Phylogenomics of eukaryotes: Impact of missing data on large alignments

Resolving the relationships between Metazoa and other eukaryotic groups as well as between metazoan phyla is central to the understanding of the origin and evolution of animals. The current view is based on limited data sets, either a single gene with many species (e.g., ribosomal RNA) or many genes but with only a few species. Because a reliable phylogenetic inference simultaneously requires numerous genes and numerous species, we assembled a very large data set containing 129 orthologous proteins (similar to30,000 aligned amino acid positions) for 36 eukaryotic species. Included in the alignments are data from the choanoflagellate Monosiga ovata, obtained through the sequencing of about 1,000 cDNAs. We provide conclusive support for choanoflagellates as the closest relative of animals and for fungi as the second closest. The monophyly of Plantae and chromalveolates was recovered but without strong statistical support. Within animals, in contrast to the monophyly of Coelomata observed in several recent large-scale analyses, we recovered a paraphyletic Coelamata, with nematodes and platyhelminths nested within. To include a diverse sample of organisms, data from EST projects were used for several species, resulting in a large amount of missing data in our alignment (about 25%). By using different approaches, we verify that the inferred phylogeny is not sensitive to these missing data. Therefore, this large data set provides a reliable phylogenetic framework for studying eukaryotic and animal evolution and will be easily extendable when large amounts of sequence information become available from a broader taxonomic range.

Differences in the activity of the muscles in the forearm of individuals with a congenital absence of the hand

The spectral content of the myoelectric signals from the muscles of the remnant forearms of three persons with congenital absences (CA) of their forearms was compared with signals from their intact contra-lateral limbs, similar muscles in three persons with acquired losses (AL) and seven persons without absences [no loss (NL)]. The observed bandwidth for the CA subjects was broader with peak energy between 200 and 300 Hz. While the signals from the contra-lateral limbs and the AL and NL subjects was in the 100-150 Hz range: The mean skew of the signals from the AL subjects was 46.3 +/- 6.7 and those with NL of 45.4 +/- 8.7, while the signals from those with CAs had a skew of 11.0 +/- 11. The structure of the muscles of one CA subject was observed ultrasonically. The muscle showed greater disruption than normally developed muscles. It is speculated that the myographic signal reflects the structure of the muscle. which has developed in a more disorganized manner as a result of the muscle not being stretched by other muscles across the missing distal joint, even in the muscles that are used regularly to control arm prostheses.

Missing the logic of the text: Lord Butler’s report on intelligence on Iraqi weapons of mass destruction

This article focuses on the final report of Lord Butler’s review of British intelligence on weapons of mass destruction (WMD), specifically on its treatment of the accuracy of the use of intelligence on Iraqi WMD in a government dossier published in September 2002 ahead of the 2003 Iraq war. In the report, the demonstration of the accuracy of the “September Dossier” hinges on the insertion of tables that compare side-by-side quotations from this document and from intelligence assessments. The analysis of the textual and visual methods by which the report is written reveals how the logic of the comparative tables is missed in the Butler report: the logic of these tables requires that the comparison between quotations from the two documents should be performed at the level of their details but the Butler report performs its comparison only at a broad and general level.

Black stem rust "...two blighted ears of wheat, which few persons would have thought it worthwhile to carry with them round the world..."

A brief survey of the history of this most severe pathogen of wheat and our developing understanding of it.

In search of the aim of the free movement of persons provisions: has the Court of Justice missed the point?

The Court of Justice has, over the years, often been vilified for exceeding the limits of its jurisdiction by interpreting the provisions of Community legislation in a way not seem originally envisaged by its drafters. A recent example of this approach was a cluster of cases in the context of the free movement of workers and the freedom of establishment (Ritter-Coulais and its progeny), where the Court included within the scope of those provisions situations which, arguably, did not present a sufficient link with their (economic) aim. In particular, in that case law the Court accepted that the mere exercise of free movement for the purpose of taking up residence in the territory of another Member State whilst continuing to exercise an economic activity in the State of origin, suffices for bringing a Member State national within the scope of Articles 39 and 43 EC. It is argued that the most plausible explanation for this approach is that the Court now wishes to re-read the economic fundamental freedoms in such a way as to include within their scope all economically active Union citizens, irrespective of whether their situation presents a sufficient link with the exercise of an economic activity in a cross-border context. It is suggested that this approach is problematic for a number of reasons. It is, therefore, concluded that the Court should revert to its orthodox approach, according to which only situations that involve Union citizens who have moved between Member States for the purpose of taking up an economic activity should be included within the scope of the market freedoms.

Are the debates on water privatization missing the point? Experiences from Africa, Asia and Latin America

This paper has two principal aims: first, to unravel some of the arguments mobilized in the controversial privatization debate, and second, to review the scale and nature of private sector provision of water and sanitation in Africa, Asia and Latin America. Despite being vigorously promoted in the policy arena and having been implemented in several countries in the South in the 1990s, privatization has achieved neither the scale nor benefits anticipated. In particular, the paper is pessimistic about the role that privatization can play in achieving the Millennium Development Goals of halving the number of people without access to water and sanitation by 2015. This is not because of some inherent contradiction between private profits and the public good, but because neither publicly nor privately operated utilities are well suited to serving the majority of low-income households with inadequate water and sanitation, and because many of the barriers to service provision in poor settlements can persist whether water and sanitation utilities are publicly or privately operated. This is not to say that well-governed localities should not choose to involve private companies in water and sanitation provision, but it does imply that there is no justification for international agencies and agreements to actively promote greater private sector participation on the grounds that it can significantly reduce deficiencies in water and sanitation services in the South.

Effect of prebiotics on the human gut microbiota of elderly persons

The colonic microbiota undergoes certain age related changes that may affect health. For example, above the age of 55–65 y, populations of bifidobacteria are known to decrease markedly. Bifidobacteria are known inhibitors of pathogenic microbes and a decrease in their activities may increase susceptibility to infections. There is therefore interest in trying to reverse their decline in aged persons. As the gut microbiota responds to dietary intervention, both probiotics and prebiotics have been tested in this regard. Probiotics are live microbes in the diet, whereas prebiotics are fermentable ingredients that specifically target components of the indigenous microbiota seen to be beneficial. We have published a recent paper demonstrating that prebiotic galactooligosaccharides can exert power effects upon bifidobacteria in the gut flora of elderly persons (both in vivo and in vitro). This addendum summarizes research that led up to this study and discusses the possible impact of prebiotics in impacting upon the gut health of aged persons.