The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins ( Pygoscelis papua ) in their natural environment

The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors

Ensuring young voices are heard in core outcome set development: international workshops with 70 children and young people.

Plain english summaryResearchers test treatments to ensure these work and are safe. They do this by studying the effects that treatments have on patients by measuring outcomes, such as pain and quality of life. Often research teams measure different outcomes even though each team is studying the same condition. This makes it hard to compare the findings from different studies and it can reduce the accuracy of the treatment advice available to patients. Increasingly, researchers are tackling this problem by developing 'core outcome sets'. These are lists of outcomes that all researchers working on a given condition should measure in their studies. It is important that patients have a voice in the development of core outcome sets and children and young people are no exception. But their voices have rarely been heard when core outcome sets are developed. Researchers are trying to address this problem and make sure that core outcome sets are developed in ways that are suitable for children and young people. As a first step, we held two international workshops with children and young people to listen to their views. They emphasised the importance of motivating young people to participate in developing core outcome sets, making them feel valued, and making the development process more interactive, enjoyable and convenient. We hope this commentary will encourage researchers to include children and young people when developing core outcome sets and to adapt their methods so these are suitable for young participants. Future research is important to examine whether these adaptations are effective.AbstractBackground Different research teams looking at treatments for the same condition often select and measure inconsistent treatment outcomes. This makes it difficult to synthesise the results of different studies, leads to selective outcome reporting and impairs the quality of evidence about treatments. 'Core outcome sets' (COS) can help to address these problems. A COS is an agreed, minimum list of outcomes that researchers are encouraged to consistently measure and report in their studies. Including children and young people (CYP) as participants in the development of COS for paediatric conditions ensures that clinically meaningful outcomes are measured and reported. However, few published COS have included CYP as participants. COS developers have described difficulties in recruiting and retaining CYP and there is a lack of guidance on optimising COS methods for them. We aimed to explore CYP's views on the methods used to develop COS and identify ways to optimise these methods.Main body This commentary summarises discussions during two workshops with approximately 70 CYP (aged 10-18 years old) at the International Children's Advisory Network Research and Advocacy Summit, 2018. Delegates described what might motivate them to participate in a COS study, including feeling valued, understanding the need for COS and the importance of input from CYP in their development, and financial and other incentives (e.g. certificates of participation). For Delphi surveys, delegates suggested that lists of outcomes should be as brief as possible, and that scoring and feedback methods should be simplified. For consensus meetings, delegates advised preparing CYP in advance, supporting them during meetings (e.g. via mentors) and favoured arrangements whereby CYP could meet separately from parents and other stakeholders. Overall, they wanted COS methods that were convenient, enjoyable and engaging.Conclusion This commentary points to the limitations of the methods currently used to develop COS with CYP. It also points to ways to motivate CYP to participate in COS studies and to enhancements of methods to make participation more engaging for CYP. Pending much needed research on COS methods for CYP, the perspectives offered in the workshops should help teams developing COS in paediatrics and child health

Stellar Coronal Spectroscopy with the Chandra HETGS

Spectroscopy with the Chandra High Energy Transmission Grating Spectrometer provides details on X-ray emission and activity from young and cool stars through resolution of emission lines from a variety of ions. We are beginning to see trends in activity regarding abundances, emission measures, and variability. Here we contrast spectra of TV Crt, a weak-lined T Tauri star, with TW Hya, a Classical T Tauri star. TV Crt has a spectrum more like magnetic activity driven coronae, relative to the TW Hya spectrum, which we have interpreted as due to accretion-produced X-rays. We have also observed the long period system, IM Pegasi to search for rotational modulation, and to compare activity in a long period active binary to shorter period systems and to the pre-main sequence stars. We detected no rotational modulation, but did see long-duration flares.Comment: 5 pages, 2 figures; to be published in IAU Symposium 219: "Stars as Suns: Activity, Evolution, Planets" (Ed. A. Dupree and A. O. Benz

Developing a weighted measure of speech sound accuracy

Purpose: To develop a system for numerically quantifying a speaker's phonetic accuracy through transcription-based measures. With a focus on normal and disordered speech in children, the authors describe a system for differentially weighting speech sound errors on the basis of various levels of phonetic accuracy using a Weighted Speech Sound Accuracy ( WSSA) score. The authors then evaluate the reliability and validity of this measure. Method: Phonetic transcriptions were analyzed from several samples of child speech, including preschoolers and young adolescents with and without speech sound disorders and typically developing toddlers. The new measure of phonetic accuracy was validated against existing measures, was used to discriminate typical and disordered speech production, and was evaluated to examine sensitivity to changes in phonetic accuracy over time. Reliability between transcribers and consistency of scores among different word sets and testing points are compared. Results: Initial psychometric data indicate that WSSA scores correlate with other measures of phonetic accuracy as well as listeners' judgments of the severity of a child's speech disorder. The measure separates children with and without speech sound disorders and captures growth in phonetic accuracy in toddlers' speech over time. The measure correlates highly across transcribers, word lists, and testing points. Conclusion: Results provide preliminary support for the WSSA as a valid and reliable measure of phonetic accuracy in children's speech. O ne of the continuing needs in the fields of developmental phonology and speech-language pathology is for accurate, sensitive, and viable measures of speech production for research and clinical practice Measurement issues are not trivial. A recent study of "independent measures" used to describe the productive phonology of toddlers withou

Horizontally acquired divergent O-antigen contributes to escape from cross-immunity in the classical bordetellae

BACKGROUND: Horizontal gene transfer (HGT) allows for rapid spread of genetic material between species, increasing genetic and phenotypic diversity. Although HGT contributes to adaptation and is widespread in many bacteria, others show little HGT. This study builds on previous work to analyze the evolutionary mechanisms contributing to variation within the locus encoding a prominent antigen of the classical bordetellae. RESULTS: We observed amongst classical bordetellae discrete regions of the lipopolysaccharide O-antigen locus with higher sequence diversity than the genome average. Regions of this locus had less than 50% sequence similarity, low dN/dS ratios and lower GC content compared to the genome average. Additionally, phylogenetic tree topologies based on genome-wide SNPs were incongruent with those based on genes within these variable regions, suggesting portions of the O-antigen locus may have been horizontally transferred. Furthermore, several predicted recombination breakpoints correspond with the ends of these variable regions. To examine the evolutionary forces that might have selected for this rare example of HGT in bordetellae, we compared in vitro and in vivo phenotypes associated with different O-antigen types. Antibodies against O1- and O2-serotypes were poorly cross-reactive, and did not efficiently kill or mediate clearance of alternative O-type bacteria, while a distinct and poorly immunogenic O-antigen offered no protection against colonization. CONCLUSIONS: This study suggests that O-antigen variation was introduced to the classical bordetellae via HGT through recombination. Additionally, genetic variation may be maintained within the O-antigen locus because it can provide escape from immunity to different O-antigen types, potentially allowing for the circulation of different Bordetella strains within the same host population

Preserving the Chesapeake: Law, Ecology, and the Bay

This event was co-sponsored by the Merhige Center for Environmental Studies, the Allen Chair of Law, the Virginia State Bar, and the Miller Center of Public Affairs. The “Historical Background” session, held from 9:30 - 10:30 a.m., was presented by the Hon. Governor Gerald L. Baliles, Director of the Miller Center of Public Affairs and 65th Governor of the Commonwealth of Virginia; Gerald McCarthy, Executive Director of the Virginia Environmental Endowment; and Russell W. Baxter, Deputy Director of the Virginia Department of Conservation and Recreation. Rodney A. Smolla, Dean of the University of Richmond School of Law, served as moderator. The “Current State of the Bay” session, held on Friday, October 20, 2006 from 10:45 - 11:45 a.m., was presented by Jonathan Z. Cannon, Director of the Center for Environmental and Land Use Law at the University of Virginia School of Law; Erin Ryan, of the Marshall-Wythe School of Law at the College of William and Mary; and Richard Batiuk, Associate Director for Science of the Chesapeake Bay Program Office, United States Environmental Protection Agency. Joel Eisen, University of Richmond School of Law, served as moderator. The Keynote was given from 11:45 a.m. - 1:15 p.m. by L. Preston Bryant, Secretary of Natural Resources of the Commonwealth of Virginia. The “Regulatory Efforts” session, held 1:15-2:15 p.m., was presented by Kathy R. Frahm, Director of the Division of Policy at the Virginia Department of Environmental Quality; Joseph J. Tannery, Virginia Staff Attorney for the Chesapeake Bay Foundation; David E. Evans, Partner at McGuireWoods LLP; and Mark Smith, Environmental Scientist with the Water Protection Division, U.S. Environmental Protection Agency. The “Future and Solutions” session, held from 2:30-3:45 p.m., was presented by Nikki Rovner, Deputy Secretary of Natural Resources for the Commonwealth of Virginia; Timothy G. Hayes, Partner at Hunton & Williams LLP; Clyde Wilbur, Principal of Greeley & Hanson; and Alexandra Dunn, General Counsel for the National Association of Clean Water Agencies. Carl W. Tobias, Williams Professor of Law University of Richmond School of Law, served as moderator

Sequence determinants of breakpoint location during HIV-1 intersubtype recombination

Retroviral recombination results from strand switching, during reverse transcription, between the two copies of genomic RNA present in the virus. We analysed recombination in part of the envelope gene, between HIV-1 subtype A and D strains. After a single infection cycle, breakpoints clustered in regions corresponding to the constant portions of Env. With some exceptions, a similar distribution was observed after multiple infection cycles, and among recombinant sequences in the HIV Sequence Database. We compared the experimental data with computer simulations made using a program that only allows recombination to occur whenever an identical base is present in the aligned parental RNAs. Experimental recombination was more frequent than expected on the basis of simulated recombination when, in a region spanning 40 nt from the 5′ border of a breakpoint, no more than two discordant bases between the parental RNAs were present. When these requirements were not fulfilled, breakpoints were distributed randomly along the RNA, closer to the distribution predicted by computer simulation. A significant preference for recombination was also observed for regions containing homopolymeric stretches. These results define, for the first time, local sequence determinants for recombination between divergent HIV-1 isolates

Development of a Model System to Identify Differences in Spring and Winter Oat

Our long-term goal is to develop a Swedish winter oat (Avena sativa). To identify molecular differences that correlate with winter hardiness, a winter oat model comprising of both non-hardy spring lines and winter hardy lines is needed. To achieve this, we selected 294 oat breeding lines, originating from various Russian, German, and American winter oat breeding programs and tested them in the field in south- and western Sweden. By assaying for winter survival and agricultural properties during four consecutive seasons, we identified 14 breeding lines of different origins that not only survived the winter but also were agronomically better than the rest. Laboratory tests including electrolytic leakage, controlled crown freezing assay, expression analysis of the AsVrn1 gene and monitoring of flowering time suggested that the American lines had the highest freezing tolerance, although the German lines performed better in the field. Finally, six lines constituting the two most freezing tolerant lines, two intermediate lines and two spring cultivars were chosen to build a winter oat model system. Metabolic profiling of non-acclimated and cold acclimated leaf tissue samples isolated from the six selected lines revealed differential expression patterns of 245 metabolites including several sugars, amino acids, organic acids and 181 hitherto unknown metabolites. The expression patterns of 107 metabolites showed significant interactions with either a cultivar or a time-point. Further identification, characterisation and validation of these metabolites will lead to an increased understanding of the cold acclimation process in oats. Furthermore, by using the winter oat model system, differential sequencing of crown mRNA populations would lead to identification of various biomarkers to facilitate winter oat breeding

Utilising Reflective Practice Groups as pedagogy in ordination training and theological development

This is an Accepted Manuscript of an article published by Taylor & Francis in Practical Theology on 3-5-19, available online: https://doi.org/10.1080/1756073X.2019.1609254With the Church of England's ([2014. Formation Criteria with Mapped Selection Criteria for Ordained Ministry in the Church of England. https://www.churchofengland.org/media/2139103/formationcriteriaforordainedministryapprovedhofbpsdec2014.docx]) recent formation criteria now requiring ordinands to have a greater degree of reflexive capability, this article considers the pedagogy of Reflective Practice Groups in ordination training and focuses on how reflexivity can be developed in a group context, towards fostering greater spiritual formation, theological reflection, self-awareness, relational practices for pastoral encounter, resilience and self-care practices for ministry. Some ‘foci for reflexivity’ are advocated for use within Reflective Practice Groups in ordination training