Analysis of 16S rDNA sequences from pathogenic Leptospira serovars and use of single nucleotide polymorphisms for rapid speciation by D-HPLC

Leptospira have a worldwide distribution and include important zoonotic pathogens yet diagnosis and differentiation still tend to rely on traditional bacteriological and serological approaches. In this study a 1.3 kb fragment of the rrs gene (16S rDNA) was sequenced from a panel of 22 control strains, representing serovars within the pathogenic species Leptospira interrogans, Leptospira borgpetersenii, and Leptospira kirschneri, to identify single nucleotide polymorphisms (SNPs). These were identified in the 5' variable region of the 16S sequence and a 181 bp PCR fragment encompassing this region was used for speciation by Denaturing High Performance Liquid Chromatography (D-HPLC). This method was applied to eleven additional species, representing pathogenic, non-pathogenic and intermediate species and was demonstrated to rapidly differentiate all but 2 of the non-pathogenic Leptospira species. The method was applied successfully to infected tissues from field samples proving its value for diagnosing leptospiral infections found in animals in the UK. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved.

Genetic diversity among Escherichia coli O157 : H7 isolates and identification of genes linked to human infections

An Escherichia coli oligonucleotide microarray based on three sequenced genomes was validated for comparative genomic microarray hybridization and used to study the diversity of E. coli O157 isolates from human infections and food and animal sources. Among 26 test strains, 24 (including both Shiga toxin [Stx]-positive and -negative strains) were found to be related to the two sequenced E. coli O157:117 strains, EDL933 and Sakai. However, these strains showed much greater genetic diversity than those reported previously, and most of them could not be categorized as either lineage I or H. Some genes were found more often in isolates from human than from nonhuman sources; e.g., ECs1202 and ECs2976, associated with stx2AB and stx1AB, were in all isolates from human sources but in only 40% of those from nonhuman sources. Some (but not all) lineage I-specific or -dominant genes were also more frequently associated with isolates from human. The results suggested that it might be more effective to concentrate our efforts on finding markers that are directly related to infection rather than those specific to certain lineages. In addition, two Stx-negative O157 cattle isolates (one confirmed to be 117) were significantly different from other Stx-positive and -negative E. coli O157:117 strains and were more similar to MG1655 in their gene content. This work demonstrates that not all E. coli O157:117 strains belong to the same clonal group, and those that were similar to E. coli K-12 might be less virulent.

A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes

Background: Microarray based comparative genomic hybridisation (CGH) experiments have been used to study numerous biological problems including understanding genome plasticity in pathogenic bacteria. Typically such experiments produce large data sets that are difficult for biologists to handle. Although there are some programmes available for interpretation of bacterial transcriptomics data and CGH microarray data for looking at genetic stability in oncogenes, there are none specifically to understand the mosaic nature of bacterial genomes. Consequently a bottle neck still persists in accurate processing and mathematical analysis of these data. To address this shortfall we have produced a simple and robust CGH microarray data analysis process that may be automated in the future to understand bacterial genomic diversity. Results: The process involves five steps: cleaning, normalisation, estimating gene presence and absence or divergence, validation, and analysis of data from test against three reference strains simultaneously. Each stage of the process is described and we have compared a number of methods available for characterising bacterial genomic diversity, for calculating the cut-off between gene presence and absence or divergence, and shown that a simple dynamic approach using a kernel density estimator performed better than both established, as well as a more sophisticated mixture modelling technique. We have also shown that current methods commonly used for CGH microarray analysis in tumour and cancer cell lines are not appropriate for analysing our data. Conclusion: After carrying out the analysis and validation for three sequenced Escherichia coli strains, CGH microarray data from 19 E. coli O157 pathogenic test strains were used to demonstrate the benefits of applying this simple and robust process to CGH microarray studies using bacterial genomes.

Escherichia coli isolates from extraintestinal organs of livestock animals harbour diverse virulence genes and belong to multiple genetic lineages

Escherichia coli, the most common cause of bacteraemia in humans in the UK, can also cause serious diseases in animals. However the population structure, virulence and antimicrobial resistance genes of those from extraintestinal organs of livestock animals are poorly characterised. The aims of this study were to investigate the diversity of these isolates from livestock animals and to understand if there was any correlation between the virulence and antimicrobial resistance genes and the genetic backbone of the bacteria and if these isolates were similar to those isolated from humans. Here 39 E. coli isolates from liver (n=31), spleen (n=5) and blood (n=3) of cattle (n=34), sheep (n=3), chicken (n=1) and pig (n=1) were assigned to 19 serogroups with O8 being the most common (n=7), followed by O101, O20 (both n=3) and O153 (n=2). They belong to 29 multi-locus sequence types, 20 clonal complexes with ST23 (n=7), ST10 (n=6), ST117 and ST155 (both n=3) being most common and were distributed among phylogenetic group A (n=16), B1 (n=12), B2 (n=2) and D (n=9). The pattern of a subset of putative virulence genes was different in almost all isolates. No correlation between serogroups, animal hosts, MLST types, virulence and antimicrobial resistance genes was identified. The distributions of clonal complexes and virulence genes were similar to other extraintestinal or commensal E. coli from humans and other animals, suggesting a zoonotic potential. The diverse and various combinations of virulence genes implied that the infections were caused by different mechanisms and infection control will be challenging.

Hcp2, a secreted protein of the phytopathogen Pseudomonas syringae pv. tomato DC3000, is required for competitive fitness against bacteria and yeasts

When analysing the secretome of the plant pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, we identified hemolysin co-regulated protein (Hcp) as one of the secreted proteins. Hcp is assumed to be an extracellular component of the type VI secretion system (T6SS). Two copies of hcp genes are present in the Pst DC3000 genome, hcp1 (PSPTO_2539) and hcp2 (PSPTO_5435). We studied the expression patterns of hcp genes and tested the fitness of hcp knock-out mutants in host plant colonization and in inter-microbial competition. We found that the hcp2 gene is expressed, most actively at the stationary growth phase, and that the Hcp2 protein is secreted via T6SS and appears in the culture medium as covalently linked dimers. Expression of hcp2 is not induced in planta and it does not contribute to virulence or colonisation in tomato or Arabidopsis plants. Instead, hcp2 is required for survival in competition with enterobacteria and yeasts, and its function is associated with suppression of the growth of these competitors. This is the first report on bacterial T6SS-associated genes functioning in competition against yeast. Our results suggest that the T6SS of P. syringae may play an important role in bacterial fitness, allowing this plant pathogen to survive in conditions where it has to compete with other micro-organisms for resources.

Revisiting Asian monsoon formation and change associated with Tibetan Plateau forcing: II. Change

Data analysis based on station observations reveals that many meteorological variables averaged over the Tibetan Plateau (TP) are closely correlated, and their trends during the past decades are well correlated with the rainfall trend of the Asian summer monsoon. However, such correlation does not necessarily imply causality. Further diagnosis confirms the existence of a weakening trend in TP thermal forcing, characterized by weakened surface sensible heat flux in spring and summer during the past decades. This weakening trend is associated with decreasing summer precipitation over northern South Asia and North China and increasing precipitation over northwestern China, South China, and Korea. An atmospheric general circulation model, the HadAM3, is employed to elucidate the causality between the weakening TP forcing and the change in the Asian summer monsoon rainfall. Results demonstrate that a weakening in surface sensible heating over the TP results in reduced summer precipitation in the plateau region and a reduction in the associated latent heat release in summer. These changes in turn result in the weakening of the near-surface cyclonic circulation surrounding the plateau and the subtropical anticyclone over the subtropical western North Pacific, similar to the results obtained from the idealized TP experiment in Part I of this study. The southerly that normally dominates East Asia, ranging from the South China Sea to North China, weakens, resulting in a weaker equilibrated Sverdrup balance between positive vorticity generation and latent heat release. Consequently, the convergence of water vapor transport is confined to South China, forming a unique anomaly pattern in monsoon rainfall, the so-called “south wet and north dry.” Because the weakening trend in TP thermal forcing is associated with global warming, the present results provide an effective means for assessing projections of regional climate over Asia in the context of global warming.

Revisiting Asian monsoon formation and change associated with Tibetan Plateau forcing: I. Formation

Numerical experiments with different idealized land and mountain distributions are carried out to study the formation of the Asian monsoon and related coupling processes. Results demonstrate that when there is only extratropical continent located between 0 and 120°E and between 20/30°N and the North Pole, a rather weak monsoon rainband appears along the southern border of the continent, coexisting with an intense intertropical convergence zone (ITCZ). The continuous ITCZ surrounds the whole globe, prohibits the development of near-surface cross-equatorial flow, and collects water vapor from tropical oceans, resulting in very weak monsoon rainfall. When tropical lands are integrated, the ITCZ over the longitude domain where the extratropical continent exists disappears as a consequence of the development of a strong surface cross-equatorial flow from the winter hemisphere to the summer hemisphere. In addition, an intense interaction between the two hemispheres develops, tropical water vapor is transported to the subtropics by the enhanced poleward flow, and a prototype of the Asian monsoon appears. The Tibetan Plateau acts to enhance the coupling between the lower and upper tropospheric circulations and between the subtropical and tropical monsoon circulations, resulting in an intensification of the East Asian summer monsoon and a weakening of the South Asian summer monsoon. Linking the Iranian Plateau to the Tibetan Plateau substantially reduces the precipitation over Africa and increases the precipitation over the Arabian Sea and the northern Indian subcontinent, effectively contributing to the development of the South Asian summer monsoon.

Pollen-based continental climate reconstructions at 6 and 21 ka: a global synthesis

Subfossil pollen and plant macrofossil data derived from 14C-dated sediment profiles can provide quantitative information on glacial and interglacial climates. The data allow climate variables related to growing season warmth, winter cold, and plant-available moisture to be reconstructed. Continental-scale reconstructions have been made for the mid-Holocene (MH, around 6 ka) and Last Glacial Maximum (LGM, around 21 ka), allowing comparison with palaeoclimate simulations currently being carried out as part of the fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change. The synthesis of the available MH and LGM climate reconstructions and their uncertainties, obtained using modern analogue, regression and model-inversion techniques, is presented for four temperature variables and two moisture variables. Reconstructions of the same variables based on surface-pollen assemblages are shown to be accurate and unbiased. Reconstructed LGM and MH climate anomaly patterns are coherent, consistent between variables, and robust with respect to the choice of technique. They support a conceptual model of the controls of Late Quaternary climate change whereby the first-order effects of orbital variations and greenhouse forcing on the seasonal cycle of temperature are predictably modified by responses of the atmospheric circulation and surface energy balance.

Multimodel estimates of intercontinental source-receptor relationships for ozone pollution

Understanding the surface O3 response over a “receptor” region to emission changes over a foreign “source” region is key to evaluating the potential gains from an international approach to abate ozone (O3) pollution. We apply an ensemble of 21 global and hemispheric chemical transport models to estimate the spatial average surface O3 response over east Asia (EA), Europe (EU), North America (NA), and south Asia (SA) to 20% decreases in anthropogenic emissions of the O3 precursors, NOx, NMVOC, and CO (individually and combined), from each of these regions. We find that the ensemble mean surface O3 concentrations in the base case (year 2001) simulation matches available observations throughout the year over EU but overestimates them by >10 ppb during summer and early fall over the eastern United States and Japan. The sum of the O3 responses to NOx, CO, and NMVOC decreases separately is approximately equal to that from a simultaneous reduction of all precursors. We define a continental-scale “import sensitivity” as the ratio of the O3 response to the 20% reductions in foreign versus “domestic” (i.e., over the source region itself) emissions. For example, the combined reduction of emissions from the three foreign regions produces an ensemble spatial mean decrease of 0.6 ppb over EU (0.4 ppb from NA), less than the 0.8 ppb from the reduction of EU emissions, leading to an import sensitivity ratio of 0.7. The ensemble mean surface O3 response to foreign emissions is largest in spring and late fall (0.7–0.9 ppb decrease in all regions from the combined precursor reductions in the three foreign regions), with import sensitivities ranging from 0.5 to 1.1 (responses to domestic emission reductions are 0.8–1.6 ppb). High O3 values are much more sensitive to domestic emissions than to foreign emissions, as indicated by lower import sensitivities of 0.2 to 0.3 during July in EA, EU, and NA when O3 levels are typically highest and by the weaker relative response of annual incidences of daily maximum 8-h average O3 above 60 ppb to emission reductions in a foreign region (<10–20% of that to domestic) as compared to the annual mean response (up to 50% of that to domestic). Applying the ensemble annual mean results to changes in anthropogenic emissions from 1996 to 2002, we estimate a Northern Hemispheric increase in background surface O3 of about 0.1 ppb a−1, at the low end of the 0.1–0.5 ppb a−1 derived from observations. From an additional simulation in which global atmospheric methane was reduced, we infer that 20% reductions in anthropogenic methane emissions from a foreign source region would yield an O3 response in a receptor region that roughly equals that produced by combined 20% reductions of anthropogenic NOx, NMVOC, and CO emissions from the foreign source region.

Commodity futures prices: more evidence on forecast power, risk premia and the theory of storage

In this paper, we examine the temporal stability of the evidence for two commodity futures pricing theories. We investigate whether the forecast power of commodity futures can be attributed to the extent to which they exhibit seasonality and we also consider whether there are time varying parameters or structural breaks in these pricing relationships. Compared to previous studies, we find stronger evidence of seasonality in the basis, which supports the theory of storage. The power of the basis to forecast subsequent price changes is also strengthened, while results on the presence of a risk premium are inconclusive. In addition, we show that the forecasting power of commodity futures cannot be attributed to the extent to which they exhibit seasonality. We find that in most cases where structural breaks occur, only changes in the intercepts and not the slopes are detected, illustrating that the forecast power of the basis is stable over different economic environments.

Ozone database in support of CMIP5 simulations: results and corresponding radiative forcing

A continuous tropospheric and stratospheric vertically resolved ozone time series, from 1850 to 2099, has been generated to be used as forcing in global climate models that do not include interactive chemistry. A multiple linear regression analysis of SAGE I+II satellite observations and polar ozonesonde measurements is used for the stratospheric zonal mean dataset during the well-observed period from 1979 to 2009. In addition to terms describing the mean annual cycle, the regression includes terms representing equivalent effective stratospheric chlorine (EESC) and the 11-yr solar cycle variability. The EESC regression fit coefficients, together with pre-1979 EESC values, are used to extrapolate the stratospheric ozone time series backward to 1850. While a similar procedure could be used to extrapolate into the future, coupled chemistry climate model (CCM) simulations indicate that future stratospheric ozone abundances are likely to be significantly affected by climate change, and capturing such effects through a regression model approach is not feasible. Therefore, the stratospheric ozone dataset is extended into the future (merged in 2009) with multimodel mean projections from 13 CCMs that performed a simulation until 2099 under the SRES (Special Report on Emission Scenarios) A1B greenhouse gas scenario and the A1 adjusted halogen scenario in the second round of the Chemistry-Climate Model Validation (CCMVal-2) Activity. The stratospheric zonal mean ozone time series is merged with a three-dimensional tropospheric data set extracted from simulations of the past by two CCMs (CAM3.5 and GISSPUCCINI)and of the future by one CCM (CAM3.5). The future tropospheric ozone time series continues the historical CAM3.5 simulation until 2099 following the four different Representative Concentration Pathways (RCPs). Generally good agreement is found between the historical segment of the ozone database and satellite observations, although it should be noted that total column ozone is overestimated in the southern polar latitudes during spring and tropospheric column ozone is slightly underestimated. Vertical profiles of tropospheric ozone are broadly consistent with ozonesondes and in-situ measurements, with some deviations in regions of biomass burning. The tropospheric ozone radiative forcing (RF) from the 1850s to the 2000s is 0.23Wm−2, lower than previous results. The lower value is mainly due to (i) a smaller increase in biomass burning emissions; (ii) a larger influence of stratospheric ozone depletion on upper tropospheric ozone at high southern latitudes; and possibly (iii) a larger influence of clouds (which act to reduce the net forcing) compared to previous radiative forcing calculations. Over the same period, decreases in stratospheric ozone, mainly at high latitudes, produce a RF of −0.08Wm−2, which is more negative than the central Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) value of −0.05Wm−2, but which is within the stated range of −0.15 to +0.05Wm−2. The more negative value is explained by the fact that the regression model simulates significant ozone depletion prior to 1979, in line with the increase in EESC and as confirmed by CCMs, while the AR4 assumed no change in stratospheric RF prior to 1979. A negative RF of similar magnitude persists into the future, although its location shifts from high latitudes to the tropics. This shift is due to increases in polar stratospheric ozone, but decreases in tropical lower stratospheric ozone, related to a strengthening of the Brewer-Dobson circulation, particularly through the latter half of the 21st century. Differences in trends in tropospheric ozone among the four RCPs are mainly driven by different methane concentrations, resulting in a range of tropospheric ozone RFs between 0.4 and 0.1Wm−2 by 2100. The ozone dataset described here has been released for the Coupled Model Intercomparison Project (CMIP5) model simulations in netCDF Climate and Forecast (CF) Metadata Convention at the PCMDI website (http://cmip-pcmdi.llnl.gov/).

Multi-agent based modeling and simulation of complex system in hospital

This study puts forward a method to model and simulate the complex system of hospital on the basis of multi-agent technology. The formation of the agents of hospitals with intelligent and coordinative characteristics was designed, the message object was defined, and the model operating mechanism of autonomous activities and coordination mechanism was also designed. In addition, the Ontology library and Norm library etc. were introduced using semiotic method and theory, to enlarge the method of system modelling. Swarm was used to develop the multi-agent based simulation system, which is favorable for making guidelines for hospital's improving it's organization and management, optimizing the working procedure, improving the quality of medical care as well as reducing medical charge costs.

The GCM–Reality Intercomparison Project for SPARC (GRIPS): scientific issues and initial results

To investigate the effects of the middle atmosphere on climate, the World Climate Research Programme is supporting the project "Stratospheric Processes and their Role in Climate" (SPARC). A central theme of SPARC, to examine model simulations of the coupled troposphere—middle atmosphere system, is being performed through the initiative called GRIPS (GCM—Reality Intercomparison Project for SPARC). In this paper, an overview of the objectives of GRIPS is given. Initial activities include an assessment of the performance of middle atmosphere climate models, and preliminary results from this evaluation are presented here. It is shown that although all 13 models evaluated represent most major features of the mean atmospheric state, there are deficiencies in the magnitude and location of the features, which cannot easily be traced to the formulation (resolution or the parameterizations included) of the models. Most models show a cold bias in all locations, apart from the tropical tropopause region where they can be either too warm or too cold. The strengths and locations of the major jets are often misrepresented in the models. Looking at three—dimensional fields reveals, for some models, more severe deficiencies in the magnitude and positioning of the dominant structures (such as the Aleutian high in the stratosphere), although undersampling might explain some of these differences from observations. All the models have shortcomings in their simulations of the present—day climate, which might limit the accuracy of predictions of the climate response to ozone change and other anomalous forcing.