Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and Aubergine

Genetic studies of Drosophila melanogaster have provided a paradigm for RNA interference (RNAi) in arthropods, in which the microRNA and antiviral pathways are each mediated by a single Argonaute (Ago1 and Ago2) and germline suppression of transposable elements is mediated by a trio of Piwi-subfamily Argonaute proteins (Ago3, Aub, and Piwi). Without a suitable evolutionary context, deviations from this can be interpreted as derived or idiosyncratic. Here we analyze the evolution of Argonaute genes across the genomes and transcriptomes of 86 Dipteran species, showing that variation in copy number can occur rapidly, and that there is constant flux in some RNAi mechanisms. The lability of the RNAi pathways is illustrated by the divergence of Aub and Piwi (182-156Ma), independent origins of multiple Piwi-family genes in Aedes mosquitoes (less than 25Ma), and the recent duplications of Ago2 and Ago3 in the tsetse fly Glossina morsitans. In each case the tissue specificity of these genes has altered, suggesting functional divergence or innovation, and consistent with the action of dynamic selection pressures across the Argonaute gene family. We find there are large differences in evolutionary rates and gene turnover between pathways, and that paralogs of Ago2, Ago3, and Piwi/Aub show contrasting rates of evolution after duplication. This suggests that Argonautes undergo frequent evolutionary expansions that facilitate functional divergence.Peer reviewe

Repeated duplication of Argonaute2 is associated with strong selection and testis specialization in Drosophila:Adaptive specialization of Drosophila Argonaute2 duplicates

Argonaute2 (Ago2) is a rapidly evolving nuclease in the Drosophila melanogaster RNA interference (RNAi) pathway that targets viruses and transposable elements in somatic tissues. Here we reconstruct the history of Ago2 duplications across the D. obscura group and use patterns of gene expression to infer new functional specialization. We show that some duplications are old, shared by the entire species group, and that losses may be common, including previously undetected losses in the lineage leading to D. pseudoobscura. We find that while the original (syntenic) gene copy has generally retained the ancestral ubiquitous expression pattern, most of the novel Ago2 paralogs have independently specialized to testis-specific expression. Using population genetic analyses, we show that most testis-specific paralogs have significantly lower genetic diversity than the genome-wide average. This suggests recent positive selection in three different species, and model-based analyses provide strong evidence of recent hard selective sweeps in or near four of the six D. pseudoobscura Ago2 paralogs. We speculate that the repeated evolution of testis specificity in obscura group Ago2 genes, combined with their dynamic turnover and strong signatures of adaptive evolution, may be associated with highly derived roles in the suppression of transposable elements or meiotic drive. Our study highlights the lability of RNAi pathways, even within well-studied groups such as Drosophila, and suggests that strong selection may act quickly after duplication in RNAi pathways, potentially giving rise to new and unknown RNAi functions in nonmodel species

Identification of Widespread Adenosine Nucleotide Binding in Mycobacterium tuberculosis

SummaryComputational prediction of protein function is frequently error-prone and incomplete. In Mycobacterium tuberculosis (Mtb), ∼25% of all genes have no predicted function and are annotated as hypothetical proteins, severely limiting our understanding of Mtb pathogenicity. Here, we utilize a high-throughput quantitative activity-based protein profiling (ABPP) platform to probe, annotate, and validate ATP-binding proteins in Mtb. We experimentally validate prior in silico predictions of >240 proteins and identify 72 hypothetical proteins as ATP binders. ATP interacts with proteins with diverse and unrelated sequences, providing an expanded view of adenosine nucleotide binding in Mtb. Several hypothetical ATP binders are essential or taxonomically limited, suggesting specialized functions in mycobacterial physiology and pathogenicity

Single-field inflation constraints from CMB and SDSS data

We present constraints on canonical single-field inflation derived from WMAP five year, ACBAR, QUAD, BICEP data combined with the halo power spectrum from SDSS LRG7. Models with a non-scale-invariant spectrum and a red tilt n_s < 1 are now preferred over the Harrison-Zel'dovich model (n_s = 1, tensor-to-scalar ratio r = 0) at high significance. Assuming no running of the spectral indices, we derive constraints on the parameters (n_s, r) and compare our results with the predictions of simple inflationary models. The marginalised credible intervals read n_s = 0.962^{+0.028}_{-0.026} and r < 0.17 (at 95% confidence level). Interestingly, the 68% c.l. contours favour mainly models with a convex potential in the observable region, but the quadratic potential model remains inside the 95% c.l. contours. We demonstrate that these results are robust to changes in the datasets considered and in the theoretical assumptions made. We then consider a non-vanishing running of the spectral indices by employing different methods, non-parametric but approximate, or parametric but exact. With our combination of CMB and LSS data, running models are preferred over power-law models only by a Delta chi^2 ~ 5.8, allowing inflationary stages producing a sizable negative running -0.063^{+0.061}_{-0.049} and larger tensor-scalar ratio r < 0.33 at the 95% c.l. This requires large values of the third derivative of the inflaton potential within the observable range. We derive bounds on this derivative under the assumption that the inflaton potential can be approximated as a third order polynomial within the observable range.Comment: 32 pages, 7 figures. v2: additional references, some typos corrected, passed to JCAP style. v3: minor changes, matches published versio

Engaging with History after Macpherson

The Race Relations Amendment Act (2000) identifies a key role for education, and more specifically history, in promoting ‘race equality’ in Britain. In this article Ian Grosvenor and Kevin Myers consider the extent of young people’s current engagement with the history of ‘diversity, change and immigration’ which underpins the commitment to ‘race equality’. Finding that in many of Britain’s schools and universities a singular and exclusionary version of history continues to dominate the curriculum, they go on to consider the reasons for the neglect of multiculturalism. The authors identify the development of an aggressive national identity that depends on the past for its legitimacy and argue that this sense of the past is an important obstacle to future progress

Strong armies, slow adaptation: civil-military relations and diffusion of military power

Why are some states more willing to adopt military innovations than others? Why, for example, were the great powers of Europe able to successfully reform their military practices to better adapt to and participate in the so-called military revolution of the sixteenth and seventeenth centuries while their most important extra-European competitor, the Ottoman Empire, failed to do so? This puzzle is best explained by two factors: civil-military relations and historical timing. In the Ottoman Empire, the emergence of an institutionally strong and internally cohesive army during the early stages of state formation—in the late fourteenth century—equipped the military with substantial bargaining powers. In contrast, the great powers of Europe drew heavily on private providers of military power during the military revolution and developed similar armies only by the second half of the seventeenth century, limiting the bargaining leverage of European militaries over their rulers. In essence, the Ottoman standing army was able to block reform efforts that it believed challenged its parochial interests. Absent a similar institutional challenge, European rulers initiated military reforms and motivated officers and military entrepreneurs to participate in the ongoing military revolution

A life in progress: motion and emotion in the autobiography of Robert M. La Follette

This article is a study of a La Follette’s Autobiography, the autobiography of the leading Wisconsin progressive Robert M. La Follette, which was published serially in 1911 and, in book form, in 1913. Rather than focusing, as have other historians, on which parts of La Follette’s account are accurate and can therefore be trusted, it explains instead why and how this major autobiography was conceived and written. The article shows that the autobiography was the product of a sustained, complex, and often fraught series of collaborations among La Follette’s family, friends, and political allies, and in the process illuminates the importance of affective ties as well as political ambition and commitment in bringing the project to fruition. In the world of progressive reform, it argues, personal and political experiences were inseparable

Microbiome sharing between children, livestock and household surfaces in western Kenya

The gut microbiome community structure and development are associated with several health outcomes in young children. To determine the household influences of gut microbiome structure, we assessed microbial sharing within households in western Kenya by sequencing 16S rRNA libraries of fecal samples from children and cattle, cloacal swabs from chickens, and swabs of household surfaces. Among the 156 households studied, children within the same household significantly shared their gut microbiome with each other, although we did not find significant sharing of gut microbiome across host species or household surfaces. Higher gut microbiome diversity among children was associated with lower wealth status and involvement in livestock feeding chores. Although more research is necessary to identify further drivers of microbiota development, these results suggest that the household should be considered as a unit. Livestock activities, health and microbiome perturbations among an individual child may have implications for other children in the household

Targeted hepatitis C antibody testing interventions: a systematic review and meta-analysis

Testing for hepatitis C virus (HCV) infection may reduce the risk of liver-related morbidity, by facilitating earlier access to treatment and care. This review investigated the effectiveness of targeted testing interventions on HCV case detection, treatment uptake, and prevention of liver-related morbidity. A literature search identified studies published up to 2013 that compared a targeted HCV testing intervention (targeting individuals or groups at increased risk of HCV) with no targeted intervention, and results were synthesised using meta-analysis. Exposure to a targeted testing intervention, compared to no targeted intervention, was associated with increased cases detected [number of studies (n) = 14; pooled relative risk (RR) 1.7, 95 % CI 1.3, 2.2] and patients commencing therapy (n = 4; RR 3.3, 95 % CI 1.1, 10.0). Practitioner-based interventions increased test uptake and cases detected (n = 12; RR 3.5, 95 % CI 2.5, 4.8; and n = 10; RR 2.2, 95 % CI 1.4, 3.5, respectively), whereas media/information-based interventions were less effective (n = 4; RR 1.5, 95 % CI 0.7, 3.0; and n = 4; RR 1.3, 95 % CI 1.0, 1.6, respectively). This meta-analysis provides for the first time a quantitative assessment of targeted HCV testing interventions, demonstrating that these strategies were effective in diagnosing cases and increasing treatment uptake. Strategies involving practitioner-based interventions yielded the most favourable outcomes. It is recommended that testing should be targeted at and offered to individuals who are part of a population with high HCV prevalence, or who have a history of HCV risk behaviour