Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene.

Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.

Demography, genetics, and decline of a spatially structured population of lekking bird.

Understanding the mechanisms underlying population decline is a critical challenge for conservation biologists. Both deterministic (e.g. habitat loss, fragmentation, and Allee effect) and stochastic (i.e. demographic and environmental stochasticity) demographic processes are involved in population decline. Simultaneously, a decrease of population size has far-reaching consequences for genetics of populations by increasing the risk of inbreeding and the strength of genetic drift, which together inevitably results in a loss of genetic diversity and a reduced effective population size ([Formula: see text]). These genetic factors may retroactively affect vital rates (a phenomenon coined 'inbreeding depression'), reduce population growth, and accelerate demographic decline. To date, most studies that have examined the demographic and genetic processes driving the decline of wild populations have neglected their spatial structure. In this study, we examined demographic and genetic factors involved in the decline of a spatially structured population of a lekking bird, the western capercaillie (Tetrao urogallus). To address this issue, we collected capture-recapture and genetic data over a 6-years period in the Vosges Mountains (France). Our study showed that the population of T. urogallus experienced a severe decline between 2010 and 2015. We did not detect any Allee effect on survival and recruitment. By contrast, individuals of both sexes dispersed to avoid small subpopulations, thus suggesting a potential behavioral response to a mate finding Allee effect. In parallel to this demographic decline, the population showed low levels of genetic diversity, high inbreeding and low effective population sizes at both subpopulation and population levels. Despite this, we did not detect evidence of inbreeding depression: neither adult survival nor recruitment were affected by individual inbreeding level. Our study underlines the benefit from combining demographic and genetic approaches to investigate processes that are involved in population decline.

Kin-dependent dispersal influences relatedness and genetic structuring in a lek system.

Kin selection and dispersal play a critical role in the evolution of cooperative breeding systems. Limited dispersal increases relatedness in spatially structured populations (population viscosity), with the result that neighbours tend to be genealogical relatives. Yet the increase in neighbours' fitness-related performance through altruistic interaction may also result in habitat saturation and thus exacerbate local competition between kin. Our goal was to detect the footprint of kin selection and competition by examining the spatial structure of relatedness and by comparing non-effective and effective dispersal in a population of a lekking bird, Tetrao urogallus. For this purpose, we analysed capture-recapture and genetic data collected over a 6-year period on a spatially structured population of T. urogallus in France. Our findings revealed a strong spatial structure of relatedness in males. They also indicated that the population viscosity could allow male cooperation through two non-exclusive mechanisms. First, at their first lek attendance, males aggregate in a lek composed of relatives. Second, the distance corresponding to non-effective dispersal dramatically outweighed effective dispersal distance, which suggests that dispersers incur high post-settlement costs. These two mechanisms result in strong population genetic structuring in males. In females, our findings revealed a lower level of spatial structure of relatedness and genetic structure in respect to males. Additionally, non-effective dispersal and effective dispersal distances in females were highly similar, which suggests limited post-settlement costs. These results indicate that kin-dependent dispersal decisions and costs have a genetic footprint in wild populations and are factors that may be involved in the evolution of cooperative courtship.

IAP Antagonists Enhance Apoptotic Response to Enzalutamide in Castration-Resistant Prostate Cancer Cells via Autocrine TNF-α Signaling.

BACKGROUND: Castration-resistant prostate cancer (CRPC) remains incurable and identifying effective treatments continues to present a clinical challenge. Although treatment with enzalutamide, a second generation androgen receptor (AR) antagonist, prolongs survival in prostate cancer patients, responses can be limited by intrinsic resistance or acquired resistance. A potential mechanism of resistance to androgen axis inhibition is evasion of apoptosis. Inhibitor of apoptosis proteins (IAPs) are found to be overexpressed in prostate cancer and function to block apoptosis and promote survival signaling. Novel, small-molecule IAP antagonists, such as AEG40995, are emerging as a strategy to induce apoptosis and increase therapeutic response in cancer. METHODS: Human prostate cancer cell lines LNCaP and C4-2 were treated with enzalutamide with or without addition of IAP antagonist AEG40995 and proliferation and survival were determined by MTS and clonogenic assay. Western blot was used to evaluate IAP protein expression changes and PARP-1 cleavage was assessed as indication of apoptosis. Flow cytometry was performed to analyze apoptosis in treated cells. Caspase activity was determined by luminescence assay. Quantitative real-time PCR and immunometric ELISA was used to assess TNF-α (transcript and protein levels, respectively) in response to treatment. RESULTS: In this study, we demonstrate that IAP antagonist AEG40995 exhibits minimal effects on prostate cancer cell proliferation or survival, but rapidly degrades cIAP1 protein. Combination treatment with enzalutamide demonstrates that AEG40995 increases apoptosis and reduces proliferation and clonogenic survival in cell line models of prostate cancer. Mechanistically, we demonstrate that apoptosis in response to enzalutamide and IAP antagonist requires activation of caspase-8, suggesting extrinsic/death receptor apoptosis signaling. Assessment of TNF-α in response to combination treatment with enzalutamide and AEG40995 reveals increased mRNA expression and autocrine protein secretion. Blocking TNF-α signaling abrogates the apoptotic response demonstrating that TNF-α plays a critical role in executing cell death in response to this drug combination. CONCLUSIONS: These findings suggest that IAP antagonists can increase sensitivity and amplify the caspase-mediated apoptotic response to enzalutamide through TNF-α signaling mechanisms. Combination with an IAP antagonist increases enzalutamide sensitivity, lowers the apoptotic threshold and may combat drug resistance in patients with prostate cancer. Prostate 77:866-877, 2017. © 2017 Wiley Periodicals, Inc.

Love wave immunosensor for the detection of carbaryl pesticide.

A Love Wave (LW) immunosensor was developed for the detection of carbaryl pesticide. The experimental setup consisted on: a compact electronic characterization circuit based on phase and amplitude detection at constant frequency; an automated flow injection system; a thermal control unit; a custom-made flow-through cell; and Quartz /SiO2 LW sensors with a 40 µm wavelength and 120 MHz center frequency. The carbaryl detection was based on a competitive immunoassay format using LIB-CNH45 monoclonal antibody (MAb). Bovine Serum Albumin-CNH (BSA-CNH) carbaryl hapten-conjugate was covalently immobilized, via mercaptohexadecanoic acid self-assembled monolayer (SAM), onto the gold sensing area of the LW sensors. This immobilization allowed the reusability of the sensor for at least 70 assays without significant signal losses. The LW immunosensor showed a limit of detection (LOD) of 0.09 µg/L, a sensitivity of 0.31 µg/L and a linear working range of 0.14-1.63 µg/L. In comparison to other carbaryl immunosensors, the LW immunosensor achieved a high sensitivity and a low LOD. These features turn the LW immunosensor into a promising tool for applications that demand a high resolution, such as for the detection of pesticides in drinking water at European regulatory levels.

863 genomes reveal the origin and domestication of chicken.

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Author Correction: 863 genomes reveal the origin and domestication of chicken.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Spatial density estimates of Eurasian lynx (Lynx lynx) in the French Jura and Vosges Mountains.

Obtaining estimates of animal population density is a key step in providing sound conservation and management strategies for wildlife. For many large carnivores however, estimating density is difficult because these species are elusive and wide-ranging. Here, we focus on providing the first density estimates of the Eurasian lynx (Lynx lynx) in the French Jura and Vosges mountains. We sampled a total of 413 camera trapping sites (with two cameras per site) between January 2011 and April 2016 in seven study areas across seven counties of the French Jura and Vosges mountains. We obtained 592 lynx detections over 19,035 trap days in the Jura mountains and 0 detection over 6,804 trap days in the Vosges mountains. Based on coat patterns, we identified a total number of 92 unique individuals from photographs, including 16 females, 13 males, and 63 individuals of unknown sex. Using spatial capture-recapture (SCR) models, we estimated abundance in the study areas between 5 (SE = 0.1) and 29 (0.2) lynx and density between 0.24 (SE = 0.02) and 0.91 (SE = 0.03) lynx per 100 km2. We also provide a comparison with nonspatial density estimates and discuss the observed discrepancies. Our study is yet another example of the advantage of combining SCR methods and noninvasive sampling techniques to estimate density for elusive and wide-ranging species, like large carnivores. While the estimated densities in the French Jura mountains are comparable to other lynx populations in Europe, the fact that we detected no lynx in the Vosges mountains is alarming. Connectivity should be encouraged between the French Jura mountains, the Vosges mountains, and the Palatinate Forest in Germany where a reintroduction program is currently ongoing. Our density estimates will help in setting a baseline conservation status for the lynx population in France.

Cost-effectiveness of bone-anchored prostheses using osseointegrated fixation: Myth or reality?

BACKGROUND: In principle, lower limb bone-anchored prostheses could alleviate expenditure associated with typical socket manufacturing and residuum treatments due to socket-suspended prostheses. OBJECTIVE: This study reports (a) the incremental costs and (b) heath gain as well as (c) cost-effectiveness of bone-anchored prostheses compared to socket-suspended prostheses. STUDY DESIGN: Retrospective individual case-controlled observations and systematic review. METHODS: Actual costs were extracted from financial records and completed by typical costs when needed over 6-year time horizon for a cohort of 16 individuals. Health gains corresponding to quality-adjusted life-year were calculated using health-related quality-of-life data presented in the literature. RESULTS: The provision of bone-anchored prostheses costed 21% ± 41% more but increased quality-adjusted life-years by 17% ± 5% compared to socket-suspended prostheses. The incremental cost-effectiveness ratio ranged between -$25,700 per quality-adjusted life-year and $53,500 per quality-adjusted life-year with indicative incremental cost-effectiveness ratio of approximately $17,000 per quality-adjusted life-year. Bone-anchored prosthesis was cost-saving and cost-effective for 19% and 88% of the participants, respectively. CONCLUSION: This study indicated that bone-anchored prostheses might be an acceptable alternative to socket-suspended prostheses at least from a prosthetic care perspective in Australian context. Altogether, this initial evidence-based economic evaluation provided a working approach for decision makers responsible for policies around care of individuals with lower limb amputation worldwide. Clinical relevance For the first time, this study provided evidence-based health economic benefits of lower limb bone-anchored prostheses compared to typical socket-suspended prostheses from a prosthetic care perspective that is essential to clinicians and decision makers responsible for policies.

Suspension-cultured BY-2 tobacco cells produce and mature immunologically active house dust mite allergens.

The replacement of crude allergen extracts by selected allergens currently represents a major goal for the improvement of allergy diagnosis and immunotherapy. Indeed, the development of molecularly defined vaccines would facilitate both standardization and enhance batch-to-batch reproducibility as well as treatment specificity. In this study, we have investigated the potential of tobacco plant cells to produce biologically active forms of the two major allergens from the house dust mite. A detailed characterization of these plant-made allergens has shown similar proteolytic maturation and folding as well as comparable immunoreactivity to their natural counterparts. Altogether, our results exemplify that suspension-cultured BY-2 tobacco cells represent a low cost and environmentally safe expression system suitable to produce recombinant allergens from Dermatophagoides pteronyssinus under a form appropriate for diagnostic and therapeutic purposes.

Clip-phen conjugates for the specific cleavage of nucleic acids.

For the first time Clip-Phen (1) was conjugated to oligonucleotides to provide very efficient tools for the cleavage of nucleic acids at specific positions. The synthesis of the conjugates as well as the cleavage experiments are reported.

Static load bearing exercises of individuals with transfemoral amputation fitted with an osseointegrated implant: Loading compliance.

BACKGROUND: Load-bearing exercises are performed by transfemoral amputees fitted with an osseointegrated implant to facilitate bone remodelling. OBJECTIVE: This study presents the loading compliance comparing loads prescribed and applied on the three axes of the implant during static load-bearing exercises with a specific emphasis on axial and vectorial comparisons. STUDY DESIGN: Cohort study. METHODS: A total of 11 fully rehabilitated unilateral transfemoral amputees fitted with an osseointegrated implant performed five trials in four loading conditions using a static standing frame. The load prescribed was monitored using a vertical single-axis strain gauge connected to an electronic display. The tri-axial forces applied on the implant were measured directly with an instrumented pylon including a six-channel transducer. The analysis included 'axial' and 'vectorial' comparisons corresponding to the difference between the force applied on the long axis of the implant and the load prescribed as well as the resultant of the three components of the load applied and the load prescribed, respectively. RESULTS: The results demonstrated that axial and vectorial differences were significant in all conditions ( p < 0.05), except for the vectorial difference for the 40 kg condition ( p = 0.182). CONCLUSION: The significant lack of axial compliance led to systematic underloading of the long axis of the implant. Clinical relevance This study contributes to a better understanding of the load applied on an osseointegrated implant during the static load-bearing exercises that could contribute to improve the design of apparatus to monitor loading exercises as well as clinical guidelines for the loading progression during rehabilitation.

Load on osseointegrated fixation of a transfemoral amputee during a fall: Determination of the time and duration of descent.

Mitigation of fall-related injuries for populations of transfemoral amputees fitted with a socket or an osseointegrated fixation is challenging. Wearing a protective device fitted within the prosthesis might be a possible solution, provided that issues with automated fall detection and time of deployment of the protective mechanism are solved. The first objective of this study was to give some examples of the times and durations of descent during a real forward fall of a transfemoral amputee that occurred inadvertently while attending a gait measurement session to assess the load applied on the residuum. The second objective was to present five semi-automated methods of detection of the time of descent using the load data. The load was measured directly at 200 Hz using a six-channel transducer. The average time and duration of descent were 242 ±â€Š42 ms (145-310 ms) and 619 ±â€Š42 ms (550-715 ms), respectively. This study demonstrated that the transition between walking and falling was characterized by times of descent that occurred sequentially. The sensitivity and specificity of an automated algorithm might be improved by combining several methods of detection based on the deviation of the loads measured from their own trends and from a template previously established.

Load on osseointegrated fixation of a transfemoral amputee during a fall: loading, descent, impact and recovery analysis.

Falling represents a health risk for lower limb amputees fitted with an osseointegrated fixation mainly because of the potential damage to the fixation. The purpose of this study was to characterize a real forward fall that occurred inadvertently to a transfemoral amputee fitted with an osseointegrated fixation while attending a gait measurement session to assess the load applied on the residuum. The objective was to analyze the load applied on the fixation with an emphasis on the sequence of events, the pattern and the magnitude of the forces and moments. The load was measured directly at 200 Hz using a six-channel transducer. Complementary video footage was also studied. The fall was divided into four phases: Loading (240 ms), descent (620 ms), impact (365 ms) and recovery (2495 ms). The main impact forces and moments occurred 870 ms and 915 ms after the heel contact, and corresponded to 133% BW and 17 % BWm, or 1.2 and 11.2 times the maximum forces and moments applied during the previous steps of the participant, respectively. This study provided key information to engineers and clinicians facing the challenge to design equipment, and rehabilitation and exercise programs to restore safely the locomotion of lower limb amputees.

New substituted aryldiazomethyl labels for high density DNA chip-based nucleic acid testing.

DNA and RNA labeling and detection are key steps in nucleic acid testing, particularly for molecular diagnostics applications. Here, we report a new class of aryldiazomethyl labels that include in their structure a biotin moiety as a detectable unit and a nitro substituted phenyl diazomethyl as a reactive group. The greatest reactivity towards phosphates of nucleic acids, the water solubility and the stability of these new molecules were demonstrated. These very important properties, which are the main requirements for nucleic acid labeling in aqueous conditions using automated protocols within integrated diagnostic devices, make them the perfect labeling tools for hybridization-based analysis, especially for high-density DNA chips.

Polymer-oligonucleotide conjugate synthesis from an amphiphilic block copolymer. Applications to DNA detection on microarray.

An amphiphilic block copolymer poly(tert-butylacrylamide-b-(N-acryloylmorpholine-N-acryloxysuccinimide)) (poly(TBAm-b-(NAM/NAS)) and a random copolymer poly(NAM/NAS), synthesized by the reversible addition-fragmentation chain transfer (RAFT) polymerization process, have been used as support for oligonucleotide (ODN) synthesis, to elaborate polymer-oligonucleotide conjugates. In a first step, starters of ODN solid-phase synthesis were coupled to activated ester functions of polymers, and second, resulting functionalized polymers were covalently grafted onto hydroxylated controlled pore glass (CPG) support to further accomplish ODN synthesis. An efficient capping of residual hydroxyl functions of CPG was performed before synthesis, with both acetic anhydride and diethoxy-N,N-diisopropyl-phosphoramidite reagents, to suppress parasite-free ODN population present in conjugate crude material and resulting from syntheses directly initiated on silica beads. After purification, conjugates were evaluated in a DNA hybridization assay on a microarray, as macromolecules being able to favor capture of the target. Conjugate coating conditions were studied on the dT25/dA25 model. The role of the hydrophobic part (poly(TBAm)) of the conjugate synthesized with the block copolymer in the orientation of the conjugate after coating was revealed by spotting experiments achieved in a mixed solvent (DMF/H(2)O). The use of block copolymer-dT25 conjugate afforded a significant sensitivity improvement of the hybridization assay.