Livrable D4.2 of the PERSEE project : Représentation et codage 3D - Rapport intermédiaire - Définitions des softs et architecture

51Livrable D4.2 du projet ANR PERSEECe rapport a été réalisé dans le cadre du projet ANR PERSEE (n° ANR-09-BLAN-0170). Exactement il correspond au livrable D4.2 du projet. Son titre : Représentation et codage 3D - Rapport intermédiaire - Définitions des softs et architectur

3D coding tools final report

Livrable D4.3 du projet ANR PERSEECe rapport a été réalisé dans le cadre du projet ANR PERSEE (n° ANR-09-BLAN-0170). Exactement il correspond au livrable D4.3 du projet. Son titre : 3D coding tools final repor

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km² resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e., offset) between in-situ soil temperature measurements, based on time series from over 1200 1-km² pixels (summarized from 8500 unique temperature sensors) across all the world’s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in-situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world\u27s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature.

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Étude de MutS à l'échelle de la molécule unique

Using single molecule micromanipulation and force measurement on DNA with a magnetic tweezer setup, this work has been devoted in part to a study of the " long patch " repair system of DNA. This repair involves the MutS, MutH and MutL proteins, and uses an as yet unidentified mechanism in order to act at a distance, between a site of mismatch (due for example to a replication error), and a proximal GATC hemimethylationsite, so that the repair is directed toward the newly synthesized strand. Some models of this action at a distance, involve the presence of a DNA loop, induced by the action of MutS on a mismatch. We have tried to explore this possibility, by studying the mechanical behavior of a long double stranded DNA, containing (or not containing) a mismatch. We have not detected any specific loop formation in DNA, i.e. only induced when a mismatch is present. This negative result seems to exclude specific loop formation induced by MutS. In a second part, we have studied the mechanical behavior of a Holliday junction (a cross-shaped DNA, involved as an intermediate during recombination). We have shown directly that it is possible to extrude a Holliday junction, by mechanically undercoiling a palindromic DNA. We have deduced the pitch of the DNA double helix from the behavior of the Holliday junction. In a last part, we have studied the influence of Ethidium Bromide, on DNA. We have shown that this intercalating agent is able to induce a non-specific attraction either intra-strand or inter-strand, in single-stranded DNA.Par micromanipulation et mesure de force sur molécule unique, avec un piège magnétique, ce travail a porté en partie sur l'étude du système de réparation « à longue distance » de l'ADN. Cette réparation fait intervenir pour son initiation les protéines MutS, MutL, et MutH et utilise un mécanisme non identifié précisément, qui lui permetd'agir à distance, entre un site de mésappariement de l'ADN (dû par exemple à une erreur de réplication), et un site proximal distant (hémi-méthylation de séquence GATC), ce qui permet de diriger la réparation sur le brin néosynthétisé. Certains modèles de l'action de la protéine MutS font intervenir une boucle dans l'ADN. Nousavons cherché à mettre en évidence une telle action sur un ADN double brin, contenant (ou ne contenant pas) un mésappariement. Nous n'avons pas mis en évidence deformation de boucle par MutS, qui soit spécifiquement liée à la présence d'un mésappariement. Ce résultat négatif semble donc exclure ce modèle de boucle spécifique. Dans une deuxième partie, nous avons effectué des expériences de micromanipulation sur une jonction de Holliday (ADN en forme de croix, intermédiaire de recombinaison). Nous avons montré directement qu'il est possible d'extruder une jonction de Holliday, en sous-enroulant mécaniquement une molécule d'ADN comportant une séquence palindromique, et avons aussi déduit de ces expériences une mesure du pas de l'hélice de l'ADN. Dans une dernière partie, nous avons étudié l'influence du bromure d'éthidium sur l'ADN. Nous avons montré que la présence de cet agent intercalant peut induire une attraction non-spécifique, intra- ou inter- simple brins d'ADN

ETUDE METALLURGIQUE D'ALLIAGES DE TITANE POUR APPLICATIONS BIOMEDICALES

RENNES-INSA (352382210) / SudocALBI-ENSTIMAC (810042301) / SudocSudocFranceF

Etude des processus physiques mis en jeu lors de la microimpression d'éléments biologiques assistée par laser

Parallèlement à l impression jet d encre et au bioplotting, l impression d'éléments biologiques assistée par laser (Laser Assisted Bioprinting : LAB) qui utilise le transfert vers l avant induit par laser (Laser Induced Forward Transfer : LIFT) a émergé comme une méthode alternative dans l assemblage et la micro structuration de biomatériaux et de cellules. Le LAB est une technique d écriture directe qui offre la possibilité d imprimer des motifs avec une haute résolution spatiale à partir d'une large gamme de matériaux solides ou liquides, tels que des diélectriques, des biomolécules et des cellules vivantes en solution.Dans nos travaux de recherche, nous avons considéré une approche expérimentale et numérique pour étudier les mécanismes physiques mis en jeu lors de la microimpression d éléments biologiques assistée par laser. Dans un premier temps nous avons défini les paramètres rhéologiques des bioencres et les conditions de transfert (composition, épaisseur et viscosité de la bioencre et énergie laser). Puis nous avons mené une analyse statistique du volume des gouttelettes déposées pour quatre viscosités de bioencre, cinq épaisseurs de bioencre et cinq énergies laser. Ensuite nous avons conçu et mis en place un système d imagerie résolue en temps pour étudier les effets de la viscosité sur la dynamique de l éjection. Nous avons ainsi différencié trois régimes d'éjection en fonction de l'énergie laser déposée dans la couche absorbante, de la viscosité et de l'épaisseur de la bioencre. Parallèlement, un modèle numérique a été mis en place pour comprendre et prédire la dynamique de l éjection en fonction de paramètres multiples : choix et épaisseur de la couche absorbante, épaisseur de la couche de bioencre, énergie laser déposée. Enfin, au regard de ces études, nous proposons un mécanisme d'éjection des microgouttelettes intervenant au cours du procédé de microimpression assistée par laser.Over this decade, cell printing strategy has emerged as one of the promising approaches to organize cells in two and three dimensional engineered tissues. In parallel with ink-jet printing and bioplotting, Laser Assisted Bioprinting (LAB) using Laser-Induced Forward Transfer (LIFT) has emerged as an alternative method in the assembly and micropatterning of biomaterials and cells. LAB is a laser direct-write technique that offers the possibility of printing micropatterns with high spatial resolution from a wide range of solid or liquid materials, such as dielectrics, biomolecules and living cells in solution. In our research works, we considered an experimental and numerical approach to study the physical mechanisms involved in the biological elements microprinting laser assisted.First we defined the rheological parameters of bioinks and the transfer conditions (composition, thickness and viscosity of the bioink and laser energy). Then we led a statistical analysis of the volume of the transfer droplets for four viscosities of bioink, five thicknesses of bioink and five laser energies. Then we designed and implemented a system for time resolved imaging to study the effects of viscosity on the dynamics of the ejection. Thus we have differentiated three ejection regimes in function of the laser energy released in the absorbing layer, the visocsity and the thickness of the bioink. In parallel, a numerical model was developed to understand and predict the dynamics of the ejection parameters according to multiple choice and thickness of the absorbing layer, thickness of the layer bioencre, energy deposited. Finally, with regard to these studies, we propose a mechanism for ejecting droplets involved in the process of laser-assisted microprinting.BORDEAUX1-Bib.electronique (335229901) / SudocSudocFranceF

Etude de MutS à l'échelle de la molécule unique

PARIS7-Bibliothèque centrale (751132105) / SudocSudocFranceF

Etude de la Micro-Impression d'Eléments Biologiques par Laser pour l'Ingénierie du Tissu Osseux

L'ingénierie tissulaire osseuse est un domaine multidisciplinaire qui vise à produire des substituts tissulaires pour la médecine régénératrice. Ce travail visait à produire des substituts osseux structurés tridimensionnels grâce à un système d'impression d'éléments biologiques par laser développé au laboratoire Inserm U577 (Projet LASIT: LASer pour L'Ingénierie Tissulaire). Les étapes de la thèse ont consisté tout d'abord à préparer des matériaux adaptés à l'impression par laser et à les caractériser au niveau physico-chimique et biologique. Il s'agissait d'hydroxyapatite nano-cristalline, de cellules humaines et d'hydrogels (alginate, matrigel). Ensuite des impressions structurées combinant ces matériaux ont été réalisées en 3 dimensions avant d'être implantés in vivo chez la souris. Les résultats ont montré que l'impression par laser d'éléments biologiques est une méthode efficace pour organiser des matériaux tridimensionnels à plusieurs composants pour l'ingénierie tissulaire.Bone Tissue Engineering is a multidisciplinary field which aims to produce artificial tissues for regenerative medicine. The purpose of this work was to produce three-dimensional bone substitute using a laser-assisted bioprinting (LAB) workstation developped in the laboratory INSERM U577 (TEAL Project: Tissue Engineering Assisted by Laser). The first step of the work consisted in the synthesis of specific materials for LAB and in the characterization of their biological and physico-chemical properties. We have prepared a nano-hydroxyapatite bioink, human cells bioinks and hydrogels bioinks. Then, three-dimensional materials have been prepared using LAB and have been implanted in vivo in mice. The results have shown that Laser Assisted Bioprinting is an efficient method fo patterning 3-D materials using biolgical elements.BORDEAUX1-Bib.electronique (335229901) / SudocSudocFranceF