Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing.

UNLABELLED: The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle. IMPORTANCE: A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria.This work was funded by an EMBO ASTF 425-2014 short-term fellowship awarded to FR and conducted in the laboratory of AJG. SPWdV and AB were funded by BBSRC grant BB/K004514/1.This is the author accepted manuscript. The final version is available from the American Society for Microbiology at http://dx.doi.org/10.1128/AEM.02281-16

'HeART of Stroke (HoS)', a community-based Arts for Health group intervention to support self-confidence and psychological well-being following a stroke: protocol for a randomised controlled feasibility study

Introduction Over 152 000 people in the UK have strokes annually and a third experience residual disability. Low mood also affects a third of stroke survivors; yet psychological support is poor. While Arts for Health interventions have been shown to improve well-being in people with mild-to-moderate depression post-stroke, their role in helping people regain sense of self, well-being and confidence has yet to be evaluated. The main aim of this study is to explore the feasibility of conducting a pragmatic multicentre randomised controlled trial to assess the effectiveness and cost-effectiveness of an Arts for Health group intervention (‘HeART of Stroke’ (HoS)) for stroke survivors. HoS is a 10-session artist-facilitated group intervention held in the community over 14 weeks. It offers a non-judgemental, supportive environment for people to explore sense of self, potentially enhancing well-being and confidence. Methods and analysis Sixty-four people, up to 2 years post-stroke, recruited via secondary care research staff or community stroke/rehabilitation teams in two UK centres will be randomised to either HoS plus usual care or usual care only. Self-reported outcomes, measured at baseline and approximately 5 months postrandomisation, will include stroke-related, well-being, mood, self-esteem, quality of life and process measures. Analyses will focus on estimating key feasibility parameters (eg, rates of recruitment, retention, intervention attendance). We will develop outcome and resource use data collection methods to inform an effectiveness and cost-effectiveness analysis in the future trial. Interviews, with a sample of participants, will explore the acceptability of the intervention and study processes, as well as experiences of the HoS group. Ethics and dissemination National Health Service (NHS), Research and Development and University ethical approvals have been obtained. Two peer-reviewed journal publications are planned plus one service user led publication. Findings will be disseminated at key national conferences, local stakeholder events and via institutional websites.This paper presents independent research funded by the National Institute for Health Research (NIHR) under its Research for Patient Benefit (RfPB) Programme (Grant Reference Number PB-PG-0212-27054)

Whisker touch guides canopy exploration in a nocturnal, arboreal rodent, the Hazel dormouse (Muscardinus avellanarius)

Dormouse numbers are declining in the UK due to habitat loss and fragmentation. We know that dormice are nocturnal, arboreal, and avoid crossing open spaces between habitats, yet how they navigate around their canopy is unknown. As other rodents use whisker touch sensing to navigate and explore their environment, this study investigates whether Hazel dormice (Muscardinus avellanarius) employ their whiskers to cross between habitats. We analysed high-speed video footage of dormice exploring freely in flat and climbing arenas in near darkness and using infrared light illumination. We confirm that, like rats and mice, dormice move their whiskers back and forth continuously (~10 Hz) in a motion called whisking and recruit them to explore small gaps (<10 cm) by increasing the amplitude and frequency of whisking and also the asymmetry of movement between the left and right whisker fields. When gaps between platforms are larger than 10-15 cm dormice spend more time travelling on the floor. These findings suggest that dormice can actively and purposively move their whiskers to gather relevant information from their canopy at night. As this species is vulnerable to threats on the ground, we also provide evidence that joining habitat patches between dormouse populations is important for promoting natural behaviours and movement between patches

Visualizing Natural Image Statistics

Natural image statistics is an important area of research in cognitive sciences and computer vision. Visualization of statistical results can help identify clusters and anomalies as well as analyze deviation, distribution and correlation. Furthermore, they can provide visual abstractions and symbolism for categorized data. In this paper, we begin our study of visualization of image statistics by considering visual representations of power spectra, which are commonly used to visualize different categories of images. We show that they convey a limited amount of statistical information about image categories and their support for analytical tasks is ineffective. We then introduce several new visual representations, which convey different or more information about image statistics. We apply ANOVA to the image statistics to help select statistically more meaningful measurements in our design process. A task-based user evaluation was carried out to compare the new visual representations with the conventional power spectra plots. Based on the results of the evaluation, we made further improvement of visualizations by introducing composite visual representations of image statistics

Genome and Plasmid Sequences of Escherichia coli KV7, an Extended-Spectrum β-Lactamase Isolate Derived from Feces of a Healthy Pig.

We present single-contig assemblies for Escherichia coli strain KV7 (serotype O27, phylogenetic group D) and its six plasmids, isolated from a healthy pig, as determined by PacBio RS II and Illumina MiSeq sequencing. The chromosome of 4,997,475 bp and G+C content of 50.75% harbored 4,540 protein-encoding genes

Motility defects in Campylobacter jejuni defined gene deletion mutants caused by second-site mutations.

Genetic variation due to mutation and phase variation has a considerable impact on the commensal and pathogenic behaviours of Campylobacter jejuni. In this study, we provide an example of how second-site mutations can interfere with gene function analysis in C. jejuni. Deletion of the flagellin B gene (flaB) in C. jejuni M1 resulted in mutant clones with inconsistent motility phenotypes. From the flaB mutant clones picked for further analysis, two were motile, one showed intermediate motility and two displayed severely attenuated motility. To determine the molecular basis of this differential motility, a genome resequencing approach was used. Second-site mutations were identified in the severely attenuated and intermediate motility flaB mutant clones: a TA-dinucleotide deletion in fliW and an A deletion in flgD, respectively. Restoration of WT fliW, using a newly developed genetic complementation system, confirmed that the second-site fliW mutation caused the motility defect as opposed to the primary deletion of flaB. This study highlights the importance of (i) screening multiple defined gene deletion mutant clones, (ii) genetic complementation of the gene deletion and ideally (iii) screening for second-site mutations that might interfere with the pathways/mechanisms under study.This work was funded by BBSRC grant RG66581.This is the final version of the article. It was first available from Society for General Microbiology via http://dx.doi.org/10.1099/mic.0.00018

Wandering behaviour prevents inter and intra oceanic speciation in a coastal pelagic fish

Small pelagic fishes have the ability to disperse over long distances and may present complex evolutionary histories. Here, Old World Anchovies (OWA) were used as a model system to understand genetic patterns and connectivity of fish between the Atlantic and Pacific basins. We surveyed 16 locations worldwide using mtDNA and 8 microsatellite loci for genetic parameters, and mtDNA (cyt b; 16S) and nuclear (RAG1; RAG2) regions for dating major lineage-splitting events within Engraulidae family. The OWA genetic divergences (0-0.4%) are compatible with intra-specific divergence, showing evidence of both ancient and contemporary admixture between the Pacific and Atlantic populations, enhanced by high asymmetrical migration from the Pacific to the Atlantic. The estimated divergence between Atlantic and Pacific anchovies (0.67 [0.53-0.80] Ma) matches a severe drop of sea temperature during the Gunz glacial stage of the Pleistocene. Our results support an alternative evolutionary scenario for the OWA, suggesting a coastal migration along south Asia, Middle East and eastern Africa continental platforms, followed by the colonization of the Atlantic via the Cape of the Good Hope.Portuguese Foundation for Science & Technology (FCT) [SFRH/BD/36600/2007]; FCT [UID/MAR/04292/2013, SFRH/BPD/65830/2009]; FCT strategic plan [UID/Multi/04326/2013]info:eu-repo/semantics/publishedVersio

Rectal Transmission of Transmitted/Founder HIV-1 Is Efficiently Prevented by Topical 1% Tenofovir in BLT Humanized Mice

Rectal microbicides are being developed to prevent new HIV infections in both men and women. We focused our in vivo preclinical efficacy study on rectally-applied tenofovir. BLT humanized mice (n = 43) were rectally inoculated with either the primary isolate HIV-1(JRCSF) or the MSM-derived transmitted/founder (T/F) virus HIV-1(THRO) within 30 minutes following treatment with topical 1% tenofovir or vehicle. Under our experimental conditions, in the absence of drug treatment we observed 50% and 60% rectal transmission by HIV-1(JRCSF) and HIV-1(THRO), respectively. Topical tenofovir reduced rectal transmission to 8% (1/12; log rank p = 0.03) for HIV-1(JRCSF) and 0% (0/6; log rank p = 0.02) for HIV-1(THRO). This is the first demonstration that any human T/F HIV-1 rectally infects humanized mice and that transmission of the T/F virus can be efficiently blocked by rectally applied 1% tenofovir. These results obtained in BLT mice, along with recent ex vivo, Phase 1 trial and non-human primate reports, provide a critically important step forward in the development of tenofovir-based rectal microbicides

The generalised anxiety stigma scale (GASS): psychometric properties in a community sample

<p>Abstract</p> <p>Background</p> <p>Although there is substantial concern about negative attitudes to mental illness, little is known about the stigma associated with Generalised Anxiety Disorder (GAD) or its measurement. The aim of this study was to develop a multi-item measure of Generalised Anxiety Disorder stigma (the GASS).</p> <p>Methods</p> <p>Stigma items were developed from a thematic analysis of web-based text about the stigma associated with GAD. Six hundred and seventeen members of the public completed a survey comprising the resulting 20 stigma items and measures designed to evaluate construct validity. Follow-up data were collected for a subset of the participants (n = 212).</p> <p>Results</p> <p>The factor structure comprised two components: Personal Stigma (views about Generalised Anxiety Disorder); and Perceived Stigma (views about the beliefs of most others in the community). There was evidence of good construct validity and reliability for each of the Generalised Anxiety Stigma Scale (GASS) subscales.</p> <p>Conclusions</p> <p>The GASS is a promising brief measure of the stigma associated with Generalised Anxiety Disorder.</p