shed a new light on its association with intracellular B. pseudomallei during the interaction with host cells.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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