Genetic islands of Streptococcus agalactiae strains NEM316 and 2603VR and their presence in other Group B Streptococcal strains

BACKGROUND: Streptococcus agalactiae (Group B Streptococcus; GBS) is a major contributor to obstetric and neonatal bacterial sepsis. Serotype III strains cause the majority of late-onset sepsis and meningitis in babies, and thus appear to have an enhanced invasive capacity compared with the other serotypes that cause disease predominantly in immunocompromised pregnant women. We compared the serotype III and V whole genome sequences, strains NEM316 and 2603VR respectively, in an attempt to identify genetic attributes of strain NEM316 that might explain the propensity of strain NEM316 to cause late-onset disease in babies. Fourteen putative pathogenicity islands were described in the strain NEM316 whole genome sequence. Using PCR- and targeted microarray- strategies, the presence of these islands were assessed in a diverse strain collection including 18 colonizing isolates from healthy pregnant women, and 13 and 8 invasive isolates from infants with early- and late-onset sepsis, respectively. RESULTS: Side-by-side comparison of the strain NEM316 and strain 2603VR genomes revealed that they are extremely similar, with the only major difference being the capsulation loci and mobile genetic elements. PCR and Comparative Genome Hybridization (CGH) were used to define the presence of each island in 39 GBS isolates. Only islands I, VI, XII, and possibly X, met criteria of a true pathogenicity island, but no significant correlation was found between the presence of any of the fourteen islands and whether the strains were invasive or colonizing. Possible associations were seen between the presence of island VI and late-onset sepsis, and island X and early-onset sepsis, which warrant further investigation. CONCLUSION: The NEM316 and 2603VR strains are remarkable in that their whole genome sequences are so similar, suggesting that the capsulation loci or other genetic differences, such as pathogenicity islands, are the main determinants of the propensity of serotype III strains to cause late-onset disease. This study supports the notion that GBS strain NEM316 has four putative pathogenicity islands, but none is absolutely necessary for disease causation, whether early- or late-onset sepsis. Mobile genetic elements are a common feature of GBS isolates, with each strain having its own peculiar burden of transposons, phages, integrases and integrated plasmids. The majority of these are unlikely to influence the disease capacity of an isolate. Serotype associated disease phenotypes may thus be solely related to differences in the capsulation loci

Towards a Formal Verification Methodology for Collective Robotic Systems

We introduce a UML-based notation for graphically modeling systems’ security aspects in a simple and intuitive way and a model-driven process that transforms graphical specifications of access control policies in XACML. These XACML policies are then translated in FACPL, a policy language with a formal semantics, and the resulting policies are evaluated by means of a Java-based software tool

MMP1 bimodal expression and differential response to inflammatory mediators is linked to promoter polymorphisms.

BACKGROUND: Identifying the functional importance of the millions of single nucleotide polymorphisms (SNPs) in the human genome is a difficult challenge. Therefore, a reverse strategy, which identifies functionally important SNPs by virtue of the bimodal abundance across the human population of the SNP-related mRNAs will be useful. Those mRNA transcripts that are expressed at two distinct abundances in proportion to SNP allele frequency may warrant further study. Matrix metalloproteinase 1 (MMP1) is important in both normal development and in numerous pathologies. Although much research has been conducted to investigate the expression of MMP1 in many different cell types and conditions, the regulation of its expression is still not fully understood. RESULTS: In this study, we used a novel but straightforward method based on agglomerative hierarchical clustering to identify bimodally expressed transcripts in human umbilical vein endothelial cell (HUVEC) microarray data from 15 individuals. We found that MMP1 mRNA abundance was bimodally distributed in un-treated HUVECs and showed a bimodal response to inflammatory mediator treatment. RT-PCR and MMP1 activity assays confirmed the bimodal regulation and DNA sequencing of 69 individuals identified an MMP1 gene promoter polymorphism that segregated precisely with the MMP1 bimodal expression. Chromatin immunoprecipitation (ChIP) experiments indicated that the transcription factors (TFs) ETS1, ETS2 and GATA3, bind to the MMP1 promoter in the region of this polymorphism and may contribute to the bimodal expression. CONCLUSIONS: We describe a simple method to identify putative bimodally expressed RNAs from transcriptome data that is effective yet easy for non-statisticians to understand and use. This method identified bimodal endothelial cell expression of MMP1, which appears to be biologically significant with implications for inflammatory disease. (271 Words).RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Homeless drug users' awareness and risk perception of peer "Take Home Naloxone" use – a qualitative study

BACKGROUND Peer use of take home naloxone has the potential to reduce drug related deaths. There appears to be a paucity of research amongst homeless drug users on the topic. This study explores the acceptability and potential risk of peer use of naloxone amongst homeless drug users. From the findings the most feasible model for future treatment provision is suggested. METHODS In depth face-to-face interviews conducted in one primary care centre and two voluntary organisation centres providing services to homeless drug users in a large UK cosmopolitan city. Interviews recorded, transcribed and analysed thematically by framework techniques. RESULTS Homeless people recognise signs of a heroin overdose and many are prepared to take responsibility to give naloxone, providing prior training and support is provided. Previous reports of the theoretical potential for abuse and malicious use may have been overplayed. CONCLUSION There is insufficient evidence to recommend providing "over the counter" take home naloxone" to UK homeless injecting drug users. However a programme of peer use of take home naloxone amongst homeless drug users could be feasible providing prior training is provided. Peer education within a health promotion framework will optimise success as current professionally led health promotion initiatives are failing to have a positive impact amongst homeless drug users

Network meta-analysis of multiple outcome measures accounting for borrowing of information across outcomes

Background: Network meta-analysis (NMA) enables simultaneous comparison of multiple treatments while preserving randomisation. When summarising evidence to inform an economic evaluation, it is important that the analysis accurately reflects the dependency structure within the data, as correlations between outcomes may have implication for estimating the net benefit associated with treatment. A multivariate NMA offers a framework for evaluating multiple treatments across multiple outcome measures while accounting for the correlation structure between outcomes. Methods: The standard NMA model is extended to multiple outcome settings in two stages. In the first stage, information is borrowed across outcomes as well across studies through modelling the within-study and between-study correlation structure. In the second stage, we make use of the additional assumption that intervention effects are exchangeable between outcomes to predict effect estimates for all outcomes, including effect estimates on outcomes where evidence is either sparse or the treatment had not been considered by any one of the studies included in the analysis. We apply the methods to binary outcome data from a systematic review evaluating the effectiveness of nine home safety interventions on uptake of three poisoning prevention practices (safe storage of medicines, safe storage of other household products, and possession of poison centre control telephone number) in households with children. Analyses are conducted in WinBUGS using Markov Chain Monte Carlo (MCMC) simulations. Results: Univariate and the first stage multivariate models produced broadly similar point estimates of intervention effects but the uncertainty around the multivariate estimates varied depending on the prior distribution specified for the between-study covariance structure. The second stage multivariate analyses produced more precise effect estimates while enabling intervention effects to be predicted for all outcomes, including intervention effects on outcomes not directly considered by the studies included in the analysis. Conclusions: Accounting for the dependency between outcomes in a multivariate meta-analysis may or may not improve the precision of effect estimates from a network meta-analysis compared to analysing each outcome separately

Investigating toxic aluminium levels in haemodialysis patients after “Day Zero” drought in Cape Town, South Africa

Introduction: Aluminium is the most abundant metallic element in the earth’s crust and can be consumed through water, medications, and by using metallic cooking utensils. Aluminium levels become a concern when they are above biological exposure limits and can present with multiple clinical complications. When patients have chronic kidney disease and are on haemodialysis, impaired aluminium excretion can lead to its accumulation. Significantly elevated serum aluminium levels were noted in patients with chronic kidney disease (stage 5) on haemodialysis at Groote Schuur Hospital, Cape Town, South Africa. This coincided with one of the worst water crises ever experienced in this metropolitan area, with extreme water restrictions being imposed and alternative water sources being accessed.Method: A multidisciplinary task force performed a systematic evaluation of aluminium concentrations throughout the dialysis water system. Additionally, a thorough investigation was performed to assess the quality of the laboratory results.Results: Possible areas of contamination and potential sources of exposure were excluded. The laboratory results were verified, and potential sources of error were excluded. The investigation verified that aluminium was truly elevated in the serum of patients, and concluded that dialysis was not the cause. Subsequently, patients’ results have declined to baseline, making it possible that there was increased environmental exposure during the drought.Conclusion: This report serves as a reminder to clinicians of acceptable serum aluminium levels in people on dialysis, and in the water system. Furthermore, it highlights the importance of a multidisciplinary collaborative team approach for the investigation of unexpected results or changes in trends

Ensemble density-functional theory for ab-initio molecular dynamics of metals and finite-temperature insulators

A new method is presented for performing first-principles molecular-dynamics simulations of systems with variable occupancies. We adopt a matrix representation for the one-particle statistical operator Gamma, to introduce a ``projected'' free energy functional G that depends on the Kohn-Sham orbitals only and that is invariant under their unitary transformations. The Liouville equation [ Gamma , H ] = 0 is always satisfied, guaranteeing a very efficient and stable variational minimization algorithm that can be extended to non-conventional entropic formulations or fictitious thermal distributions.Comment: 5 pages, two-column style with 2 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#nm_meta

Secondary schooling and rural youth transitions in Lesotho and Zimbabwe

Based on case studies centred on two rural secondary schools in Lesotho and Zimbabwe, this paper examines the gendered impacts of schooling on young people’s transitions to adulthood. School attendance is shown, first, to disrupt the conventional pathways to adulthood: young people attending school may leave home sooner than they otherwise would, and take responsibility for their day-to-day survival, while marriage and childbearing are often delayed. More significantly, secondary schooling reflects, and contributes to, a growing sense that adulthood itself is not fixed. An alternative version of adulthood is promoted through schools in which formal sector employment is central. Yet while young people are encouraged to opt for, and work towards, this goal, only a minority are able to obtain paid employment. The apparent possibility of determining one’s own lifecourse serves to cast the majority of young people as failures in their transitions to adulthood

Long term drought and warming alter soil bacterial and fungal communities in an upland heathland

The response of soil microbial communities to a changing climate will impact global biogeochemical cycles, potentially leading to positive and negative feedbacks. However, our understanding of how soil microbial communities respond to climate change and the implications of these changes for future soil function is limited. Here, we assess the response of soil bacterial and fungal communities to long-term experimental climate change in a heathland organo-mineral soil. We analysed microbial communities using Illumina sequencing of the 16S rRNA gene and ITS2 region at two depths, from plots undergoing 4 and 18 years of in situ summer drought or warming. We also assessed the colonisation of Calluna vulgaris roots by ericoid and dark septate endophytic (DSE) fungi using microscopy after 16 years of climate treatment. We found significant changes in both the bacterial and fungal communities in response to drought and warming, likely mediated by changes in soil pH and electrical conductivity. Changes in the microbial communities were more pronounced after a longer period of climate manipulation. Additionally, the subsoil communities of the long-term warmed plots became similar to the topsoil. Ericoid mycorrhizal colonisation decreased with depth while DSEs increased; however, these trends with depth were removed by warming. We largely ascribe the observed changes in microbial communities to shifts in plant cover and subsequent feedback on soil physicochemical properties, especially pH. Our results demonstrate the importance of considering changes in soil microbial responses to climate change across different soil depths and after extended periods of time

Interactions between human immunodeficiency virus (HIV)-1 Vpr expression and innate immunity influence neurovirulence

<p>Abstract</p> <p>Background</p> <p>Viral diversity and abundance are defining properties of human immunodeficiency virus (HIV)-1's biology and pathogenicity. Despite the increasing availability of antiretroviral therapy, HIV-associated dementia (HAD) continues to be a devastating consequence of HIV-1 infection of the brain although the underlying disease mechanisms remain uncertain. Herein, molecular diversity within the HIV-1 non-structural gene, Vpr, was examined in RNA sequences derived from brain and blood of HIV/AIDS patients with or without HIV-associated dementia (HAD) together with the ensuing pathobiological effects.</p> <p>Results</p> <p>Cloned brain- and blood-derived full length <it>vpr </it>alleles revealed that amino acid residue 77 within the brain-derived alleles distinguished HAD (77Q) from non-demented (ND) HIV/AIDS patients (77R) (<it>p </it>< 0.05) although <it>vpr </it>transcripts were more frequently detected in HAD brains (<it>p </it>< 0.05). Full length HIV-1 clones encoding the 77R-ND residue induced higher <it>IFN-α</it>, <it>MX1 </it>and <it>BST-2 </it>transcript levels in human glia relative to the 77Q-HAD encoding virus (<it>p </it>< 0.05) but both viruses exhibited similar levels of gene expression and replication. Myeloid cells transfected with 77Q-(p<it>Vpr77Q-HAD</it>), 77R (p<it>Vpr77R-ND</it>) or Vpr null (p<it>Vpr</it>^<it>(-)</it>)-containing vectors showed that the p<it>Vpr77R-ND </it>vector induced higher levels of immune gene expression (<it>p </it>< 0.05) and increased neurotoxicity (<it>p </it>< 0.05). Vpr peptides (amino acids 70-96) containing the 77Q-HAD or 77R-ND motifs induced similar levels of cytosolic calcium activation when exposed to human neurons. Human glia exposed to the 77R-ND peptide activated higher transcript levels of <it>IFN-α</it>, <it>MX1</it>, <it>PRKRA </it>and <it>BST-2 </it>relative to 77Q-HAD peptide (<it>p </it>< 0.05). The Vpr 77R-ND peptide was also more neurotoxic in a concentration-dependent manner when exposed to human neurons (<it>p </it>< 0.05). Stereotaxic implantation of full length Vpr, 77Q-HAD or 77R-ND peptides into the basal ganglia of mice revealed that full length Vpr and the 77R-ND peptide caused greater neurobehavioral deficits and neuronal injury compared with 77Q-HAD peptide-implanted animals (<it>p </it>< 0.05).</p> <p>Conclusions</p> <p>These observations underscored the potent neuropathogenic properties of Vpr but also indicated viral diversity modulates innate neuroimmunity and neurodegeneration.</p