The gain and loss of chromosomal integron systems in the Treponema species

BACKGROUND: Integron systems are now recognized as important agents of bacterial evolution and are prevalent in most environments. One of the human pathogens known to harbor chromosomal integrons, the Treponema spirochetes are the only clade among spirochete species found to carry integrons. With the recent release of many new Treponema genomes, we were able to study the distribution of chromosomal integrons in this genus. RESULTS: We find that the Treponema spirochetes implicated in human periodontal diseases and those isolated from cow and swine intestines contain chromosomal integrons, but not the Treponema species isolated from termite guts. By examining the species tree of selected spirochetes (based on 31 phylogenetic marker genes) and the phylogenetic tree of predicted integron integrases, and assisted by our analysis of predicted integron recombination sites, we found that all integron systems identified in Treponema spirochetes are likely to have evolved from a common ancestor—a horizontal gain into the clade. Subsequent to this event, the integron system was lost in the branch leading to the speciation of T. pallidum and T. phagedenis (the Treponema sps. implicated in sexually transmitted diseases). We also find that the lengths of the integron attC sites shortened through Treponema speciation, and that the integron gene cassettes of T. denticola are highly strain specific. CONCLUSIONS: This is the first comprehensive study to characterize the chromosomal integron systems in Treponema species. By characterizing integron distribution and cassette contents in the Treponema sps., we link the integrons to the speciation of the various species, especially to the pathogens T. pallidum and T. phagedenis

Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites

BACKGROUND: Ciliates employ massive chromatid breakage and de novo telomere formation during generation of the somatic macronucleus. Positions flanking the 81-MAC locus are reproducibly cut. But those flanking the Common Region are proposed to often escape cutting, generating three nested macronuclear chromosomes, two retaining "arms" still appended to the Common Region. Arm-distal positions must differ (in cis) from the Common Region flanks. RESULTS: The Common-Region-flanking positions also differ from the arm-distal positions in that they are "multi-TAS" regions: anchored PCR shows heterogeneous patterns of telomere addition sites, but arm-distal sites do not. The multi-TAS patterns are reproducible, but are sensitive to the sequence of the allele being processed. Thus, random degradation following chromatid cutting does not create this heterogeneity; these telomere addition sites also must be dictated by cis-acting sequences. CONCLUSIONS: Most ciliates show such micro-heterogeneity in the precise positions of telomere addition sites. Telomerase is believed to be tightly associated with, and act in concert with, the chromatid-cutting nuclease: heterogeneity must be the result of intervening erosion activity. Our "weak-sites" hypothesis explains the correlation between alternative chromatid cutting at the Common Region boundaries and their multi-TAS character: when the chromatid-breakage machine encounters either a weak binding site or a weak cut site at these regions, then telomerase dissociates prematurely, leaving the new end subject to erosion by an exonuclease, which pauses at cis-acting sequences; telomerase eventually heals these resected termini. Finally, we observe TAS positioning influenced by trans-allelic interactions, reminiscent of transvection

Written education materials for stroke patients and their carers: perspectives and practices of health professionals

Inadequacies in the provision of written education materials to stroke patients and their carers have been reported. In this study, 20 stroke team health professionals were surveyed regarding their use of and perspectives on written education materials. Seventy percent of participants provided materials to 25% or fewer stroke patients and 90% believed that patients and carers are only occasionally or rarely provided with sufficient written information. Health professionals were uncertain which team members provided written information and identified the need to improve the quality of materials used. Stroke teams should implement a system that facilitates the routine provision of quality written materials to patients and carers, communication among team members, and documentation and verbal reinforcement of the information provided

Paper 4: Instabilities in downslope propagating gravity currents

In this paper, the stability of a gravity current propagating down an inclined channel is explored. The gravity current is generated through a partial lock release. A local analysis of the flow about the lock is conducted using classical methodologies in two-layer shallow water theory, which is here developed to allow for drag and an angled channel. A global analysis of the flow is done by exploring the long-time forced steady state, using non-linear simulations solving the full three-dimensional Navier-Stokes equations. A steady state is forced through the inclusion of a so-called mask function. For sufficiently large slope angles, wave-like instabilities are observed on the density interface (pycnocline) of the generated gravity current. Spectral Proper-Orthogonal Decomposition of the time-series data provides evidence that instability arises via the interaction of two asymmetric vorticity waves, occurring on either side of a critical layer, akin to a spatially evolving Kelvin-Helmholtz instability. The work in this paper is exploratory in nature and motivates further investigation

Calculation of dopant solubilities and phase diagrams of X–Pb–Se (X = Br, Na) limited to defects with localized charge

The control of defects, particularly impurities, to tune the concentrations of electrons and holes is of utmost importance in the use of semiconductor materials. To estimate the amount of dopant that can be added to a semiconductor without precipitating secondary phases, a detailed phase diagram is needed. The ability of ab initio computational methods to predict defect stability can greatly accelerate the discovery of new semiconductors by calculating phase diagrams when time-consuming experimental ones are not available. DFT defect energy calculations are particularly successful in identifying doping strategies by determining the energy of multiple defect charge states in large band gap semiconductors and insulators. In metals, detailed phase diagrams can be determined from such calculations but only one, uncharged defect is needed. In this work, we have calculated dopant solubilities of Br and Na in the thermoelectric material PbSe by mapping its solvus boundaries in different regions of the respective ternary phase diagrams using DFT defect energy calculations. The narrow gap PbSe provides an example where defects with nominal charge state (based on valence counting) have properly-localized charge states. However, defects with unexpected charge states produce delocalized electrons, which are then, in effect, defects with the expected charge state. Simply applying the methods for calculating multiple defect charge states in PbSe and treating them as separate defects fails to predict properties measured by experiments. Performing thermodynamic calculations using only the expected charge states, excluding others, enables accurate prediction of experimentally measured doping efficiencies and phase diagrams. Identifying which defect charge states to include in thermodynamic calculations will expedite the use of such calculations for other semiconductors in understanding phase diagrams and devising effective doping strategies

Dose, exposure time, and resolution in Serial X-ray Crystallography

The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available molecular and X-ray fluxes and molecular alignment. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent X-ray imaging. We find that multiple single-file protein beams will be needed for sub-nanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 0.7 nm should be possible with short exposures.Comment: 19 pages, 7 figures, 1 tabl

Influence of dna repair on nonlinear dose-responses for mutation

Recent evidence has challenged the default assumption that all DNA-reactive alkylating agents exhibit a linear dose-response. Emerging evidence suggests that the model alkylating agents methyl- and ethylmethanesulfonate and methylnitrosourea (MNU) and ethylnitrosourea observe a nonlinear dose-response with a no observed genotoxic effect level (NOGEL). Follow-up mechanistic studies are essential to understand the mechanism of cellular tolerance and biological relevance of such NOGELs. MNU is one of the most mutagenic simple alkylators. Therefore, understanding the mechanism of mutation induction, following low-dose MNU treatment, sets precedence for weaker mutagenic alkylating agents. Here, we tested MNU at 10-fold lower concentrations than a previous study and report a NOGEL of 0.0075μg/ml (72.8nM) in human lymphoblastoid cells, quantified through the hypoxanthine (guanine) phosphoribosyltransferase assay (OECD 476). Mechanistic studies reveal that the NOGEL is dependent upon repair of O6-methylguanine (O6MeG) by the suicide enzyme O6MeG-DNA methyltransferase (MGMT). Inactivation of MGMT sensitizes cells to MNU-induced mutagenesis and shifts the NOGEL to the left on the dose axis. © The Author 2013. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved

Translating Scientific Advances in the AOP Framework to Decision Making for Nanomaterials

Much of the current innovation in advanced materials is occurring at the nanoscale, specifically in manufactured nanomaterials (MNs). MNs display unique attributes and behaviors, and may be biologically and physically unique, making them valuable across a wide range of applications. However, as the number, diversity and complexity of MNs coming to market continue to grow, assessing their health and environmental risks with traditional animal testing approaches is too time- and cost-intensive to be practical, and is undesirable for ethical reasons. New approaches are needed that meet current requirements for regulatory risk assessment while reducing reliance on animal testing and enabling safer-by-design product development strategies to be implemented. The adverse outcome pathway (AOP) framework presents a sound model for the advancement of MN decision making. Yet, there are currently gaps in technical and policy aspects of AOPs that hinder the adoption and use for MN risk assessment and regulatory decision making. This review outlines the current status and next steps for the development and use of the AOP framework in decision making regarding the safety of MNs. Opportunities and challenges are identified concerning the advancement and adoption of AOPs as part of an integrated approach to testing and assessing (IATA) MNs, as are specific actions proposed to advance the development, use and acceptance of the AOP framework and associated testing strategies for MN risk assessment and decision making. The intention of this review is to reflect the views of a diversity of stakeholders including experts, researchers, policymakers, regulators, risk assessors and industry representatives on the current status, needs and requirements to facilitate the future use of AOPs in MN risk assessment. It incorporates the views and feedback of experts that participated in two workshops hosted as part of an Organization for Economic Cooperation and Development (OECD) Working Party on Manufactured Nanomaterials (WPMN) project titled, “Advancing AOP Development for Nanomaterial Risk Assessment and Categorization”, as well as input from several EU-funded nanosafety research consortia