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Leveraging Comparative Phylogenetics for Evolutionary Medicine: Applications to Comparative Oncology
No full textInternational audienceAbstract Comparative phylogenetics provides a wealth of computational tools to understand evolutionary processes and their outcomes. Advances in these methodologies have occurred in parallel with a surge in cross-species genomic and phenotypic data. To date, however, the majority of published studies have focused on classical questions in evolutionary biology, such as speciation and the ecological drivers of trait evolution. Here, we argue that evolutionary medicine in general, and our understanding of the origin and diversification of disease traits in particular, would be greatly expanded by a wider integration of phylogenetic comparative methods (PCMs). We use comparative oncology – the study of cancer across the tree of life – as a case study to demonstrate the power of the approach and show that implementing PCMs can highlight the mode and tempo of the evolutionary changes in intrinsic, species-level disease vulnerabilities
Linguistique coréenne et japonaise : dynamiques contrastives. Introduction
No full textInternational audienceThe Korean and Japanese languages, although typologically, geographically, and culturally close, are still too rarely contrasted or compared. This volume aims to help fill this gap. To that end, it brings together seventeen articles that reflect the current state of Francophone research on issues of contrastive or comparative linguistics based on one of these two languages; that address broader linguistic questions from Korean or Japanese perspectives; or that provide an in-depth analysis of specific linguistic features in one of the two languages. The volume includes works by linguists from diverse theoretical backgrounds, research domains, and generations. As the title of this collection indicates, the target languages are Korean and Japanese, but the contributions are not limited to these two: readers will also find articles that draw on Chinese, Spanish, English, and, of course, French, as well as another Japonic variety—the Hachijō language.Les langues coréenne et japonaise, bien que typologiquement, géographiquement, et culturellement proches sont encore trop rarement contrastées ou comparées. Ce volume souhaite contribuer à combler cette lacune. A cet effet, il rassemble 17 articles qui reflètent l’état de la recherche francophone actuelle sur des questions delinguistique contrastive ou comparative à partir de l’une de ces deux langues, qui abordent des questions linguistiques plus générales à partir des perspectives coréenne ou japonaise, ou bien, enfin, qui traitent en profondeur tel ou tel point de linguistique de l’une des deux langues. On y lira des travaux de linguistes de tous horizons théoriques, de tous domaines, et de toutes générations. Comme le titre du présent volume l’indique, les langues cibles sont le coréen et le japonais, mais les contributions ne se limitent pas à ces dernières, puisqu’on trouvera des articles qui convoquent le chinois, l’espagnol, l’anglais, en plus, bien évidemment, du français, ainsi qu’une autre variété japonique, la langue de Hachijō
Long–term sedimentary earthquake records along the northern branch of the North Anatolian Fault in the Sea of Marmara (NW Türkiye)
No full textInternational audienceGeological earthquake records are important for probabilistic seismic risk assessment. Such records can be obtained from studies of turbidites triggered by seismic activity in marine and lake basins. The Sea of Marmara (SoM), located on the North Anatolian Fault (NAF), serves as an important laboratory for subaqueous palaeoseismological research. This is because it has 2500 yrs. of historical earthquake records that can be correlated with radiometrically dated sedimentary earthquake records. Additionally, the relatively high sedimentation rate (∼3 mm/yr) in the deep subbasins allows the recognition of individual events. Following the destructive 1912 Mw 7.4 Şarköy–Mürefte and 1999 Mw 7.4 Izmit and Mw 7.2 Düzce earthquakes, the main submerged part of the NAF in the SoM represents a seismic gap, where the long–term earthquake history is of crucial importance for earthquake risk assessment.We have studied nine cores recovered along the most active northern strand of the NAF (i.e. the Main Marmara Fault: MMF), using high resolution digital X–ray radiography, μ–XRF core scanning, MSCL physical properties and grain–size analyses. The chronology was determined using accelerated mass spectrometry (AMS) radiocarbon and radionuclide methods. In the cores, coseismic turbidites commonly consist of a basal part with multiple sand–silt laminae above a sharp and often erosional base and an overlying graded mud part (homogenite). The basal parts exhibit high gamma density and MS, and are often enriched in one or more elements, such as Si, K, Fe, Ti, Zr, Ca and Sr, indicative of coarse siliciclastic and carbonate shell fragments.Radionuclide- and radiocarbon-dated coseismic turbidites in different SoM subbasins extending back to more than 5000 yrs. indicate an average earthquake recurrence time between 220 and 300 yrs. along the different segments of the MMF. These results are compatible with the GPS velocities and geological slip rates. However, the intervals between two consecutive events vary widely between 50 and 695 yrs. for the different northern NAF segments.Integration of our results with previous studies indicates that the M > 7 events recorded are the 1999, 1509, 1296 and 740 earthquakes on the İzmit Gulf segment; the 1894, 1509, 1343, 1090 and 740 earthquakes on the Prince Islands segment in the Çınarcık Basin; the 1894, 1766, 1509, 989, 869 or 862, 740 and 447 earthquakes on the Central High segment and in the Central Basin; and the 1912, 1766, 1344, 989 and 447 earthquakes on the western Marmara segment. The 1912 Şarköy–Mürefte earthquake record is absent in the Central Basin, which suggests that the earthquake rupture did not extend beyond the western end of the Western High. The distribution of the 2500 yr-long sedimentary earthquake records matched with the historical earthquakes along the MMF indicates the common occurrence of multiple-segment ruptures, and suggests that presently, the most earthquake–prone part of the MMF is the Central High segment, located SW of Istanbul
Potagers urbains et amendements: Gestion et challenges environnementaux et sanitaires
No full textInternational audienceL’étude visait à évaluer l’intérêt d’amendements organiques et minéraux pour gérer des sols de potagers urbains présentant des contaminations géogènes et/ou anthropiques. Il s’agissait plus spécifiquement d’évaluer le potentiel de ces amendements pour réduire de façon durable la phytodisponibilité des éléments en trace ainsi que l’exposition des jardiniers et de leur famille via l’ingestion de particules de terre ou de légumes autoproduits et les risques sanitaires associés. Pour déterminer l’intérêt global de l’utilisation des 10 amendements testés, leur impact a été évalué sur des aspects environnementaux, agronomiques et d’exposition humaine. L’étude, réalisée sur trois jardins urbains, a montré que chaque situation est unique et qu’une étude spécifique, de l’expérimentation en pots jusqu’au sol en place, est nécessaire afin de sélectionner un amendement adéquat au contexte pédo-géo-climatique du jardin. Cette démarche a été plutôt concluante avec l’apport de compost pour le site présentant principalement une contamination en As et Pb d’origine géogène, mais reste toutefois limitée car n’entraînant pas de réel bénéfice quant à la réduction des expositions et des risques sanitaires pour le jardinier. La démarche d’apporter un ou des amendements sur un site n’est pas opérationnelle pour l’instant et lorsqu’elle est mise en oeuvre, elle doit être réfléchie au cas par cas et selon un programme de surveillance de la qualité des végétaux sur plusieurs années
Opening Pandora's box in Workshop "IEA EBC Annex 86: a Rating Ecology for IAQ Management in Residential Buildings"
No full textInternational audienc
From cities to vineyards: sex-specific phenotypic differences between habitats in a generalist bird species, the great tit (Parus major)
No full textInternational audienceIn vertebrates, habitats differ in many biotic and abiotic factors with potential important consequences on fitness. Measuring phenotypic differences between habitats is a relevant approach to assess habitat quality for multiple categories of individuals such as males and females. Morphological traits have, for example, been used to successfully assess the impact of urbanization on birds. Surprisingly, this approach has rarely been used in farmlands, although it could be useful to assess the constraints of agricultural practices (i.e. habitat alteration, pesticides). We investigated the phenotypic differences between three habitats (forest, urban, vineyard) in male and female great tits (Parus major) to assess the constraints that occur in small cities and intensive vineyards, and to test if one sex may be more sensitive than the other to habitat-specific constraints. We measured three traits that integrate environmental constraints (body size, body condition, carotenoid-based plumage colouration). We found that urban great tits are of lower phenotypic quality (size, condition, plumage brightness) than their forest counterparts even when they live in small cities. Despite intensive agricultural practices, we found no difference in body size and plumage colouration between vineyard and forest birds, and vineyard birds were even in better condition than forest ones. We found that the differences in body condition between habitats were more pronounced for females relative to males. This supports the idea that females may be more sensitive to habitat-specific constraints than males. Our study suggests that food availability is probably not limited for this generalist species in vineyards, contrary to cities
High‐throughput microfluidic real‐time PCR as a promising tool in disease ecology
No full textInternational audienceAmong recent advances in molecular biology for studying infectious diseases, the microfluidic high‐throughput real‐time polymerase chain reaction (Htrt PCR) has emerged as an efficient first‐line tool for the detection of a wide range of infectious agents (IA) in a host system. This technology allows large batches of samples to be screened simultaneously for tens of targeted IA by real‐time PCR. It represents a promising tool in disease ecology. As a proof of concept, we present here the development steps and initial application of a microfluidic Htrt PCR system for the detection of DNA from 28 selected IA in a set of wild vertebrates. We applied this approach to 497 samples (mainly mucosal swabs and necropsy tissues) from 274 seabirds and 80 mammals from Southern Ocean islands. This ecosystem is of particular interest for disease ecology and biodiversity conservation due to the high host densities of breeding colonies, within and among which pathogens may spread rapidly. Positive samples were subsequently confirmed for each PCR system using a secondary real‐time or conventional PCR system and/or sequencing. Fourteen targeted IA were detected. The approach allowed an efficient screening of host species for known seabird pathogens, including Pasteurella multocida (avian cholera) (9.9% [6.6–14.0] in seabirds, 18.3% [9.5–30.4] in mammals) and Erysipelothrix amsterdamensis (15% [11–19.8] in seabirds, 2.1% [0.4–6.1] in mammals) in cloacal and rectal swabs. Their detection on islands where they were not known previously raised conservation concerns. IA not previously known to be circulating in the system were detected at high prevalence, notably Chlamydiaceae on all colonies (32.1% [26.6–38] in seabirds and 21.3% [12.9–31.8] in mammals, in cloacal and rectal swabs). Prevalence and diversity of targeted IA could be compared among sites and host species, highlighting the usefulness of the approach to explore drivers of IA community dynamics, but also to identify specific hosts as potential epidemiological sentinels or reservoirs. Htrt PCR is a powerful and versatile tool that can be used in disease ecology for exploring the composition of IA communities within host communities, but also for addressing other important basic and applied questions in multi‐host, multi‐pathogen systems.Parmi les progrès récents de la biologie moléculaire dans l'étude des maladies infectieuses, la PCR en temps réel microfluidique à haut débit (Htrt PCR) apparaît comme un outil de première intention efficace pour la détection d'un large panel d'agents infectieux (IA) dans un système donné. Cette technologie permet de tester simultanément un grand nombre d'échantillons pour des dizaines d'agents infectieux ciblés par PCR en temps réel et représente donc un outil prometteur en écologie des maladies infectieuses. Comme preuve de concept, nous présentons ici la mise en place et l'application d'un système Htrt PCR pour la détection de 28 IA à ADN dans des populations de vertébrés sauvages. Cette approche a été appliquée à 497 échantillons (écouvillons de cloacaux et tissus d'autopsie) provenant de 368 oiseaux marins et mammifères des îles subantarctiques. Cet écosystème présente un intérêt particulier en écologie des maladies infectieuse en raison notamment des fortes densités des colonies au sein desquelles la circulation des IA peut être importante. Tous les échantillons positifs en Htrt PCR ont été confirmés secondairement par des PCR en temps réel ou classiques et/ou par séquençage. Quatorze des IA ciblés ont été détectés. L'approche a permis de rechercher efficacement certains IA connus pour être associés à des mortalités d'oiseaux marins, comme l'agent du choléra aviaire ( Pasteurella multocida ) (9,9% [6,6‐14,0] chez les oiseaux marins et 18,3% [9,5‐30,4] chez les mammifères) ou la bactérie Erysipelothrix amsterdamensis (15% [11–19,8] chez les oiseaux marins et 2,1% [0,4‐6,1] chez les mammifères). Leur détection sur des îles jusqu'à présent considérées comme indemnes soulève avec de fortes implications dans la conservation des espèces. Certains IA, dont la circulation dans ce système n'était pas connue auparavant, ont été détectées avec de fortes prévalences, comme la famille des Chlamydiaceae sur toutes les colonies (32,1% [26,6–38] chez les oiseaux marins et 21,3% [12,9‐31,8] chez les mammifères). La prévalence et la diversité des IA ciblés ont pu être comparées entre les sites et les espèces hôtes, soulignant l'utilité de l'approche dans l'exploration des dynamiques des communautés d'IA, ainsi que dans l'identification de potentielles espèces sentinelles épidémiologiques ou réservoirs. La PCR Htrt semble être un outil intéressant pour l'écologie des maladies infectieuses, permettant d'explorer la composition des communautés d'IA au sein des communautés d'hôtes, tout en abordant des questions fondamentales et/ou appliquées sur les systèmes multi‐hôtes et multi‐pathogènes
