Culture-independent methods for identifying microbial communities in cheese

International audienceThis review focuses on the culture-independent methods available for the description of both bacterial and fungal communities in cheese. Important steps of the culture-independent strategy, which relies on bulk DNA extraction from cheese and polymerase chain reaction (PCR) amplification of selected sequences, are discussed. We critically evaluate the identification techniques already used for monitoring microbial communities in cheese, including PCR-denaturing gradient gel electrophoresis (PCR-DGGE), PCR-temporal temperature gradient gel electrophoresis (PCR-TTGE) or single-strand conformation polymorphism-PCR (SSCP-PCR) as well as some other techniques that remain to be adapted to the study of cheese communities. Further, our analysis draws attention to the lack of data available on suitable DNA sequences for identifying fungal communities in cheese and proposes some potential DNA targets

Step interactions on Pt(111) vicinal surfaces determined by grazing incidence x-ray diffraction: influence of the step orientation

International audienceWe have studied the step–step interactions on the Pt(997) vicinal surface. Grazing incidence X-ray diffraction (GIXD) allowed us to measure the elastic atomic relaxations near the surface due to the steps. By means of the model of buried elastic dipoles, within the framework of anisotropic linear elasticity (ALE) calculations, the surface stress of Pt(111), and the elastic interaction between steps are deduced. The values so-obtained are compared to the values previously measured on the Pt(779) surface with the same technique. The comparison shows the strong influence of step geometry on step interactions

Tumor classification and prediction using robust multivariate clustering of multiparametric MRI

International audienceIn neuro-oncology, the use of multiparametric MRI may better characterize brain tumor heterogeneity. To fully exploit multiparametric MRI (e.g. tumor classification), appropriate analysis methods are yet to be developed. In this work, we show on small animals data that advanced statistical learning approaches can help 1) in organizing existing data by detecting and excluding outliers and 2) in building a dictionary of tumor fingerprints from a clustering analysis of their microvascular features

Monitoring glioma heterogeneity during tumor growth using clustering analysis of multiparametric MRI data

International audienceSynopsis Brain tumor heterogeneity plays a major role during gliomas growth and for the tumors resistance to therapies. The goal of this study was to demonstrate the ability of clustering analysis applied to multiparametric MRI (mpMRI) data to summarize and quantify intralesional heterogeneity during tumor growth. A mpMRI dataset of rats bearing glioma was acquired during the tumor growth (5 maps, 8 animals and 6 time points). After co-registration of every MR data over time, a clustering analysis was performed using a Gaussian mixture distribution model. Although preliminary, our results show that clustering analysis of mpMRI has a great potential to monitor quantitatively intralesional heterogeneity during the growth of tumors. Introduction For tumor diagnosis, histology often remains the reference, but due to tumor heterogeneity, it is widely acknowledged that biopsies are not reliable. There is thus a strong interest in monitoring quantitatively intralesional brain tumor heterogeneity. MRI has demonstrated its ability to quantitatively map structural information like diiusion (ADC) as well as functional characteristics such as the blood volume (BVf), vessel size (VSI), the oxygen saturation of the tissue (StO), or the blood brain barrier permeability. In a recent study (1), these MR parameters were analyzed independently from each other to demonstrate the great potential of a multiparametric MR (mpMRI) protocol to monitor combined radio-and chemo-therapies. However, to summarize and quantify all the information contained in an mpMRI protocol while preserving information about tumor heterogeneity, new methods to extract information need to be developed. The goal of this study is to demonstrate the ability of clustering analysis (2) applied to longitudinal mpMRI to summarize and quantify intralesional heterogeneity during tumor growth. Methods Animal model: The local IRB committee approved all studies. 9L tumors were implanted in 8 rats and imaging was performed every 2 days between day 7 and day 17 post tumor implantation on a 4.7T Bruker system (D7, D9, D11, D13, D15 and D17; respectively). The following mpMRI protocol was acquired at each MR session: a T2-weighted spin echo sequence to obtain structural information over the whole brain, a diiusion weighted EPI sequence to map the Apparent Diiusion Coeecient (ADC) and multiple spin/gradient echo sequences to map T2 and T2*. A Gradient Echo Sampling of the FID and Spin Echo (GESFIDE) sequence was acquired pre-and post-injection of USPIO (133 µmol/kg). A dynamic contrast enhancing sequence was acquired using a RARE sequence (T1w images; n=15, 15.6 sec per image). After the acquisition of 4 images, a bolus of gadolinium-chelate was administered (100µmol/kg). Parametric maps: for each MR session, BVf and VSI maps were computed using the approach described in (3), StO using the method described in (4) and the vessel permeability maps (Perm) was calculated as the percentage of enhancement (voxel-wise) within 3 min post injection of gadolinium (cf. g1-a). Co-registration: each parametric map of each MR session was co-registered to that acquired at the previous time point using rigid registration (SPM toolbox and Matlab). ROI: tumor was manually delineated using the T2w images (Tumor-ROI; Red line in g1-a). Cluster analysis: parameter values were centered and normalized. Then, a Gaussian mixture distribution (Matlab function called: tgmdist) was use to performed the clustering analysis of all voxels included in the tumor-ROI. The number of classes inside the mixture was selected by minimizing the Bayesian information criterion (BIC). Results Firstly, we performed the clustering analysis 9 times using 1 to 9 classes. The optimal classes number, deened by the BIC was 5. Each cluster may be seen as a tissue type, as described Fig.1-E. The result of the clustering analysis is illustrated Fig1-A for one animal. For each of the ve clusters (labeled K1 to K5), the evolution of the mean cluster volume over the entire population of tumor is presented Fig 1-B. Note that the sum of the ve cluster volumes represents the whole tumor volume. Fig.1-C illustrates the longitudinal evolution of the 5 clusters in 2 animals with diierent tumor growth rate (slow on the top and high on the bottom). Although the cluster analysis analyzed every voxel independently from each other, one can see that the clustering results are spatially consistent at 1 time point but also over time. Indeed, clusters are spatially grouped: for example, the green cluster is mostly located in the center of the tumor (Fig1-C). Our result shows a diierence in cluster composition between the slow and the high growth rate tumors (Fig.1-C,D). For example, in the slow growth rate tumor, the yellow cluster takes more and more space in the tumor overtime (up to 49% at D17) whereas, in the high growth rate tumor, it is the green one. The main diierence between the yellow and the green cluster is the strong reduction in StO in the green cluster versus the yellow cluster (cf. Fig.1-E). Conclusions To our knowledge, it is a rst study demonstrating the feasibility of performing a clustering analysis on mpMRI data to monitor the evolution of brain tumor heterogeneity in vivo. This approach highlights the type of tissue, which mostly contributes to the development of the tumor. The composition in tissue type could be used to reene the evaluation of chemo and radiotherapies and could contribute to improve tumor prognosis

Chapitre 13. Séquestration du carbone et usage durable des savanes ouest-africaines : synergie ou antagonisme ?

Introduction Les écosystèmes de savane ouest-africaine couvrent de vastes superficies (5.106 km2), en grande majorité exploitées par l’agriculture et le pastoralisme (Mayaux et al., 2004). Ils associent des systèmes herbacés et arborés, les faciès de végétation étant fortement pilotés par la pluviosité annuelle selon un gradient latitudinal. Dans ces écosystèmes, pour des raisons principalement démographiques et techniques – et, demain, sans doute climatiques – les ressources carbonées se rar..

Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

Background Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~253K SNPs) in order to reconstruct pedigrees. Results Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as 'Ribston Pippin', 'White Transparent' and 'Braeburn' were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely 'Reinette Franche' and 'Margil', and one North-Eastern Europe cultivar from the 1700s, 'Alexander'. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the 19th century onwards. Conclusions The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection

Optimizing signal patterns for MR vascular fingerprinting

International audienceMR vascular fingerprinting proposes to map vascular properties such as blood volume fraction, average vessel radius or blood oxygenation saturation (SO). The fingerprint pattern used in previous studies provides low sensitivity on SO. We optimised signal patterns built from pre and post USPIO acquisitions. Concatenation of different echoes associated with higher dimensional dictionaries led to better estimates in both healthy and tumoral tissues

Considérations ontogénétiques et phylogénétiques concernant l'origine de la parole. Prédiction de la capacité des conduits vocaux de fossiles reconstitués à produire des sons de parole

http://primatologie.revues.org/797National audienceOntogenetic and phylogenetic considerations concerning the origin of speech The end of the XXth century and the beginning of this century saw a reorganization of the researches in the field of speech and language emergence (SLE). Naturalism is the kernel of this new approach. It consists in describing the relations between biological aspects (in every sense of the word) on the one hand and speech and language, on the other hand, by an accumulation of hypotheses and evidence derived from a huge range of data collected thanks to interdisciplinary collaborations. As is the case for researches on the origin of Man, a theoretical profusion of hypotheses has arisen which sometimes leads to very hypothetical developments, based on fragile results and on too little data, and proposed in related but not fully mastered or too much simplified disciplines. This is why regular critical overviews do not seem superfluous. First, we propose a classification (push and pull theory) that provides a new reading of the various theories which have been proposed for half a century. In the present state of knowledge it is not possible to infer when our ancestors acquired the FacultyofSpeechandLanguageandSpeech: control of speech articulators, coordination between larynx and vocal tract, phonology, syntax, semantic and recursivity. Among old unsolved questions: Why is our species alone in having speech and language? Many others questions are (for the moment?) ill posed problems: we do not have sufficiently data to answer. Perhaps these questions will remain unsolved. But we think that the following question can be solved: If we suppose that our ancestors (and distant cousins) controlled their larynx and vocal tract in the same way as present-day humans, did the geometry of their vocal tract allow them to produce the universal sound structures of the languages spoken today? We analyzed 31 skulls from now to 1.5 Ma (millions years) BP (Before Present) for fossil hominids available at the Muséedel'Homme in Paris or in the literature: (1) 10-30 ka BP: modern humans: Paleolithic; (2) 90-200 ka BP: anatomically modern humans; (3) 45-90 ka BP: Neanderthals; (4) 1.5 Ma BP: Homoergaster; These skulls are all well kept and possess a jaw in the majority of cases but the vertebral column has been reconstituted. We attempt to: (1) Localize hyoid bone and then glottis position; (2) Reconstitute a vocal tract model in a plausible way using an articulatory model; (3) Quantify the acoustic capabilities of this reconstituted vocal tract. For this purpose, we combine phylogenesis and ontogenesis. We are in a position to state that our ancestors and distant cousins were equipped with a vocal tract that could produce the same variety of vowel sounds as we can today: the vowels /i a u/. The vocal tract morphology has been favorable to the emergence and production of speech since several hundreds of thousands of years. But how to know to what extent they mastered the control skills needed to produce speech? New lines of research are proposed in which orofacial abilities necessary to the emergence of speech are linked to a precursor mechanism dedicated to feeding (masticating-swallowing movements).La fin du XXe et le tout début de ce siècle révèlent une véritable réarticulation des recherches dans le domaine de l'émergence de la parole et du langage. Le naturalisme, qui est au centre de cette approche, se propose de décrire les relations entre la biologie (au sens très large du terme) d'une part, la parole et le langage, d'autre part, par une accumulation d'hypothèses, de données et de preuves formulées et établies grâce à de multiples collaborations interdisciplinaires. Comme pour les travaux sur l'origine de l'Homme (la découverte d'un nouveau fossile entraînant souvent une remise en question des théories précédentes), on assiste à un foisonnement théorique qui entraîne parfois des développements très hypothétiques, s'appuyant sur des résultats fragiles et sur trop peu de données, proposés dans des disciplines connexes mais non maîtrisées ou trop simplifiées. C'est pourquoi les bilans réguliers, les mises en perspectives critiques ne nous semblent pas superflus. Dans un premier temps nous proposerons une classification qui permet une lecture des différentes théories proposées depuis un demi-siècle (théorie push-pull). Dans l'état actuel des connaissances, il n'est pas possible d'inférer quand nos ancêtres, voire nos lointains ont acquis la faculté de langage et de parole : le contrôle des articulateurs, la coordination entre le larynx et le conduit vocal, la phonologie, la syntaxe, la sémantique et la récursivité. Parmi les questions qui se posent, il en est une qui reste sans réponse : pourquoi notre espèce est actuellement la seule à posséder langue et parole ? De nombreuses questions font partie des problèmes mal posés, comme le sont les questions du type: Quelle(s) langue(s) parlaient nos prédécesseurs ? Possédaient-ils une langue unique ? En effet, on ne dispose pas (pour le moment) de suffisamment de données pour pouvoir y répondre. Peut-être même que ces questions ne trouveront pas de solution. Actuellement, il est quand même possible de répondre à la question suivante : si nous supposons que nos ancêtres (et cousins lointains) contrôlaient leur larynx et leur conduit vocal de la même manière que les Hommes actuels, est-ce que la géométrie de leur conduit leur permettaient de produire les structures sonores qui sont pratiquement présentes dans toutes les langues du monde ? Nous présenterons ensuite nos travaux qui participent à la nouvelle réarticulation avec une approche véritablement axée sur la pluridisciplinarité. Ils s'inscrivent dans le domaine des relations entre la morphologie des organes de la production de la parole et son contrôle. Nous présentons de nouveaux résultats concernant la croissance du conduit vocal de la naissance à l'âge adulte puis des reconstructions du conduit vocal pour des fossiles qui couvrent la période de 10.000 ans à un million et demi d'années BP (Before Present). À partir du crâne, de la mandibule et des vertèbres cervicales nous essaierons de manière plausible (1) de localiser l'os hyoïde, support de la langue, et la position de la glotte, (2) de reconstituer un conduit vocal, à l'aide d'un modèle articulatoire, (3) d'induire les possibilités acoustiques de tous ces conduits. En combinant phylogenèse et ontogenèse il est possible de représenter l'anatomie du tractus en synthétisant deux remodelages qui renvoient à l'ontogenèse et à la phylogenèse. Nous montrerons que tous ces conduits ont les mêmes potentialités acoustiques, ils peuvent produire les voyelles /i a u/ qui sont pratiquement présentes dans toutes les langues du monde : un triangle à l'intérieur duquel se situent toutes les autres voyelles. Quand aux consonnes les plus fréquentes /p t k/, /b d g/ elles sont aussi à la portée de tous ces conduits vocaux à partir de gestes de fermeture dans des régions précises (lèvres, zone alvéodentale, zone vélaire). De nouvelles pistes de recherche sont proposées qui tendraient à montrer qu'il y a vraisemblablement plusieurs centaines de milliers, voire plusieurs millions d'années que le conduit vocal présente une morphologie favorable à l'émergence et à la production de la parole. Un cadre est posé dans lequel les capacités orofaciales nécessaire à la parole pourraient être reliées au mécanisme précurseur d'ingestion (mastication-déglutition)