Authenticated DNA from Ancient Wood Remains

• Background The reconstruction of biological processes and human activities during the last glacial cycle relies mainly on data from biological remains. Highly abundant tissues, such as wood, are candidates for a genetic analysis of past populations. While well-authenticated DNA has now been recovered from various fossil remains, the final ‘proof' is still missing for wood, despite some promising studies. • Scope The goal of this study was to determine if ancient wood can be analysed routinely in studies of archaeology and palaeogenetics. An experiment was designed which included blind testing, independent replicates, extensive contamination controls and rigorous statistical tests. Ten samples of ancient wood from major European forest tree genera were analysed with plastid DNA markers. • Conclusions Authentic DNA was retrieved from wood samples up to 1000 years of age. A new tool for real-time vegetation history and archaeology is ready to us

Measurement and comparison of individual external doses of high-school students living in Japan, France, Poland and Belarus -- the "D-shuttle" project --

Twelve high schools in Japan (of which six are in Fukushima Prefecture), four in France, eight in Poland and two in Belarus cooperated in the measurement and comparison of individual external doses in 2014. In total 216 high-school students and teachers participated in the study. Each participant wore an electronic personal dosimeter "D-shuttle" for two weeks, and kept a journal of his/her whereabouts and activities. The distributions of annual external doses estimated for each region overlap with each other, demonstrating that the personal external individual doses in locations where residence is currently allowed in Fukushima Prefecture and in Belarus are well within the range of estimated annual doses due to the background radiation level of other regions/countries

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Rangewide phylogeography of a bird-dispersed Eurasian shrub : contrasting Mediterranean and temperate glacial refugia

We studied the phylogeography of alder buckthorn (Frangula alnus), a bird-dispersed shrub or small tree distributed over most of Europe and West Asia and present in three of the four main refugia of West Palaearctic temperate woody plants: the Iberian Peninsula, the Balkans and Anatolia. A total of 78 populations from 21 countries were analysed for chloroplast DNA variation using polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP), and 21 different haplotypes were distinguished. We found a very strong overall population differentiation (GST = 0.81) and phylogeographical struc- ture, and a sharp contrast between the haplotype-rich refugia and the almost completely uniform area of postglacial colonization. The haplotype network comprises three lineages made up of haplotypes from the Iberian Peninsula, Anatolia with the Caucasus, and tem- perate Europe. The Iberian and the Anatolian branches represent parts of a major lineage that spans over the whole northern Mediterranean Basin and some neighbouring areas and probably dates back to the Tertiary. Many haplotypes of this lineage are distributed locally and most populations are fixed for a single haplotype; these populations have apparently been very stable since their establishment, experiencing negligible gene flow and few mutations. The temperate European lineage consists of one very widespread and abundant plus six locally distributed haplotypes. Four of them are located in Southeast Europe, the putative refugium of all extant temperate European populations. Contrary to populations from Iberia and Anatolia, F. alnus populations from the southeastern European refugium have most genetic variation within populations. Bird-mediated seed dispersal has apparently allowed not only a very rapid postglacial expansion of F. alnus but also subsequent regular seed exchanges between populations of the largely continuous species range in temperate Europe. In contrast, the disjunct F. alnus populations persisting in Mediterranean mountain ranges seem to have experienced little gene flow and have therefore accumulated a high degree of differentiation, even at short distances. Populations from the southern parts of the glacial refugia have contributed little to the postglacial recolonization of Europe, but their long- term historical continuity has allowed them to maintain a unique store of genetic variationPeer reviewe

Data from: Detecting the footprints of divergent selection in oaks with linked markers

Genome scans are increasingly used to study ecological speciation, providing a useful genome-wide perspective on divergent selection in the presence of gene flow. Here, we compare current approaches to detect footprints of divergent selection in closely related species. We analyzed 192 individuals from two interfertile European temperate oak species using 30 genomic microsatellites from eight linkage groups. These markers present little intraspecific differentiation and can be used in combination to assign individual genotypes to species. We first show that different outlier detection tests give somewhat different results, possibly due to model constraints. Second, using linkage information for these markers, we further characterize the signature of divergent selection in the presence of gene flow. In particular, we show that recombination estimates for regions with outlier markers are lower than those for a control region, in line with a prediction from ecological speciation theory. Most importantly, we show that analyses at the haplotype level can distinguish between truly divergent (bi-directional) selection and positive selection in one of the two species, offering a new and improved method for characterizing the speciation process

Invoking adaptation to decipher the genetic legacy of past climate change

Persistence of natural populations during periods of climate change is likely to depend on migration (range shifts) or adaptation. These responses were traditionally considered discrete processes and conceptually divided into the realms of ecology and evolution. In a milestone paper, Davis and Shaw (2001) Science 292:673 argued that the interplay of adaptation and migration was central to biotic responses to Quaternary climate, but since then there has been no synthesis of efforts made to set up this research program. Here we review some of the salient findings from molecular genetic studies assessing ecological and evolutionary responses to Quaternary climate change. These studies have revolutionized our understanding of population processes associated with past species migration. However, knowledge remains limited about the role of natural selection for local adaptation of populations to Quaternary environmental fluctuations and associated range shifts, and for the footprints this might have left on extant populations. Next‐generation sequencing technologies, high‐resolution paleoclimate analyses, and advances in population genetic theory offer an unprecedented opportunity to test hypotheses about adaptation through time. Recent population genomics studies have greatly improved our understanding of the role of contemporary adaptation to local environments in shaping spatial patterns of genetic diversity across modern‐day landscapes. Advances in this burgeoning field provide important conceptual and methodological bases to decipher the historical role of natural selection and assess adaptation to past environmental variation. We suggest that a process called “temporal conditional neutrality” has taken place: some alleles favored in glacial environments become selectively neutral in modern‐day conditions, whereas some alleles that had been neutral during glacial periods become under selection in modern environments. Building on this view, we present a new integrative framework for addressing the interplay of demographic and adaptive evolutionary responses to Quaternary climate dynamics, the research agenda initially envisioned by Davis and Shaw (2001) Science 292:673

Survival of bioaerosols in HVAC system photocatalytic filters

AIR+SPI:SPE:CGU:FSIInternational audienceThe survival of an experimental bioaerosol in photocatalytic and non-photocatalytic filters was investigated under UV-A or UV-C radiation exposure. To ensure the generation of reproducible bioaerosols in real operating conditions of Heating, Ventilation and Air Conditioning (HVAC) systems and their homogeneous coating on filters, a reactor with an optimal geometry was developed. The bacterial aerosol was generated from standardised bacterial suspensions and the Gram-negative bacterial model Escherichia coli was used as the experimental organism. The bioaerosol was characterised in terms of particle size distribution, reproducibility and stability over time. The coating of aerosolised cells on the filters was then studied. The total number of aerosolised E. coli cells was different from the amount of cultivable bacterial cells extracted from filters, probably resulting from the stress of the aerosolisation process. Damages to the outer membrane of E. coli cells were clearly observed through SEM and epifluorescent microscopy analysis. The influence of important physical parameters in the reactor-aerosolisation duration, frontal velocity and relative humidity- on the amount of aerosolised cells coated on filters were also investigated. Finally, the effects of UV-A or UV-C radiation were assessed on aerosolised microorganisms coated on HEPA photocatalytic filters and on photocatalytic or non-photocatalytic filters containing activated charcoal. The HEPA photocatalytic filters demonstrated a better disinfection efficiency with full damages of the aerosolised bacterial cells, probably resulting from an optimal contact between TiO2 coating and the microorganisms. In contrast, the use of filters with activated charcoal resulted in the apparition of an inactivation threshold that could be attributed to the penetration of aerosolised cells within the activated charcoal layer and the absence of contact with the photocatalyst. However, UV-C photocatalysis was able to inactivate faster and, at the same time, mineralise biological pollutants than UV-A. (C) 2013 Elsevier B.V. All rights reserved

Efficiency of (photo)catalytic filters to remove bioaerosols : application to HVAC system

International @ EAU+CGU:FSIInternational audienceIndoor air quality has become a major public health concern and it potentially poses a threat to the health of all types of populations. Actually, populations in developed countries spend more than 80 % of their time in confined indoor environments. Indoor air pollutants emanate from various sources, chemical or biological. Most of the studies deal with the removal of chemical sources but biological treatment of indoor air remains an emerging research theme. Indeed, the removal of biological agents is a complex issue. None of the traditional technologies for indoor air decontamination, such as activated charcoal filters, HEPA filters with or without UV radiation, ozonation, air ionization, are completely effective. Moreover, these technologies still need further investigation. The aim is not only to trap the microorganisms present in the indoor air, but also to alter them irreversibly. In this context, the combination, within air treatment plants, of both the photocatalytic and the filtering process is a promising technology that would combine the benefits of both processes to efficiently trap and alter chemical and microbiological pollutants through total mineralisation. Our researches deals with the effects of UV-A and UV-C radiation on the coating of aerosolised cells of fungal spores before and after their germination but also on an experimental bioaerosol of bacteria in presence of photocatalytic and non-photocatalytic air filters commonly used in Heating, Ventilating, and Air Conditioning (HVAC) systems. E.coli and Aspergillus Niger are used as model of bacteria and fungi because E.coli is commonly used to evaluate indoor air cleaning technologies and A.Niger is known for its resistance to any environmental stress conditions, and especially the spores which contain a black fungal spore pigment, protecting them from UV radiation exposure. In presence of E.coli or A.Niger the photocatalytic filters without charcoal demonstrated better disinfection efficiency with full damages of the cells, probably resulting from an optimal contact between TiO2 coating and the microorganisms. In contrast, the use of filters with activated charcoal, even with UV-C, resulted in the apparition of an inactivation threshold that could be attributed to the penetration of cells within the activated charcoal layer and the absence of contact with the photocatalyst. However, UV-C photocatalysis was able to inactivate faster and, at the same time, mineralise biological pollutants than UV-A. In the case of A.Niger, the effects of UV radiation were also assessed on spore germination for both types of filters. The inactivation of spores in illuminated photocatalytic filters resulted in an irreversible inhibition of the fungal germination under UV-A or UV-C radiation. In contrast, fungal spores were able to germinate in non-photocatalytic filters despite previous exposure to both types of UV radiation. After spore germination disinfection efficiency is lower than experiments whereby spores had just been applied onto the filters, due to the absence of contact between the biological pollutants and the photocatalyst coating. Our results demonstrated the interest to use photocatalytic filters ensuring optimal contact between pollutants and TiO2 coating to lead to a total inactivation of fungal spores in filters of HVAC systems