Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.

Epidemiological and nutrition transition in developing countries: impact on human health and development

Whereas common infectious and parasitic diseases such as malaria and the HIV/AIDS pandemic remain major unresolved health problems in many developing countries, emerging non-communicable diseases relating to diet and lifestyle have been increasing over the last two decades, thus creating a double burden of disease and impacting negatively on already over-stretched health services in these countries. Prevalence rates for type 2 diabetes mellitus and CVD in sub-Saharan Africa have seen a 10-fold increase in the last 20 years. In the Arab Gulf current prevalence rates are between 25 and 35% for the adult population, whilst evidence of the metabolic syndrome is emerging in children and adolescents. The present review focuses on the concept of the epidemiological and nutritional transition. It looks at historical trends in socio-economic status and lifestyle and trends in nutrition-related non-communicable diseases over the last two decades, particularly in developing countries with rising income levels, as well as the other extreme of poverty, chronic hunger and coping strategies and metabolic adaptations in fetal life that predispose to non-communicable disease risk in later life. The role of preventable environmental risk factors for obesity and the metabolic syndrome in developing countries is emphasized and also these challenges are related to meeting the millennium development goals. The possible implications of these changing trends for human and economic development in poorly-resourced healthcare settings and the implications for nutrition training are also discussed.

RED COATS AND WILD BIRDS: MILITARY CULTURE AND ORNITHOLOGY ACROSS THE NINETEENTH-CENTURY BRITISH EMPIRE

“Red coats and wild birds: military culture and ornithology across the nineteenth-century British Empire” investigates the intersections between British military culture and the practices and ideas of ornithology, with a particular focus on the British Mediterranean. Considering that British officers often occupied several imperial sites over the course of their military careers, to what extent did their movements shape their ornithological knowledge and identities at “home” and abroad? How did British military naturalists perceive different local cultures (with different attitudes to hunting, birds, field science, etc.) and different local natures (different sets of birds and environments)? How can trans-imperial careers be written using not only textual sources (for example, biographies and personal correspondence) but also traces of material culture? In answering these questions, I centre my work on the Mediterranean region as a “colonial sea” in the production of hybrid identities and cultural practices, and the mingling of people, ideas, commodities, and migratory birds. I focus on the life geographies of four military officers: Thomas Wright Blakiston, Andrew Leith Adams, L. Howard Lloyd Irby, and Philip Savile Grey Reid. By the mid-nineteenth century, the Mediterranean region emerged as a crucial site for the security of the British “empire route” to India and South Asia, especially with the opening of the Suez Canal in 1869. Military stations served as trans-imperial sites, connecting Britain to India through the flow of military manpower, commodities, information, and bodily experiences across the empire. By using a “critical historical geopolitics of empire” to examine the material remnants of the “avian imperial archive,” I demonstrate how the practices and performances of British military field ornithology helped to: materialize the British Mediterranean as a moral “semi-tropical” place for the physical and cultural acclimatization of British officers en route to and from India; reinforce imperial presence in the region; and make “visible in new ways” the connectivity of North Africa to Europe through the geographical distribution of birds. I also highlight the ways in which the production of ornithological knowledge by army officers was entwined with forms of temperate martial masculinity.

Conservation of substrate specificities among coronavirus main proteases.

The key enzyme in coronavirus replicase polyprotein processing is the coronavirus main protease, 3CL(pro). The substrate specificities of five coronavirus main proteases, including the prototypic enzymes from the coronavirus groups I, II and III, were characterized. Recombinant main proteases of human coronavirus (HCoV), transmissible gastroenteritis virus (TGEV), feline infectious peritonitis virus, avian infectious bronchitis virus and mouse hepatitis virus (MHV) were tested in peptide-based trans-cleavage assays. The determination of relative rate constants for a set of corresponding HCoV, TGEV and MHV 3CL(pro) cleavage sites revealed a conserved ranking of these sites. Furthermore, a synthetic peptide representing the N-terminal HCoV 3CL(pro) cleavage site was shown to be effectively hydrolysed by noncognate main proteases. The data show that the differential cleavage kinetics of sites within pp1a/pp1ab are a conserved feature of coronavirus main proteases and lead us to predict similar processing kinetics for the replicase polyproteins of all coronaviruses.

The natural plasma testosterone profile of male blue tits during the breeding season and its relation to song output

In male birds, the gonadal hormone testosterone (T) is known to influence territorial and mating behaviour. Plasma levels of T show seasonal fluctuations which vary in relation to mating system and social instability. First, we determined the natural T profile of male blue tits Parus caeruleus during the breeding season. We found that plasma levels of T increased at the onset of nest building. Thus, the increase in circulating T was not associated with territory establishment, nor with the fertile period of the males' mates. In most individuals, T levels dropped to values close to zero during the period of chick feeding. Second, we investigated the relationship between plasma levels of T and male age, size, and singing behaviour. During the mating period, T levels did not differ between 1 yr old and older males and did not correlate with body size or condition. However, song output during the dawn chorus tended to be positively correlated with T levels. Therefore, if high T levels are costly, song output might be an honest indicator of male quality in blue tits. Finally, we show that plasma levels of T are significantly higher during the night than during the day. This pattern has also been observed in captive non-passerine birds, but its functional significance remains unknown.

Habitat for Humanity: Calibrating Best Practice Against the MDGs

Poverty alleviation lies at the heart of contemporary international initiatives on development. The key to development is the creation of an environment in which people can develop their potential, leading productive, creative lives in accordance with their needs, interests and faith. This entails, on the one hand, protecting the vulnerable from things that threaten their survival, such as inadequate nutrition, disease, conflict, natural disasters and the impact of climate change, thereby enhancing the poor’s capabilities to develop resilience in difficult conditions. On the other hand, it also requires a means of empowering the poor to act on their own behalf, as individuals and communities, to secure access to resources and the basic necessities of life such as water, food, shelter, sanitation, health and education. ‘Development’, from this perspective, seeks to address the sources of human insecurity, working towards ‘freedom from want, freedom from fear’ in ways that empower the vulnerable as agents of development (not passive recipients of benefaction).

Recognition of the magnitude of the problems confronted by the poor and failure of past interventions to tackle basic issues of human security led the United Nations (UN) in September 2000 to set out a range of ambitious, but clearly defined, development goals to be achieved by 2015. These are known as the Millennium Development Goals (MDGs). The intention of the UN was to mobilise multilateral international organisations, non-governmental organisations and the wider international community to focus attention on fulfilling earlier promises to combat global poverty. This international framework for development prioritises: the eradication of extreme poverty and hunger; achieving universal primary education; promoting gender equality and empowering women; reducing child mortality; improving maternal health; combating HIV/AIDS, malaria and other diseases; ensuring environmental sustainability; and developing a global partnership for development. These goals have been mapped onto specific targets (18 in total) against which outcomes of associated development initiatives can be measured and the international community held to account. If the world achieves the MDGs, more than 500 million people will be lifted out of poverty. However, the challenges the goals represent are formidable. Interim reports on the initiative indicate a need to scale-up efforts and accelerate progress.
Only MDG 7, Target 11 explicitly identifies shelter as a priority, identifying the need to secure ‘by 2020 a significant improvement in the lives of at least 100 million slum dwellers’. This raises a question over how Habitat for Humanity’s commitment to tackling poverty housing fits within this broader international framework designed to allievate global poverty. From an analysis of HFH case studies, this report argues that the processes by which Habitat for Humanity tackles poverty housing directly engages with the agenda set by the MDGs. This should not be regarded as a beneficial by-product of the delivery of decent, affordable shelter, but rather understood in terms of the ways in which Habitat for Humanity has translated its mission and values into a participatory model that empowers individuals and communities to address the interdependencies between inadequate shelter and other sources of human insecurity. What housing can deliver is as important as what housing itself is.

Examples of the ways in which Habitat for Humanity projects engage with the MDG framework include the incorporation of sustainable livelihoods strategies, up-grading of basic infrastructure and promotion of models of good governance. This includes housing projects that have also offered training to young people in skills used in the construction industry, microfinanced loans for women to start up their own home-based businesses, and the provision of food gardens. These play an important role in lifting families out of poverty and ensuring the sustainability of HFH projects. Studies of the impact of improved shelter and security of livelihood upon family life and the welfare of children evidence higher rates of participation in education, more time dedicated to study and greater individual achievement. Habitat for Humanity projects also typically incorporate measures to up-grade the provision of basic sanitation facilities and supplies of safe, potable drinking water. These measures not only directly help reduce mortality rates (e.g. diarrheal diseases account for around 2 million deaths annually in children under 5), but also, when delivered through HFH project-related ‘community funds’, empower the poor to mobilise community resources, develop local leadership capacities and even secure de facto security of tenure from government authorities.

In the process of translating its mission and values into practical measures, HFH has developed a range of innovative practices that deliver much more than housing alone. The organisation’s participatory model enables both direct beneficiaries and the wider community to tackle the insecurities they face, unlocking latent skills and enterprise, building sustainable livelihood capabilities. HFH plays an important role as a catalyst for change, delivering through the vehicle of housing the means to address the primary causes of poverty itself. Its contribution to wider development priorities deserves better recognition. In calibrating the success of HFH projects in terms of units completed or renovated alone, the significance of the process by which HFH realises these outcomes is often not sufficiently acknowledged, both within the organisation and externally. As the case studies developed in the report illustrate, the methodologies Habitat for Humanity employs to address the issue of poverty housing within the developing world, place the organisation at the centre of a global strategic agenda to address the root causes of poverty through community empowerment and the transformation of structures of governance.

Given this, the global network of HFH affiliates constitutes a unique organisational framework to faciliate sharing resources, ideas and practical experience across a diverse range of cultural, political and institutional environments. This said, it is apparent that work needs to be done to better to faciliate the pooling of experience and lessons learnt from across its affiliates. Much is to be gained from learning from less successful projects, sharing innovative practices, identifying strategic partnerships with donors, other NGOs and CBOs, and engaging with the international development community on how housing fits within a broader agenda to alleviate poverty and promote good governance.

Microtubules as antiparasitic drug targets

Background: Parasitic diseases including malaria, leishmaniasis and schistosomiasis take a terrible toll of human life, health and productivity, especially in tropical and subtropical regions, and are also highly significant in animal health worldwide. Antiparasitic drugs are the mainstays of control of most of these diseases, but in many cases current therapies are inadequate and in some the situation is deteriorating because of drug resistance. Microtubules, as essential components of almost all eukaryotic cells, are proven drug targets in many helminth diseases and show promise as targets for the development of new antiprotozoal drugs. Objective: This article reviews the chemistry of the microtubule inhibitors in current use and under investigation as antiparasitic agents, their activities against the major parasites and their mechanisms of action. New directions in both inhibitor chemistry and biological evaluation are discussed. Conclusions: The most promising immediate avenues for discovery and design appear to lie in development of novel benzimidazoles for helminth parasites and compounds based on antimitotic herbicides for protozoal parasites. New understanding from functional genomics, structural biology and microtubular imaging will help accelerate the development of completely novel antiparasitic drugs targeting microtubules.

Future novel threats and opportunities facing UK biodiversity identified by horizon scanning

1. Horizon scanning is an essential tool for environmental scientists if they are to contribute to the evidence base for Government, its agencies and other decision makers to devise and implement environmental policies. The implication of not foreseeing issues that are foreseeable is illustrated by the contentious responses to genetically modified herbicide-tolerant crops in the UK, and by challenges surrounding biofuels, foot and mouth disease, avian influenza and climate change.

Further evidence for visual landmark involvement in the pigeon's familiar area map

In previous experiments suggesting that previewing visual landscapes speeds homing from familiar release sites, restricted access to olfactory cues may have artefactually encouraged homing pigeons, Calumba livia, to resort to visual landmark orientation. Since evidence for the role of visual landmarks in wide-ranging avian orientation is still equivocal, Braithwaite & Guilford's (1991, Proc. R. Sec. Lond. Ser. B, 245, 183-186) 'previewing' experiments were replicated: birds were allowed or denied visual access to a familiar site prior to release, but allowed ample access to olfactory cues. In experiment 1, allowing birds to preview familiar sites for 5 min prior to release enhanced homing speeds by about 12%. In experiment 2, modified to reduce between-day effects on variation, previewing enhanced homing speeds by about 16%. These experiments support the conclusion that visual landmarks remote from sight of the loft are an important component of the familiar area map, although the nature of the landmarks and how they are encoded remain to be determined. (C) 1997 The Association for the Study of Animal Behaviour.

Biogeographical conditions, the transition to agriculture and long-run growth

We use new data on the timing of the transition to agriculture, developed by Putterman and Trainor (2006), to test the theory of Diamond (1997) and Olsson and Hibbs (2005) that an earlier transition is reflected in higher incomes today. Our results confirm the theory, even after controlling for institutional quality and other geographical factors. The date of transition is correlated with prehistoric biogeography (the availability of wild grasses and large domesticable animal species). The factors conducive to high per capita incomes today are good institutions, an early transition to agriculture, access to the sea and a low incidence of fatal malaria. Geographical influences have been at work in all of these proximate determinants of per capita income.

Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase

Plasmodium falciparum parasites are responsible for the major global disease malaria, which results in > 2 million deaths each year. With the rise of drug-resistant malarial parasites, novel drug targets and lead compounds are urgently required for the development of new therapeutic strategies. Here, we address this important problem by targeting the malarial neutral aminopeptidases that are involved in the terminal stages of hemoglobin digestion and essential for the provision of amino acids used for parasite growth and development within the erythrocyte. We characterize the structure and substrate specificity of one such aminopeptidase, PfA-M1, a validated drug target. The X-ray crystal structure of PfA-M1 alone and in complex with the generic inhibitor, bestatin, and a phosphinate dipeptide analogue with potent in vitro and in vivo antimalarial activity, hPheP[CH2] Phe, reveals features within the protease active site that are critical to its function as an aminopeptidase and can be exploited for drug development. These results set the groundwork for the development of antimalarial therapeutics that target the neutral aminopeptidases of the parasite.

Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases

Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the x-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here, we present the x-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with antimalarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centers in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA- M17 active sites now permits a rational approach in the development of a unique class of two-target and/or combination antimalarial therapy.

Metallo-aminopeptidase inhibitors

Aminopeptidases are enzymes that selectively hydrolyze an amino acid residue from the N-terminus of proteins and peptides. They are important for the proper functioning of prokaryotic and eukaryotic cells, but very often are central players in the devastating human diseases like cancer, malaria and diabetes. The largest aminopeptidase group include enzymes containing metal ion(s) in their active centers, which often determines the type of inhibitors that are the most suitable for them. Effective ligands mostly bind in a non-covalent mode by forming complexes with the metal ion(s). Here, we present several approaches for the design of inhibitors for metallo-aminopeptidases. The optimized structures should be considered as potential leads in the drug discovery process against endogenous and infectious diseases. Crown Copyright (C) 2010 Published by Elsevier Masson SAS. All rights reserved.

‘Invasional meltdown’: evidence for unexpected consequences and cumulative impacts of multispecies invasions

Empirical support for ‘invasional meltdown’, where the presence of one invading species facilitates another and compounds negative impacts on indigenous species, is equivocal with few convincing studies. In Ireland, the bank vole was introduced 80 years ago and now occupies a third of the island. The greater white-toothed shrew arrived more recently within the invasive range of the bank vole. We surveyed the abundance of both invasive species and two indigenous species, the wood mouse and pygmy shrew, throughout their respective ranges. The negative effects of invasive on indigenous species were strong and cumulative bringing about species replacement. The greater white-toothed shrew, the second invader, had a positive and synergistic effect on the abundance of the bank vole, the first invader, but a negative and compounding effect on the abundance of the wood mouse and occurrence of the pygmy shrew. The gradual replacement of the wood mouse by the bank vole decreased with distance from the point of the bank vole’s introduction whilst no pygmy shrews were captured where both invasive species were present. Such interactions may not be unique to invasions but characteristic of all multispecies communities. Small mammals are central in terrestrial food webs and compositional changes to this community in Ireland are likely to reverberate throughout the ecosystem. Vegetation composition and structure, invertebrate communities and the productivity of avian and mammalian predators are likely to be affected. Control of these invasive species may only be effected through landscape and habitat management.