Coalescent-based genome analyses resolve the early branches of the euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods

Expanding the phenotype in argininosuccinic aciduria: need for new therapies

OBJECTIVES: This UK-wide study defines the natural history of argininosuccinic aciduria and compares long-term neurological outcomes in patients presenting clinically or treated prospectively from birth with ammonia-lowering drugs. METHODS: Retrospective analysis of medical records prior to March 2013, then prospective analysis until December 2015. Blinded review of brain MRIs. ASL genotyping. RESULTS: Fifty-six patients were defined as early-onset (n = 23) if symptomatic < 28 days of age, late-onset (n = 23) if symptomatic later, or selectively screened perinatally due to a familial proband (n = 10). The median follow-up was 12.4 years (range 0-53). Long-term outcomes in all groups showed a similar neurological phenotype including developmental delay (48/52), epilepsy (24/52), ataxia (9/52), myopathy-like symptoms (6/52) and abnormal neuroimaging (12/21). Neuroimaging findings included parenchymal infarcts (4/21), focal white matter hyperintensity (4/21), cortical or cerebral atrophy (4/21), nodular heterotopia (2/21) and reduced creatine levels in white matter (4/4). 4/21 adult patients went to mainstream school without the need of additional educational support and 1/21 lives independently. Early-onset patients had more severe involvement of visceral organs including liver, kidney and gut. All early-onset and half of late-onset patients presented with hyperammonaemia. Screened patients had normal ammonia at birth and received treatment preventing severe hyperammonaemia. ASL was sequenced (n = 19) and 20 mutations were found. Plasma argininosuccinate was higher in early-onset compared to late-onset patients. CONCLUSIONS: Our study further defines the natural history of argininosuccinic aciduria and genotype-phenotype correlations. The neurological phenotype does not correlate with the severity of hyperammonaemia and plasma argininosuccinic acid levels. The disturbance in nitric oxide synthesis may be a contributor to the neurological disease. Clinical trials providing nitric oxide to the brain merit consideration

Emerging roles and competencies of district and sub-district pharmacists: a case study from Cape Town

District and sub-district pharmacist positions were created during health sector reform in South Africa. High prevalence of HIV/AIDS, tuberculosis and increasing chronic non-communicable diseases have drawn attention to their pivotal roles in improving accessibility and appropriate use of medicines at the primary level. This research describes new roles and related competencies of district and sub-district pharmacists in Cape Town. Between 2008 and 2011, the author (HB) conducted participatory action research in Cape Town Metro District, an urban district in the Western Cape Province of South Africa, partnering with pharmacists and managers of the two government primary health care (PHC) providers. The two providers function independently delivering complementary PHC services across the entire geographic area, with one provider employing district pharmacists and the other sub-district pharmacists. After an initiation phase, the research evolved into a series of iterative cycles of action and reflection, each providing increasing understanding of district and sub-district pharmacists’ roles and competencies. Data was generated through workshops, semi-structured interviews and focus groups with pharmacists and managers which were recorded and transcribed. Thematic analysis was carried out iteratively during the 4-year engagement and triangulated with document reviews and published literature. Five main roles for district and sub-district pharmacists were identified: district/sub-district management; planning, co-ordination and monitoring of pharmaceuticals; information and advice; quality assurance and clinical governance; and research (district pharmacists)/dispensing at clinics (sub-district pharmacists). Although the roles looked similar, there were important differences, reflecting the differing governance and leadership models and services of each provider. Five competency clusters were identified: professional pharmacy practice; health system and public health; management; leadership; and personal, interpersonal and cognitive competencies. Whilst professional pharmacy competencies were important, generic management and leadership competencies were considered critical for pharmacists working in these positions. Similar roles and competencies for district and sub-district pharmacists were identified in the two PHC providers in Cape Town, although contextual factors influenced precise specifications. These insights are important for pharmacists and managers from other districts and sub-districts in South Africa and inform health workforce planning and capacity development initiatives in countries with similar health systems.Web of Scienc

Use of Praziquantel as an Adjuvant Enhances Protection and Tc-17 Responses to Killed H5N1 Virus Vaccine in Mice

BACKGROUND: H5N1 is a highly pathogenic influenza A virus, which can cause severe illness or even death in humans. Although the widely used killed vaccines are able to provide some protection against infection via neutralizing antibodies, cytotoxic T-lymphocyte responses that are thought to eradicate viral infections are lacking. METHODOLOGY/PRINCIPAL FINDINGS: Aiming to promote cytotoxic responses against H5N1 infection, we extended our previous finding that praziquantel (PZQ) can act as an adjuvant to induce IL-17-producing CD8(+) T cells (Tc17). We found that a single immunization of 57BL/6 mice with killed viral vaccine plus PZQ induced antigen-specific Tc17 cells, some of which also secreted IFN-γ. The induced Tc17 had cytolytic activities. Induction of these cells was impaired in CD8 knockout (KO) or IFN-γ KO mice, and was even lower in IL-17 KO mice. Importantly, the inoculation of killed vaccine with PZQ significantly reduced virus loads in the lung tissues and prolonged survival. Protection against H5N1 virus infection was obtained by adoptively transferring PZQ-primed wild type CD8(+) T cells and this was more effective than transfer of activated IFN-γ KO or IL-17 KO CD8(+) T cells. CONCLUSIONS/SIGNIFICANCE: Our results demonstrated that adding PZQ to killed H5N1 vaccine could promote broad Tc17-mediated cytotoxic T lymphocyte activity, resulting in improved control of highly pathogenic avian influenza virus infection

Long-term durability of alumina ceramic heads in THA

Background: The optimal type of bearing for hip arthroplasty remains a matter of debate. Ceramic-on-polyethylene (CoP) bearings are frequently used in younger and more active patients to reduce wear and increase biocompatibility compared to Metal-on-Polyethylene (MoP) bearings. However, in comparison to metal heads, the fracture risk of ceramic heads is higher. In addition, ceramic head fractures pose a serious complication which often necessitates major revision surgery. To date, there are no long-term data (>20 years of follow-up) reporting fracture rates of the ceramic femoral heads in CoP bearings. The purpose of this research was to investigate long-term CoP fracture rate. Methods: We evaluated the clinical and radiographic results of 348 cementless THAs treated with 2nd generation Biolox® Al2O3 Ceramic-on-Polyethylene (CoP) bearings consecutively implanted between January 1985 and December 1989. The mean age at implantation was 57 years. The patients were followed for a minimum of 20 years. At the final 111 had died, and 5 were lost to follow-up. The cumulative incidence of ceramic head fractures in the long-term was estimated using a competing risk analysis. Results: The cumulative incidence of ceramic head fracture after 22-years was estimated with a competing risk analysis at 0.29% after 22-years (SE = 2.09%; 95% - CI: 0.03-1.5%). The radiographic analysis revealed no impending failures at final follow-up. Discussion/Conclusion: The fracture rate of second-generation ceramic heads using a CoP articulation remains very low into the third decade after cementless THA

MPA in Labor: Securing the Pearl Cays of Nicaragua

Implementation of Marine Protected Areas (MPAs) has always a step-zero, i.e., an initial phase when the idea is incepted, communicated and negotiated among stakeholders. What happens during this phase is likely to have an impact later on. If not done right, the management of the MPA may encounter problems at later stage that will be difficult to correct. Inspired by this working theory, this article describes the effort to establish the Pearl Cays off the Caribbean coast of Nicaragua as a protected area. This case-study illustrates the critical actions to be taken during step-zero, i.e., what needs to be considered and done before an MPA is formally declared. The area investigated consists of a number of small islands (cays) and coral reefs, fishing grounds and marine turtle nesting areas. Throughout history, the cays have played an important role in sustaining livelihoods of nearby communities. Although the idea of an MPA was originally conservation, the communities saw it as an opportunity to regain ownership and control of the cays. By Nicaraguan law, in order to establish protected areas, consultation and approval from local people is required. In the case of the Pearl Cays, this has proved difficult. The article demonstrates how MPA initiatives must sometimes relate to already ongoing complex social processes in the area where they are to be instigated

Heritagization of the Camino to Finisterre

This chapter focuses on one of the objectives of the Finisterre route research project: to compare the concept of heritage conveyed in regional and municipal heritage policies with that of other local actors. The ethnographic studies carried out in the villages and towns with pilgrim hostels show that there is a gap between the two concepts. This chapter deals with two aspects of the disparity. Firstly, some politicians construct a sophisticated discourse on heritage regarding the Camino de Santiago, which contrasts with the lack of a term to name ‘heritage’ at a local level. The second aspect is related to the concept of heritage itself. Politicians and heritage managers have a limited concept of heritage, and therefore they dedicate their heritage policies and funding to building restoration and maintenance of the route itself. On the other hand, the local residents’ idea of heritage is broader, and includes cultural practices such as festivals and religious celebrations as well as other elements of heritage that are more difficult to catalogue, such as ‘continuing to work the land,’ ‘the rural landscape,’ or ‘our local water supplies.’ In addition, this chapter analyses various levels of conflict around heritage and the Camino.Peer reviewe

Impaired Thymic Selection and Abnormal Antigen-Specific T Cell Responses in Foxn1Δ/Δ Mutant Mice

Foxn1(Δ/Δ) mutant mice have a specific defect in thymic development, characterized by a block in TEC differentiation at an intermediate progenitor stage, and blocks in thymocyte development at both the DN1 and DP cell stages, resulting in the production of abnormally functioning T cells that develop from an atypical progenitor population. In the current study, we tested the effects of these defects on thymic selection.We used Foxn1(Δ/Δ); DO11 Tg and Foxn1(Δ/Δ); OT1 Tg mice as positive selection and Foxn1(Δ/Δ); MHCII I-E mice as negative selection models. We also used an in vivo system of antigen-specific reactivity to test the function of peripheral T cells. Our data show that the capacity for positive and negative selection of both CD4 and CD8 SP thymocytes was reduced in Foxn1(Δ/Δ) mutants compared to Foxn1(+/Δ) control mice. These defects were associated with reduction of both MHC Class I and Class II expression, although the resulting peripheral T cells have a broad TCR Vβ repertoire. In this deficient thymic environment, immature CD4 and CD8 SP thymocytes emigrate from the thymus into the periphery. These T cells had an incompletely activated profile under stimulation of the TCR signal in vitro, and were either hypersensitive or hyporesponsive to antigen-specific stimulation in vivo. These cell-autonomous defects were compounded by the hypocellular peripheral environment caused by low thymic output.These data show that a primary defect in the thymic microenvironment can cause both direct defects in selection which can in turn cause indirect effects on the periphery, exacerbating functional defects in T cells

Application of a Mathematical Model to Describe the Effects of Chlorpyrifos on Caenorhabditis elegans Development

The nematode Caenorhabditis elegans is being assessed as an alternative model organism as part of an interagency effort to develop better means to test potentially toxic substances. As part of this effort, assays that use the COPAS Biosort flow sorting technology to record optical measurements (time of flight (TOF) and extinction (EXT)) of individual nematodes under various chemical exposure conditions are being developed. A mathematical model has been created that uses Biosort data to quantitatively and qualitatively describe C. elegans growth, and link changes in growth rates to biological events. Chlorpyrifos, an organophosphate pesticide known to cause developmental delays and malformations in mammals, was used as a model toxicant to test the applicability of the growth model for in vivo toxicological testing.L1 larval nematodes were exposed to a range of sub-lethal chlorpyrifos concentrations (0-75 microM) and measured every 12 h. In the absence of toxicant, C. elegans matured from L1s to gravid adults by 60 h. A mathematical model was used to estimate nematode size distributions at various times. Mathematical modeling of the distributions allowed the number of measured nematodes and log(EXT) and log(TOF) growth rates to be estimated. The model revealed three distinct growth phases. The points at which estimated growth rates changed (change points) were constant across the ten chlorpyrifos concentrations. Concentration response curves with respect to several model-estimated quantities (numbers of measured nematodes, mean log(TOF) and log(EXT), growth rates, and time to reach change points) showed a significant decrease in C. elegans growth with increasing chlorpyrifos concentration.Effects of chlorpyrifos on C. elegans growth and development were mathematically modeled. Statistical tests confirmed a significant concentration effect on several model endpoints. This confirmed that chlorpyrifos affects C. elegans development in a concentration dependent manner. The most noticeable effect on growth occurred during early larval stages: L2 and L3. This study supports the utility of the C. elegans growth assay and mathematical modeling in determining the effects of potentially toxic substances in an alternative model organism using high-throughput technologies