Gathering and Analyzing Surface Parameters for Diet Identification Purposes

International audienceModern surface acquisition devices, such as interferometers and confocal microscopes, make it possible to have accurate three-dimensional (3D) numerical representations of real surfaces. The numerical dental surfaces hold details that are related to the microwear that is caused by food processing. As there are numerous surface parameters that describe surface properties and knowing that a lot more can be built, is it possible to identify the ones that can separate taxa based on their diets? Until now, the candidates were chosen from among those provided by metrology software, which often implements International Organization for Standardization (ISO) parameters. Moreover, the way that a parameter is declared as diet-discriminative differs from one researcher to another. The aim of the present work is to propose a framework to broaden the investigation of relevant parameters and subsequently a procedure that is based on statistical tests to highlight the best of them. Many parameters were tested in a previous study. Here, some were dropped and others added to the classical ones. The resulting set is doubled while considering two derived surfaces: the initial one minus a second order and an eighth order polynomial. The resulting surfaces are then sampled—256 samples per surface—making it possible to build new derived parameters that are based on statistics. The studied dental surfaces belong to seven sets of three or more groups with known differences in diet. In almost all cases, the statistical procedure succeeds in identifying the most relevant parameters to reflect the group differences. Surprisingly, the widely used Area-scale fractal complexity (Asfc) parameter—despite some improvements—cannot differentiate the groups as accurately. The present work can be used as a standalone procedure, but it can also be seen as a first step towards machine learning where a lot of training data is necessary, thus making the human intervention prohibitive

Specifying and verifying reactive systems in a multi-language environment

Abstract The multi-language environment Synchronie supports the design and formal verification of synchronous reactive systems. It integrates three synchronous languages and also three ways to specify properties: the temporal logic with future operators CTL, the temporal logic with past operators Past TL, and observers, which are particular synchronous programs. It is argued that this multi-language feature provides an answer to two major issues of formal verification: facility of formalizing properties and facility of verifying large systems. The approach is illustrated with the case study of a time-triggered protocol

Dynamiques démographiques contemporaines de la Polynésie française : héritage colonial, pluri-ethnisme et macrocéphalie urbaine

Après avoir connu une longue crise démographique au XIXe siècle, la Polynésie française a progressivement retrouvé le niveau de peuplement qui était le sien avant l’arrivée des Européens. Ce rattrapage est lié à des comportements démographiques qui, de l’Entre-deux-guerres jusqu’aux années 1970, furent comparables à ceux des pays en voie de développement. Associée à la forte concentration de l’essor économique aux îles du Vent, cette croissance démographique a confirmé l’organisation de l’esp..

L'écologie alimentaire d'Eucladoceros ctenoides : un outil pour suivre les variations environnementales régionales en Europe au Pléistocène inférieur

The early Pleistocene is represented by a succession of glacial-interglacial cycles character-ized by a general tendency towards global cooling, with increasing aridity and seasonality.The large deer Eucladoceros is found in abundance in Europe during this period of faunaldispersions. The dietary plasticity of Eucladoceros and how it can mirror early Pleistoceneclimatic variations will be explored here using Dental Microwear Texture Analysis. Thewide range of dental microwear textures for Eucladoceros reflects a low selectivity and highplasticity in its diet. It is an appropriate proxy to track vegetal resource availability. Oscil-lations were identified between a browsing and a grazing signal. This study proposes thata browsing signal is associated with a fossil assemblage deposited during an interglacialevent characterized by warmer temperatures and deciduous vegetation. A grazing signalmore likely indicates a glacial event with cooler temperatures and a developed herbaceous,bushy layer.Le Pléistocène inférieur correspond à une succession de cycles glaciaires-interglaciairescaractérisée par une tendance générale au refroidissement global, avec une aridité et unesaisonnalité croissantes. Le cervidé de grande taille Eucladoceros est abondant en Europedurant cette période de dispersions fauniques. Grâce à l'analyse de texture de la micro-usuredentaire, nous explorons la plasticité alimentaire d'Eucladoceros et la manière dont celle-ci reflète les variations climatiques du Pléistocène inférieur. La large gamme de texturesde micro-usure dentaire d'Eucladoceros reflète sa faible sélectivité et sa forte plasticité ali-mentaire. De fait, il constitue un outil approprié pour aborder la disponibilité en ressources végétales dans le milieu. Nous identifions des oscillations entre un signal brouteur et unsignal paisseur. Nous proposons qu'un signal brouteur soit associé à un assemblage fossiledéposé lors d'un évènement interglaciaire caractérisé par des températures plus chaudeset une végétation décidue, tandis qu'un signal paisseur correspondrait plutôt à un évène-ment glaciaire, avec des températures plus froides et la présence d?une strate herbacée etarbustive développée.This project was supported by the “Agence nationale dela recherche” (ANR TRIDENT: grant number: ANR-13-JSV7-0008-01; PI.: Gildas Merceron)

Etude moléculaire et structurale d'une intégrase rétrovirale pour le développement de nouveaux antirétroviraux et étude cristallographique d' -galactosidases thermostables issues du microorganisme Geobacillus stearothermophilus

Integrase (IN) is a key protein in the retrovirus life cycle and constitutes an important therapeutic target for the development of antiretroviral compounds. This enzyme is involved in the early phase of theretroviral replication cycle and catalyses the retrotranscribed viral DNA integration into the host cell genome.The teams of BioCrystallography and Retrovirology of Lyon Gerland demonstrated by X ray crystallography, the existence of a new dimeric assembly of the central catalytic domain (CCD) of Rous Associated Virus type 1integrase or RAV 1 IN. As part of my thesis work, a protocol of overproduction and purification of the H103Cisolated catalytic domain mutant was developed to demonstrate the existence of this dimeric assembly insolution stabilized by an inter molecular disulfide bond. Biochemical and biophysical methods were developed to test the ability of small molecules of interest to bind and stabilize this "new" assembly. A protocol ofoverproduction and purification of full length RAV1 integrase was developed. Crystallization trials and SAXSstudies were undertaken. The H103C mutant of the entire protein was produced to verify the formation of the"new" interface on the full length protein.The microorganism Geobacillus stearothermophilus produces two thermostable ɑ-galactosidases named AgaA and AgaB, which belong to theGH36 glycoside hydrolase family. These two isoenzymes share97% sequence identity, but have different catalytic properties. A collaborative study was initiated with theInstitute of Industrial Genetics, University of Stuttgart (Germany),to better understand the catalytic specificity of these two isoenzymes. The crystal structures of AgaA and AgaB were solved in two different crystal systems.The crystal structure of the mutant AgaA A355E, which has catalytic properties similar of those of AgaB, wasalso determined. These three structures show that the A355E substitution results in a signifiant displacement of the W336 tryptophan residue from the catalytic subsite -1. This could explain the catalytic specificities of the two isoenzymesL'intégrase (IN) est une protéine clé du cycle de réplication des rétrovirus et constitue une cible thérapeutique importante. Nous avons découvert par cristallographie aux rayons X, une nouvelle possibilité d'assemblage dimérique du domaine central catalytique de l'intégrase du Rous associated virus type I (RAV-1 IN). Dans le cadre de mon travail de thèse, un protocole de surproduction et de purification d'un mutant du domaine catalytique isolé (H103C) a été optimisé, afin de démontrer l'existence de cet assemblage en solution grâce à un pont disulfure inter-moléculaire. Différentes méthodes ont été mises au point, afin de tester la ca pacité de petites molécules d'intérêt à se lier et à stabiliser ce "nouvel" assemblage. Un protocole de surproduction et de purification de l'IN entière du RAV-1 a également été développé et mis au point. Des études structurales ont été réalisées. Un mutant H103C de la protéine entière a été produit, afin de vérifier la formation de la "nouvelle" interface sur la protéine entière. Le microorganisme Geobacillus stearothermophilus produit deux ɑ-galactosidases, AgaA et AgaB, qui appartiennent à la famille GH36 des glycosides hydrolases. Ces deux isoenzymes partagent 97 % d'identité de séquence, mais ont des activités catalytiques différentes. Les structures cristallines d'AgaA et AgaB ont été résolues ainsi que la structures du mutant AgaA et AgaB ont été résolues ainsi que la structure du mutant AgaA A355E, qui présente des caractéristiques enzymatiques similaires de AgaB. L'analyse de ces trois structures montre que la substitution A355E entraîne un déplacement significatif du tryptophane du sous-site catalytiques -1. Ce mouvement peut expliquer les spécificités catalytiques des deux isoenzymes