What is the relative importance of physical, biological environment and geographic distance in shaping medium and large fauna assemblages in lowland Amazonia?

Understanding the response of communities to spatially heterogeneous environmental conditions is an important challenge for ecologists. Whereas broad-scale Amazonian forest types have been shown to influence the structure of the communities of mediumto large-sized vertebrates, their natural heterogeneity within the terra firme rainforests remains poorly investigated. Here we question the drivers of the diversity and composition of medium and large fauna assemblages from a species-neutral, functional and phylogenetic perspective. In this study, we disentangled the effects of various physical, biological and spatial covariates on the composition and diversity of 21 communities of 19 medium- and large-sized vertebrates in neotropical terra firme rainforests, French Guiana (~84,000 km²). We sampled each local vertebrates community using standardized line transects (sampling effort of ~5,000 km). We estimated species densities using distance sampling method taking into account temporary emigration and imperfect detection. Raw population density data were used to analyse species-neutral assemblages. Functional compositions and diversities were estimated from 9 morphological and behavioral traits while phylogenetic ones were measured from discrepancies between taxonomic levels (from species to classes). Physical environmental conditions were extracted from remote sensing data (e.g. mean landforms slope, mean elevation). Biological environmental conditions were estimated in the field (e.g. biomass, dominant tree families). Finally, geographic distances between sites were calculated to assess spatial effects on the structure of communities. We implemented variation partitioning to determine the relative importance of each covariate in shaping fauna assemblages. At this spatial extent, we can hypothesize that biological conditions explain better composition and diversities than physical conditions because of their potentially direct influences on fauna. In addition, these results should allow us to better understand how much environmental filtering and geographical processes shape patterns of medium- and large-sized vertebrates distribution. (Texte intégral

Hybrid hierarchical patterns of gold nanoparticles and poly(ethylene glycol) microstructures

Hybrid surface micro-patterns composed of topographic structures of polyethylene glycol (PEG)-hydrogels and hierarchical lines of gold nanoparticles (Au NPs) were fabricated on silicon wafers. Micro-sized lines of Au NPs were first obtained on the surface of a silicon wafer via “micro-contact deprinting”, a method recently developed by our group. Topographic micro-patterns of PEG, of both low and high aspect ratio (AR up to 6), were then aligned on the pre-patterned surface via a procedure adapted from the soft lithographic method MIMIC (Micro-Molding in Capillaries), which is denoted as “adhesive embossing”. The result is a complex surface pattern consisting of alternating flat Au NP lines and thick PEG bars. Such patterns provide novel model surfaces for elucidating the interplay between (bio)chemical and physical cues on cell behavior

Genetic Correlation with the DNA Repair Assay in Mice Exposed to High-LET

We hypothesize that DNA damage induced by high local energy deposition, occurring when cells are traversed by high-LET (Linear Energy Transfer) particles, can be experimentally modeled by exposing cells to high doses of low-LET. In this work, we validate such hypothesis by characterizing and correlating the time dependence of 53BP1 radiation-induced foci (RIF) for various doses and LET across 72 primary skin fibroblast from mice. This genetically diverse population allows us to understand how genetic may modulate the dose and LET relationship. The cohort was made on average from 3 males and 3 females belonging to 15 different strains of mice with various genetic backgrounds, including the collaborative cross (CC) genetic model (10 strains) and 5 reference mice strains. Cells were exposed to two fluences of three HZE (High Atomic Energy) particles (Si 350 megaelectronvolts per nucleon, Ar 350 megaelectronvolts per nucleon and Fe 600 megaelectronvolts per nucleon) and to 0.1, 1 and 4 grays from a 160 kilovolt X-ray. Individual radiation sensitivity was investigated by high throughput measurements of DNA repair kinetics for different doses of each radiation type. The 53BP1 RIF dose response to high-LET particles showed a linear dependency that matched the expected number of tracks per cell, clearly illustrating the fact that close-by DNA double strand breaks along tracks cluster within one single RIF. By comparing the slope of the high-LET dose curve to the expected number of tracks per cell we computed the number of remaining unrepaired tracks as a function of time post-irradiation. Results show that the percentage of unrepaired track over a 48 hours follow-up is higher as the LET increases across all strains. We also observe a strong correlation between the high dose repair kinetics following exposure to 160 kilovolts X-ray and the repair kinetics of high-LET tracks, with higher correlation with higher LET. At the in-vivo level for the 10-CC strains, we observe that drops in the number of T-cells and B-cells found in the blood of mice 24 hours after exposure to 0.1 gray of 320 kilovolts X-ray correlate well with slower DNA repair kinetics in skin cells exposed to X-ray. Overall, our results suggest that repair kinetics found in skin is a surrogate marker for in-vivo radiation sensitivity in other tissue, such as blood cells, and that such response is modulated by genetic variability

Lymphoid Tumors of Xenopus laevis with Different Capacities for Growth in Larvae and Adults

Three new lymphoid tumors offering an assortment of variants in terms of MHC class I expressions, MHC class II expression, and Ig gene transcription have been discovered in the amphibian Xenopus. One was developed in an individual of the isogenic LG15 clone (LG15/0), one in a frog of the LG15/40 clone (derived from a small egg recombinant of LG15), and one (ff-2) in a male ff sib of the individual in which MAR1, the first lymphoid tumor in Xenopus was found 2 years ago. These tumors developed primarily as thymus outgrowths and were transplantable in histocompatible tadpoles but not in nonhistocompatible hosts. Whereas LG15/0 and LG15/40 tumor cells also grow in adult LG15 frogs, the ff-2 tumor, like the MAR1 cell line, is rejected by adult ff animals. Using flow cytometry with fluorescence-labeled antibodies and immunoprecipitation analysis, we could demonstrate that, like MAR1, these three new tumors express on their cell surface lymphopoietic markers recognized by mAbs FIF6 and RC47, as well as T-cell lineage markers recognized by mAbs AM22 (CD8-1ike) and X21.2, but not by immunologobulin (Ig) nor MHC class II molecules. Another lymphocyte-specific marker AM15 is expressed by 15/0 and 15/40 but not ff-2 tumor cells. The ff-2 tumor cell expresses MHC class molecule in association with β2-microglobulin on the surface, 15/40 cells contain cytoplasmic I α chain that is barely detected at the cell surface by fluocytometry, and 15/0 cells do not synthesize class I α chain at all. The three new tumors all produce large amounts of IgM mRNA of two different sizes but no Ig protein on the membrane nor in the cytoplasm. All tumor cell types synthesize large amount of Myc mRNA and MHC class I-like transcripts considered to be non classical

Développement d'un algorithme de simulation en dynamique des fluides basé sur la méthode de Boltzman sur réseau

Équations de Navier-Stokes -- Simulation d'écoulements au niveau microscopique par la méthode des automates de gaz sur réseau -- Des automates de gaz sur réseau à la méthode de Boltzmann sur réseau -- Méthode de Boltzmann sur réseau -- But et objectifs -- Théorie associée à la méthode de Boltzmann sur réseau -- Principe de base de la méthode de Boltzmann sur réseau -- Équation de transport de Boltzmann et ses simplifications -- L'équation de Boltzmann sur réseau -- Méthode de Boltzmann sur réseau BGK -- Application de la méthode de Boltzmann sur réseau D2Q9 -- Simulation avec le modèle D2Q9 -- Conditions aux limites appliquées au modèle D2Q9 -- Améliorations de la méthode de Boltzmann sur réseau D2Q9 -- Simulations numériques par la méthode de Boltzmann sur réseau -- Cavité entraînée, vérification de la formulation de base de la méthode de Boltzmann sur réseau -- Cylindre dans un canal, vérification des améliorations de la méthode de Boltzmann sur réseau -- Profils NACA, comparaison à d'autres méthodes de simulation -- Remontée libre d'une particule dans un fluide par poussée d'Archimède

Etude des mécanismes cellulaires et moléculaires de la migration des macrophages humains dans des environnements en trois dimensions

L'infiltration tissulaire des macrophages est un facteur aggravant dans de nombreuses pathologies telles que les maladies inflammatoires chroniques ou le cancer. Les macrophages qui infiltrent les tumeurs de façon continue sont appelés macrophages associés aux tumeurs (TAMs). Ils favorisent la croissance tumorale, l'angiogenèse, l'invasion tumorale et la formation de métastases. L'inhibition de l'infiltration des macrophages est donc devenue une évidence thérapeutique. Récemment, l'équipe a démontré que les macrophages utilisent le mode migratoire amiboïde (dépendant de ROCK) ou mésenchymal (dépendant des protéases) selon l'architecture de la matrice extracellulaire (MEC) en trois-dimensions (3D) qu'ils traversent. De plus, l'étude du mode migratoire mésenchymal a montré qu'il est dépendant de Hck (une tyrosine kinase spécifique des phagocytes) et de sa capacité à réorganiser les podosomes en rosettes (structures riches en actine dégradant la MEC). Mon projet de thèse s'est articulé autour de deux axes de recherche : 1) l'identification des substrats de Hck et la caractérisation de leur rôle dans l'organisation des podosomes et la migration 3D des macrophages, et 2) l'étude de la migration 3D des monocytes/macrophages primaires humains dans un modèle mimant le microenvironnement tumoral : les sphéroïdes tumoraux. Par une approche protéomique j'ai identifié des partenaires et substrats potentiels de Hck dont la Filamine A (FLNa), une protéine assurant notamment la liaison entre le cytosquelette d'actine et les intégrines. En utilisant différents outils (protéines recombinantes, anticorps, shRNA...) j'ai montré que : 1) Hck phosphoryle la FLNa in vitro, 2) la FLNa est associée aux podosomes et est nécessaire à leur organisation en rosettes sous le contrôle de Hck, 3) les podosomes des cellules déficientes en Flna ont une durée de vie plus courte, et 4) l'expression de la FLNa est nécessaire à la migration mésenchymale, mais pas à la migration amiboïde des macrophages dans une MEC en 3D. Ainsi la FLNa est impliquée dans la formation et à la stabilisation des podosomes, à leur organisation en rosettes, la migration mésenchymale des macrophages et pourrait se situer dans la voie de signalisation de Hck. En parallèle, j'ai mis au point un modèle de sphéroïdes tumoraux qui m'a permis de montrer que l'infiltration des monocytes ou des macrophages, dans ce modèle tissulaire in vitro, est dépendante de ROCK et des protéases, signature de l'utilisation des deux modes migratoires. Puis en incubant ces sphéroïdes au sein de MEC, j'ai démontré que la présence de macrophages infiltrés dans les sphéroïdes est nécessaire pour déclencher le pouvoir invasif des cellules tumorales qui émigrent des sphéroïdes en suivant les macrophages et infiltrent la MEC environnante. Les macrophages Hck-/- présentant un défaut de migration mésenchymale, sont significativement moins efficaces dans la promotion de l'invasion des cellules tumorales. Ces résultats indiquent que l'activité de migration et de remodelage de la matrice exercée par les macrophages est prépondérante dans l'invasion tumorale in vitro. Ces résultats ont permis d'établir le mode migratoire des macrophages infiltrant un modèle tissulaire in-vitro et de démontrer le mécanisme d'action des macrophages dans l'invasion tumorale. Ainsi, mes travaux de thèse ont permis de progresser dans la caractérisation des mécanismes moléculaires et cellulaires de la migration 3D des macrophages humains. En effet, j'ai pu 1) identifier une protéine nécessaire à la migration mésenchymale des macrophages, 2) mettre en évidence l'utilisation par les macrophages des modes migratoires amiboïde et mésenchymal lors de leur infiltration dans un modèle de tumeur en trois-dimensions, les sphéroïdes tumoraux et 3) montrer que le remodelage de la matrice par les macrophages, lors de leur migration, joue un rôle prépondérant dans l'invasion tumorale.Tissue infiltration of macrophages is an aggravating factor in many diseases such as chronic inflammation and cancer. Macrophages that infiltrate tumors are called tumor-associated macrophages (TAMs). They promote tumor growth, angiogenesis, invasion and metastasis. Thus, inhibition of macrophage infiltration has become a therapeutic goal. Recently, the team demonstrated that macrophages use the amoeboid (depending on ROCK) or the mesenchymal (depending on proteases) migratory mode according to the extracellular matrix (ECM) architecture in three dimensions (3D). In addition, the study of the mesenchymal migration mode showed that it is dependent on Hck (a phagocyte-specific tyrosine kinase) and its ability to reorganize podosomes (ECM-degrading actin-rich structures) into rosettes. My thesis project was organized around two axes 1) the identification of substrates of Hck and the characterization of their role in the organization of podosomes and 3D migration of macrophages, and 2) the study of the 3D migration mechanisms of primary human monocytes/ macrophages within an in vitro tumor model: tumor cell spheroids. By a proteomic approach, I have identified potential partners and substrates of Hck, including the protein Filamin A (FLNa), a protein interacting with the actin cytoskeleton and integrins. Using different tools (recombinant proteins, antibodies, shRNA ...) I showed that: 1) Hck phosphorylates FLNa in vitro, 2) FLNa is localized to podosomes and is necessary for their organization as rosettes under the control of Hck, 3) the podosomes of FLNa-deficient cells have a shorter life span, and 4) the expression of FLNa is required for mesenchymal migration, but not for amoeboid migration of macrophages in a 3D ECM. Thus, FLNa could be a substrate of Hck necessary for the formation and stabilization of podosomes and their organization as rosettes, and is required for the mesenchymal migration of macrophages. In parallel, I developed a model of tumor cell spheroids, which allowed me to show that the infiltration of monocytes or macrophages in this in vitro tissue model of tumor is dependent on ROCK and proteases, signature of the use of the two migration modes. Then, when spheroids were embedded into ECM, I demonstrated that the presence of macrophages infiltrated into the spheroids is necessary to trigger the invasiveness of tumor cells. Indeed, macrophages infiltrate first the surrounding ECM and tumor cells follow macrophages in the matrix outside of the spheroid. Hck-/- macrophages, that are defective in mesenchymal migration, are significantly less effective in promoting the invasion of tumor cells. These results indicate that the activity of migration and matrix remodeling exerted by macrophages is prominent in tumor invasion. These results have established the migratory mode of macrophages infiltrating an in vitro tumor model and a mechanism required for tumor invasiveness promoted by macrophages. Thus during my thesis, I characterized the molecular and cellular mechanisms of 3D migration of human macrophages. Indeed, I have been able to: 1) identify a protein necessary for the mesenchymal migration of macrophages, 2) highlight the use by macrophages of the amoeboid and mesenchymal migration modes during their infiltration into an in vitro tumor model in 3D and 3) show that the matrix remodeling activity of macrophages during their migration plays a critical role in tumor cell invasion

Seasonal variability in global industrial fishing effort

Unidad de excelencia María de Maeztu MdM-2015-0552Identificadors digitals: Digital object identifier for the 'European Research Council' (http://dx.doi.org/10.13039/501100000781) Digital object identifier for 'Horizon 2020' (http://dx.doi.org/10.13039/501100007601) - BIGSEA PROJECTHuman beings are the dominant top predator in the marine ecosystem. Throughout most of the global ocean this predation is carried out by industrial fishing vessels, that can now be observed in unprecedented detail via satellite monitoring of Automatic Identification System (AIS) messages. The spatial and temporal distribution of this fishing effort emerges from the coupled interaction of ecological and socio-economic drivers and can therefore yield insights on the dynamics of both the ecosystem and fishers. Here we analyze temporal variability of industrial fishing effort from 2015-2017 as recorded by global AIS coverage, and differentiated by fishing gear type. The strongest seasonal signal is a reduction of total deployed effort during the annual fishing moratorium on the numerically-dominant Chinese fleet, which occurs during boreal summer. An additional societally-controlled reduction of effort occurs during boreal winter holidays. After accounting for these societal controls, the total deployed effort is relatively invariant throughout the year for all gear types except squid jiggers and coastal purse seiners. Despite constant deployment levels, strong seasonal variability occurs in the spatial pattern of fishing effort for gears targeting motile pelagic species, including purse seiners, squid jiggers and longliners. Trawlers and fixed gears target bottom-associated coastal prey and show very little overall seasonality, although they exhibit more seasonal variation at locations that are further from port. Our results suggest that societal controls dominate the total deployment of fishing effort, while the behavior of pelagic fish, including seasonal migration and aggregation, is likely the most prominent driver of the spatial seasonal variations in global fishing effort

Bioenergetic influence on the historical development and decline of industrial fisheries

Unidad de excelencia María de Maeztu CEX2019-000940-MIdentificadors digitals: Digital object identifier for the 'European Research Council' (http://dx.doi.org/10.13039/501100000781) Digital object identifier for 'Horizon 2020' (http://dx.doi.org/10.13039/501100007601) - BIGSEA projectThe global wild capture fishery expanded rapidly over the 20th century as fishing technology improved, peaking in the 1990s as most fisheries transitioned to fully- or over-exploited status. Historical records for individual large marine ecosystems (LMEs) tend to echo this same progression, but with local variations in the timing and abruptness of catch peaks. Here, we provide objective descriptions of these catch peaks, which generally progressed from high- to low-latitude LMEs, and attribute the temporal progression to a combination of economic and ecological factors. We show that the ecological factors can be remarkably strong by using a spatially resolved, observationally-constrained, coupled macroecological-economic model to which we impose an idealized, globally homogeneous increase in catchability. The globally-uniform technology creep produces a spatial progression of fishing from high-to-low latitudes that is similar to observations, primarily due to the impact of temperature on ecosystem metabolism. In colder LMEs, low respiration rates allow the build-up of larger pristine standing stocks, so that high-latitude fisheries are profitable earlier, at lower levels of fishing technology. We suggest that these bioenergetic characteristics contributed significantly to the historical progression of this human-ecological system

Instrumentalisations de la sémiotique

Depuis les travaux de Roland Barthes la sémiotique a pris une place considérable dans les champs professionnels de la publicité et du marketing. Au travers d'exemples théoriques et pratiques il s'agit d'étudier comment les mondes professionnels et universitaires s'interpénétrent