Detecting evolutionarily significant units above the species level using the generalised mixed Yule coalescent method

1. There is renewed interest in inferring evolutionary history by modelling diversification rates using phylogenies. Understanding the performance of the methods used under different scenarios is essential for assessing empirical results. Recently, we introduced a new approach for analysing broadscale diversity patterns, using the generalised mixed Yule coalescent (GMYC) method to test for the existence of evolutionarily significant units above the species (higher ESUs). This approach focuses on identifying clades as well as estimating rates, and we refer to it as clade-dependent. However, the ability of the GMYC to detect the phylogenetic signature of higher ESUs has not been fully explored, nor has it been placed in the context of other, clade-independent approaches. 2. We simulated >32 000 trees under two clade-independent models: constant-rate birth-death (CRBD) and variable-rate birth-death (VRBD), using parameter estimates from nine empirical trees and more general parameter values. The simulated trees were used to evaluate scenarios under which GMYC might incorrectly detect the presence of higher ESUs. 3. The GMYC null model was rejected at a high rate on CRBD-simulated trees. This would lead to spurious inference of higher ESUs. However, the support for the GMYC model was significantly greater in most of the empirical clades than expected under a CRBD process. Simulations with empirically derived parameter values could therefore be used to exclude CRBD as an explanation for diversification patterns. In contrast, a VRBD process could not be ruled out as an alternative explanation for the apparent signature of hESUs in the empirical clades, based on the GMYC method alone. Other metrics of tree shape, however, differed notably between the empirical and VRBD-simulated trees. These metrics could be used in future to distinguish clade-dependent and clade-independent models. 4. In conclusion, detection of higher ESUs using the GMYC is robust against some clade-independent models, as long as simulations are used to evaluate these alternatives, but not against others. The differences between clade-dependent and clade-independent processes are biologically interesting, but most current models focus on the latter. We advocate more research into clade-dependent models for broad diversity patterns

Grey Literature and Professional Knowledge Making

International audienceWhat does grey literature mean? What role does it play in the production and dissemination of practitioner knowledge? How do reports, presentations and communications, working papers and other un-published material contribute to professional, extra-academic knowledge making? The following paper tries to provide some elements for a better understanding of grey literature, with examples from different collections and disciplines. Moreover, it puts the focus on critical issues like standards, identifiers and quality, and it discusses the impact of open science, i.e. the movement to make scientific research, data and dissemination accessible to all levels of an inquiring society, amateur or professional

Freeze-Drying of Mononuclear Cells Derived from Umbilical Cord Blood Followed by Colony Formation

BACKGROUND: We recently showed that freeze-dried cells stored for 3 years at room temperature can direct embryonic development following cloning. However, viability, as evaluated by membrane integrity of the cells after freeze-drying, was very low; and it was mainly the DNA integrity that was preserved. In the present study, we improved the cells' viability and functionality after freeze-drying. METHODOLOGY/PRINCIPAL FINDINGS: We optimized the conditions of directional freezing, i.e. interface velocity and cell concentration, and we added the antioxidant EGCG to the freezing solution. The study was performed on mononuclear cells (MNCs) derived from human umbilical cord blood. After freeze-drying, we tested the viability, number of CD34(+)-presenting cells and ability of the rehydrated hematopoietic stem cells to differentiate into different blood cells in culture. The viability of the MNCs after freeze-drying and rehydration with pure water was 88%-91%. The total number of CD34(+)-presenting cells and the number of colonies did not change significantly when evaluated before freezing, after freeze-thawing, and after freeze-drying (5.4 x 10(4)+/-4.7, 3.49 x 10(4)+/-6 and 6.31 x 10(4)+/-12.27 cells, respectively, and 31+/-25.15, 47+/-45.8 and 23.44+/-13.3 colonies, respectively). CONCLUSIONS: This is the first report of nucleated cells which have been dried and then rehydrated with double-distilled water remaining viable, and of hematopoietic stem cells retaining their ability to differentiate into different blood cells

A content analysis of thinspiration, fitspiration, and bonespiration imagery on social media

Background On social media, images such as thinspiration, fitspiration, and bonespiration, are shared to inspire certain body ideals. Previous research has demonstrated that exposure to these groups of content is associated with increased body dissatisfaction and decreased self-esteem. It is therefore important that the bodies featured within these groups of content are more fully understood so that effective interventions and preventative measures can be informed, developed, and implemented. Method A content analysis was conducted on a sample of body-focussed images with the hashtags thinspiration, fitspiration, and bonespiration from three social media platforms. Results The analyses showed that thinspiration and bonespiration content contained more thin and objectified bodies, compared to fitspiration which featured a greater prevalence of muscles and muscular bodies. In addition, bonespiration content contained more bone protrusions and fewer muscles than thinspiration content. Conclusions The findings suggest fitspiration may be a less unhealthy type of content; however, a subgroup of imagery was identified which idealised the extremely thin body type and as such this content should also be approached with caution. Future research should utilise qualitative methods to further develop understandings of the body ideals that are constructed within these groups of content and the motivations behind posting this content

Anhydrobiosis-Associated Nuclear DNA Damage and Repair in the Sleeping Chironomid: Linkage with Radioresistance

Anhydrobiotic chironomid larvae can withstand prolonged complete desiccation as well as other external stresses including ionizing radiation. To understand the cross-tolerance mechanism, we have analyzed the structural changes in the nuclear DNA using transmission electron microscopy and DNA comet assays in relation to anhydrobiosis and radiation. We found that dehydration causes alterations in chromatin structure and a severe fragmentation of nuclear DNA in the cells of the larvae despite successful anhydrobiosis. Furthermore, while the larvae had restored physiological activity within an hour following rehydration, nuclear DNA restoration typically took 72 to 96 h. The DNA fragmentation level and the recovery of DNA integrity in the rehydrated larvae after anhydrobiosis were similar to those of hydrated larvae irradiated with 70 Gy of high-linear energy transfer (LET) ions (4He). In contrast, low-LET radiation (gamma-rays) of the same dose caused less initial damage to the larvae, and DNA was completely repaired within within 24 h. The expression of genes encoding the DNA repair enzymes occurred upon entering anhydrobiosis and exposure to high- and low-LET radiations, indicative of DNA damage that includes double-strand breaks and their subsequent repair. The expression of antioxidant enzymes-coding genes was also elevated in the anhydrobiotic and the gamma-ray-irradiated larvae that probably functions to reduce the negative effect of reactive oxygen species upon exposure to these stresses. Indeed the mature antioxidant proteins accumulated in the dry larvae and the total activity of antioxidants increased by a 3–4 fold in association with anhydrobiosis. We conclude that one of the factors explaining the relationship between radioresistance and the ability to undergo anhydrobiosis in the sleeping chironomid could be an adaptation to desiccation-inflicted nuclear DNA damage. There were also similarities in the molecular response of the larvae to damage caused by desiccation and ionizing radiation

Potential therapeutic implications of new insights into respiratory syncytial virus disease

Viral bronchiolitis is the most common cause of hospitalization in infants under 6 months of age, and 70% of all cases of bronchiolitis are caused by respiratory syncytial virus (RSV). Early RSV infection is associated with respiratory problems such as asthma and wheezing later in life. RSV infection is usually spread by contaminated secretions and infects the upper then lower respiratory tracts. Infected cells release proinflammatory cytokines and chemokines, including IL-1, tumor necrosis factor-α, IL-6, and IL-8. These activate other cells and recruit inflammatory cells, including macrophages, neutrophils, eosinophils, and T lymphocytes, into the airway wall and surrounding tissues. The pattern of cytokine production by T lymphocytes can be biased toward 'T-helper-1' or 'T-helper-2' cytokines, depending on the local immunologic environment, infection history, and host genetics. T-helper-1 responses are generally efficient in antiviral defense, but young infants have an inherent bias toward T-helper-2 responses. The ideal intervention for RSV infection would be preventive, but the options are currently limited. Vaccines based on protein subunits, live attenuated strains of RSV, DNA vaccines, and synthetic peptides are being developed; passive antibody therapy is at present impractical in otherwise healthy children. Effective vaccines for use in neonates continue to be elusive but simply delaying infection beyond the first 6 months of life might reduce the delayed morbidity associated with infantile disease

Emissions generated by sugarcane burning promote genotoxicity in rural workers: a case study in Barretos, Brazil

Background: To determine the possible genotoxic effect of exposure to the smoke generated by biomass burning on workers involved in manual sugar cane harvesting. Methods: The frequency of micronuclei in exfoliated buccal cells and peripheral blood lymphocytes was determined in sugarcane workers in the Barretos region of Brazil, during the harvest season and compared to a control population, comprised of administrative employees of Barretos Cancer Hospital. Results: The frequency of micronuclei was higher in the sugar cane workers. The mean frequency in blood lymphocytes (micronuclei/1000 cells) in the test group was 8.22 versus 1.27 in the control group. The same effect was observed when exfoliated buccal cells were considered (22.75 and 9.70 micronuclei/1000 cells for sugar cane workers and controls, respectively). Conclusion: Exposure to emissions produced by the burning of sugar cane during harvesting induces genomic instability in workers, indicating the necessity of adopting more advanced techniques of harvesting sugar cane to preserve human health.We thank the Researcher Support Center of Barretos Cancer Hospital, especially the statistician Zanardo C. for assisting in the statistical analysis. We thank Oliveira R. for technical support, and we acknowledge financial support from FAPESP Proc. 2010/10192-6