Age-related shifts in bacterial diversity in a reef coral

This study investigated the relationship between microbial communities in differently sized colonies of the massive coral Coelastrea aspera at Phuket, Thailand where colony size could be used as a proxy for age. Results indicated significant differences between the bacterial diversity (ANOSIM, R = 0.76, p = 0.001) of differently sized colonies from the same intertidal reef habitat. Juvenile and small colonies (28 cm mean diam). Bacterial diversity increased in a step-wise pattern from juvenilessmallmedium colonies, which was then followed by a slight decrease in the two largest size classes. These changes appear to resemble a successional process which occurs over time, similar to that observed in the ageing human gut. Furthermore, the dominant bacterial ribotypes present in the tissues of medium and large sized colonies of C. aspera, (such as Halomicronema, an Oscillospira and an unidentified cyanobacterium) were also the dominant ribotypes found within the endolithic algal band of the coral skeleton; a result providing some support for the hypothesis that the endolithic algae of corals may directly influence the bacterial community present in coral tissues.Barbara Brown recieved funding from the Leverhulme Trust [www.leverhulme.ac.uk]; Grant number: EM-2013-058. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

T cell development comprises a stepwise process of commitment from a multipotent precursor. To define molecular mechanisms controlling this progression, we probed five stages spanning the commitment process using RNA-seq and ChIP-seq to track genome-wide shifts in transcription, cohorts of active transcription factor genes, histone modifications at diverse classes of cis-regulatory elements, and binding repertoire of GATA-3 and PU.1, transcription factors with complementary roles in T cell development. The results highlight potential promoter-distal cis-regulatory elements in play and reveal both activation sites and diverse mechanisms of repression that silence genes used in alternative lineages. Histone marking is dynamic and reversible, and though permissive marks anticipate, repressive marks often lag behind changes in transcription. In vivo binding of PU.1 and GATA-3 relative to epigenetic marking reveals distinctive factor-specific rules for recruitment of these crucial transcription factors to different subsets of their potential sites, dependent on dose and developmental context

Consensual Qualitative Research: An Update

The authors reviewed the application of consensual qualitative research (CQR) in 27 studies published since the method’s introduction to the field in 1997 by C. E. Hill, B. J. Thompson, and E. N. Williams (1997). After first describing the core components and the philosophical underpinnings of CQR, the authors examined how it has been applied in terms of the consensus process, biases, research teams, data collection, data analysis, and writing up the results and discussion sections of articles. On the basis of problems that have arisen in each of these areas, the authors made recommendations for modifications of the method. The authors concluded that CQR is a viable qualitative method and suggest several ideas for research on the method itself

Divergence or convergence? Health inequalities and policy in a devolved Britain

Since the advent of political devolution in the UK, it has been widely reported that markedly different health policies have emerged. However, most of these analyses are based on a comparison of health care policies and, as such, only tell part of a complex and evolving story. This paper considers official responses to a shared public health policy aim, the reduction of health inequalities, through an examination of national policy statements produced in England, Scotland and Wales respectively since 1997. The analysis suggests that the relatively consistent manner in which the ‘policy problem’ of health inequalities has been framed combined with the dominance of a medical model of health have constrained policy responses. Our findings differ from existing analyses, raising some important questions about the actuality of, and scope for, policy divergence since devolution

The Culture of Poverty Debate: Some Additional Data

In this paper we briefly review relevant research on the culture of poverty and set our findings within the general context of culture of poverty arguments. Data from a community survey in a Southwestern city are analyzed using Oscar Lewis’ four major culture of poverty dimensions: 1) the individual, 2) the family, 3) the slum community, and 4) the community’s relation to society. In our study a sample of 271 black respondents was divided into two groups, here termed the “poor” and the “non-poor.” In noting all the broad traits studied in all dimensions taken together, some support for Lewis’ culture of poverty was found in less than half of the cases; and in several cases our findings were in direct opposition to culture of poverty predictions. In addition, we have suggested that the majority of those traits that did lend support to Lewis’ argument might be better classified as situational conditions of poverty rather than as a part of a bona fide “culture” of poverty. The findings of this paper may call into question the use of the “culture of poverty” perspective as a basis for policy decisions

Transcription factor redundancy and tissue-specific regulation: Evidence from functional and physical network connectivity

Two major transcriptional regulators of Caenorhabditis elegans bodywall muscle (BWM) differentiation, hlh-1 and unc-120, are expressed in muscle where they are known to bind and regulate several well-studied muscle-specific genes. Simultaneously mutating both factors profoundly inhibits formation of contractile BWM. These observations were consistent with a simple network model in which the muscle regulatory factors drive tissue-specific transcription by binding selectively near muscle-specific targets to activate them. We tested this model by measuring the number, identity, and tissue-specificity of functional regulatory targets for each factor. Some joint regulatory targets (218) are BWM-specific and enriched for nearby HLH-1 binding. However, contrary to the simple model, the majority of genes regulated by one or both muscle factors are also expressed significantly in non-BWM tissues. We also mapped global factor occupancy by HLH-1, and created a genetic interaction map that identifies hlh-1 collaborating transcription factors. HLH-1 binding did not predict proximate regulatory action overall, despite enrichment for binding among BWM-specific positive regulatory targets of hlh-1. We conclude that these tissue-specific factors contribute much more broadly to the transcriptional output of muscle tissue than previously thought, offering a partial explanation for widespread HLH-1 occupancy. We also identify a novel regulatory connection between the BWM-specific hlh-1 network and the hlh-8/twist nonstriated muscle network. Finally, our results suggest a molecular basis for synthetic lethality in which hlh-1 and unc-120 mutant phenotypes are mutually buffered by joint additive regulation of essential target genes, with additional buffering suggested via newly identified hlh-1 interacting factors

Dallas with balls: televized sport, soap opera and male and female pleasures

Two of the most popular of television genres, soap opera and sports coverage have been very much differentiated along gender lines in terms of their audiences. Soap opera has been regarded very much as a 'gynocentric' genre with a large female viewing audience while the audiences for television sport have been predominantly male. Gender differentiation between the genres has had implications for the popular image of each. Soap opera has been perceived as inferior; as mere fantasy and escapism for women while television sports has been perceived as a legitimate, even edifying experience for men. In this article the authors challenge the view that soap opera and television sport are radically different and argue that they are, in fact, very similar in a number of significant ways. They suggest that both genres invoke similar structures of feeling and sensibility in their respective audiences and that television sport is a 'male soap opera'. They consider the ways in which the viewing context of each genre is related to domestic life and leisure, the ways in which the textual structure and conventions of each genre invoke emotional identification, and finally, the ways in which both genres re-affirm gender identities

Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements

RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to quantify transcriptome-wide epistasis that reflects the underlying interactions and which can be interpreted intuitively. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans. From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes with HIF-1–dependent expression that have opposite changes in expression in mutants of two genes that cooperate to negatively regulate HIF-1 abundance; however, the double mutant of these genes exhibits suppression epistasis. This class violates the classical model of HIF-1 regulation but can be explained by postulating a role of hydroxylated HIF-1 in transcriptional control