Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations

Indexación: Web of Science; Scopus.Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.https://www.nature.com/articles/s41598-017-02845-

Analysis of large oxygenated and nitrated polycyclic aromatic hydrocarbons formed under simulated diesel engine exhaust conditions (by compound fingerprints with SPE/LC-API-MS)

The analysis of organic compounds in combustion exhaust particles and the chemical transformation of soot by nitrogen oxides are key aspects of assessment and mitigation of the climate and health effects of aerosol emissions from fossil fuel combustion and biomass burning. In this study we present experimental and analytical techniques for efficient investigation of oxygenated and nitrated derivatives of large polycyclic aromatic hydrocarbons (PAHs), which can be regarded as well-defined soot model substances. For coronene and hexabenzocoronene exposed to nitrogen dioxide under simulated diesel exhaust conditions, several reaction products with high molecular mass could be characterized by liquid chromatography-atmospheric pressure chemical (and photo) ionization-mass spectrometry (LC-APCI-MS and LC-APPI-MS). The main products of coronene contained odd numbers of nitrogen atoms (m/z 282, 256, 338), whereas one of the main products of hexabenzocoronene exhibited an even number of nitrogen atoms (m/z 391). Various reaction products containing carbonyl and nitro groups could be tentatively identified by combining chromatographic and mass spectrometric information, and changes of their relative abundance were observed to depend on the reaction conditions. This analytical strategy should highlight a relatively young technique for the characterization of various soot-contained, semi-volatile, and semi-polar reaction products of large PAHs

The Treatment of Uncertainties in Reactive Pollution Dispersion Models at Urban Scales

The ability to predict NO2 concentrations ([NO¬2]) within urban street networks is important for the evaluation of strategies to reduce exposure to NO2. However, models aiming to make such predictions involve the coupling of several complex processes: traffic emissions under different levels of congestion; dispersion via turbulent mixing; chemical processes of relevance at the street-scale. Parameterisations of these processes are challenging to quantify with precision. Predictions are therefore subject to uncertainties which should be taken into account when using models within decision making. This paper presents an analysis of mean [NO¬2] predictions from such a complex modelling system applied to a street canyon within the city of York, UK including the treatment of model uncertainties and their causes. The model system consists of a micro-scale traffic simulation and emissions model, a Reynolds Averaged turbulent flow model coupled to a reactive Lagrangian particle dispersion model. The analysis focuses on the sensitivity of predicted in-street increments of [NO¬2] at different locations in the street to uncertainties in the model inputs. These include physical characteristics such as background wind direction, temperature and background ozone concentrations; traffic parameters such as overall demand and primary NO2 fraction; as well as model parameterisations such as roughness lengths, turbulent time- and length-scales and chemical reaction rate coefficients. Predicted [NO¬2] is shown to be relatively robust with respect to model parameterisations, although there are significant sensitivities to the activation energy for the reaction NO+O3 as well as the canyon wall roughness length. Under off-peak traffic conditions, demand is the key traffic parameter. Under peak conditions where the network saturates, road-side [NO¬2] is relatively insensitive to changes in demand and more sensitive to the primary NO2 fraction. The most important physical parameter was found to be the background wind direction. The study highlights the key parameters required for reliable [NO¬2] estimations suggesting that accurate reference measurements for wind direction should be a critical part of air quality assessments for in-street locations. It also highlights the importance of street scale chemical processes in forming road-side [NO¬2], particularly for regions of high NOx emissions such as close to traffic queues

The value of health care – a matter of discussion in Germany

BACKGROUND: Interest in assessing the value of health-care services in Germany has considerably increased since the foundation of the Institut für Qualität und Wirtschaftlichkeit im Gesundheitswesen, IQWiG (Institute for Quality and Efficiency in Health Care). The practical application of value assessment illustrates how problematic the process can be. In all decisions made for the provision of health care, data concerning the measurable dimensions (quantity and quality of efficacy and effectiveness, validity of the results and costs) flow into a complex and not yet standardized decision-making process concerning public financing. Some of these decisions are based on data of uncertain validity, unknown reproducibility and unclear appropriateness. DISCUSSION: In this paper we describe the theoretical aspects of value from psychological and economic viewpoints and discuss national and international approaches. Methodic details and difficulties in assessing the value of health-care services are analysed. A definition of the intangible value of health-care services will be proposed which contains only three factors: the absolute risk reduction (usually a measure of efficacy), the validity of the scientific papers examined and the type of the expected effectiveness (prevention of death and disability, restitution of well-being). The intangible value describes the additional benefit when comparing two possible actions, like treatment or observation only. CONCLUSION: The description of intangible value from the viewpoint of different stakeholders is a useful measure for subsequent steps (not discussed here) – the evaluation of costs and of patient benefit. A standardised, transparent, fair and democratic evaluation is essential for the definition of a basic benefit package

Factors associated with self-assessed increase in tobacco consumption among over-indebted individuals in Germany: a cross-sectional study

Background Over-indebtedness is an increasing phenomenon in industrialised nations causing individual hardship and societal problems. Nonetheless, few studies have explored smoking among over-indebted individuals. Methods A cross-sectional survey (n=949) on retrospectively assessed changes in tobacco consumption was carried out in 2006 and 2007 among clients of 84 officially approved debt and insolvency counselling centres in Germany (response rate 39.7%). Logistic regressions were performed to explore factors associated with reports of increased smoking after onset of over-indebtedness. Results 63% of all respondents stated daily or occasional tobacco consumption. Almost one fifth reported an increase in smoking after becoming over-indebted. Females were less likely to report increased smoking than men (aOR 0.66, 95% CI 0.44-0.99) whereas respondents who had been over-indebted for more than 10 years were more likely to report increased smoking than those who had been over-indebted for less than five years (aOR 1.66; 95%-CI 1.00-2.76). The odds of increased smoking were also elevated among those who reported that their families and friends had withdrawn from them as a consequence of their over-indebtedness (aOR 1.82; 95%-CI 1.06-3.14). Conclusions The study identifies over-indebted individuals and particularly over-indebted men as a high-risk group of smokers. Low levels of social embeddedness/support were associated with a further increase in smoking after becoming over-indebted. Given recent increases of over-indebtedness, the findings highlight the need to develop appropriate public health policies

Different Domains of the RNA Polymerase of Infectious Bursal Disease Virus Contribute to Virulence

BACKGROUND: Infectious bursal disease virus (IBDV) is a pathogen of worldwide significance to the poultry industry. IBDV has a bi-segmented double-stranded RNA genome. Segments A and B encode the capsid, ribonucleoprotein and non-structural proteins, or the virus polymerase (RdRp), respectively. Since the late eighties, very virulent (vv) IBDV strains have emerged in Europe inducing up to 60% mortality. Although some progress has been made in understanding the molecular biology of IBDV, the molecular basis for the pathogenicity of vvIBDV is still not fully understood. METHODOLOGY, PRINCIPAL FINDINGS: Strain 88180 belongs to a lineage of pathogenic IBDV phylogenetically related to vvIBDV. By reverse genetics, we rescued a molecular clone (mc88180), as pathogenic as its parent strain. To study the molecular basis for 88180 pathogenicity, we constructed and characterized in vivo reassortant or mosaic recombinant viruses derived from the 88180 and the attenuated Cu-1 IBDV strains. The reassortant virus rescued from segments A of 88180 (A88) and B of Cu-1 (BCU1) was milder than mc88180 showing that segment B is involved in 88180 pathogenicity. Next, the exchange of different regions of BCU1 with their counterparts in B88 in association with A88 did not fully restore a virulence equivalent to mc88180. This demonstrated that several regions if not the whole B88 are essential for the in vivo pathogenicity of 88180. CONCLUSION, SIGNIFICANCE: The present results show that different domains of the RdRp, are essential for the in vivo pathogenicity of IBDV, independently of the replication efficiency of the mosaic viruses

Large-Eddy Simulation of Flow and Pollutant Transport in Urban Street Canyons with Ground Heating

Our study employed large-eddy simulation (LES) based on a one-equation subgrid-scale model to investigate the flow field and pollutant dispersion characteristics inside urban street canyons. Unstable thermal stratification was produced by heating the ground of the street canyon. Using the Boussinesq approximation, thermal buoyancy forces were taken into account in both the Navier–Stokes equations and the transport equation for subgrid-scale turbulent kinetic energy (TKE). The LESs were validated against experimental data obtained in wind-tunnel studies before the model was applied to study the detailed turbulence, temperature, and pollutant dispersion characteristics in the street canyon of aspect ratio 1. The effects of different Richardson numbers (Ri) were investigated. The ground heating significantly enhanced mean flow, turbulence, and pollutant flux inside the street canyon, but weakened the shear at the roof level. The mean flow was observed to be no longer isolated from the free stream and fresh air could be entrained into the street canyon at the roof-level leeward corner. Weighed against higher temperature, the ground heating facilitated pollutant removal from the street canyon.Singapore-MIT Alliance for Research and Technology. Center for Environmental Sensing and Monitorin

The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Background: The NORMAN Association (https://www.norman-.network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-.network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https:// zenodo.org/communities/norman-.sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA's CompTox Chemicals Dashboard (https://comptox. epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101).Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the "one substance, one assessment" approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-.network.com/nds/SLE/)

Advances in mass spectrometry-based post-column bioaffinity profiling of mixtures

In the screening of complex mixtures, for example combinatorial libraries, natural extracts, and metabolic incubations, different approaches are used for integrated bioaffinity screening. Four major strategies can be used for screening of bioactive mixtures for protein targets—pre-column and post-column off-line, at-line, and on-line strategies. The focus of this review is on recent developments in post-column on-line screening, and the role of mass spectrometry (MS) in these systems. On-line screening systems integrate separation sciences, mass spectrometry, and biochemical methodology, enabling screening for active compounds in complex mixtures. There are three main variants of on-line MS based bioassays: the mass spectrometer is used for ligand identification only; the mass spectrometer is used for both ligand identification and bioassay readout; or MS detection is conducted in parallel with at-line microfractionation with off-line bioaffinity analysis. On the basis of the different fields of application of on-line screening, the principles are explained and their usefulness in the different fields of drug research is critically evaluated. Furthermore, off-line screening is discussed briefly with the on-line and at-line approaches