Recherche de mutations ponctuelles de l'ADN mitochondrial dans l'os pour une détermination de l'âge

In recent years, numbers of reports have suggested that during individual natural aging, heteroplasmic point mutations accumulate in the control region of mitochondrial DNA (mtDNA) of some tissue types. In the present study, we searched to evaluate the most efficient method for detecting low levels of heteroplasmy, determine whether these mutations were really age-related and assess the possible implications of heteroplasmies in anthropological and forensic studies. In first time, in two tissue types, muscle samples and buccal cells, we carried out the sensitive detection and quantification of point mutation A189G with peptid nucleic acid (PNA) and Real Time PCR (qPCR) together. Our results give additional information on the increase in mutation frequency with age in muscle tissue and revealed that the PNA/Real Time PCR is a largely more sensitive method than DNA sequencing for heteroplasmy detection, confirmed by Southern blot. In second time, we worked on bone tissues, on the one hand, from individuals where age was known in forensic identification, on the other hand, from ancient skeletons of the Eastern Siberia, where age determination was done using bone indicators. We showed the A189G heteroplasmy accumulation on individuals of 70 years old or more, when age is known, and on identified old individuals by bone indicators. The automatic sequencing revealed two other heteroplasmies (T72C and A73G) on individuals of 50 years old or more, in muscle and bone tissues, heteroplasmies already described in literature. These investigations could be of interest in the detection and interpretation of mtDNA heteroplasmy in anthropological and forensic studies.Ces dernières années, de nombreux travaux ont démontré la présence de mutations mitochondriales en relation avec l'âge dans divers types tissulaires. Le sujet de notre travail consiste à démontrer de manière fiable et spécifique la détection de telles mutations, d'établir leurs relations avec l'âge, et de déterminer si elles peuvent présenter un intérêt en Médecine Légale ou en Anthropologie afin d'augmenter les indices de détermination de l'âge. Dans un premier temps, sur le tissu musculaire et les cellules buccales, nous avons mis au point une technique combinant la technologie PNA (Peptid Nucleic Acid) et la PCR en Temps Réel (qPCR), démontrant une détection sensible et une quantification des taux de mutation de l'hétéroplasmie A189G, et la relation avec l'âge dans le tissu musculaire. Ces résultats ont démontré la meilleure sensibilité de la technique PNA/qPCR par rapport à la technique de séquençage automatique pour la détection d'hétéroplasmie et ont pu être confirmés par la technique de Southern blot. Dans un deuxième temps, nous avons travaillé à partir de tissu osseux provenant d'une part d'individus d'âge connu dans le cadre d'identification en Médecine Légale et d'autre part de squelettes de Sibérie Orientale identifiés par l'analyse de marqueurs ostéologiques du vieillissement. Nous avons démontré l'accumulation de l'hétéroplasmie A189G dans les individus âgés de plus de 70 ans pour ceux dont l'âge est connu, et dans les individus âgés identifiés comme tel par les indicateurs ostéologiques. Le séquençage automatique nous a permis d'identifier deux autres hétéroplasmies (T72C et A73G) présentes dans des individus âgés de plus de 50 ans dans le tissu musculaire et osseux, hétéroplasmies déjà décrites dans la littérature. L'ensemble de ces résultats peut présenter un intérêt dans la détection et l'interprétation de l'hétéroplasmie de l'ADN mitochondrial dans les études médico-légale et anthropologique

Changing patterns of public research funding in France

In this paper, we critically assess the specificity of the French research system and of its funding mode, which is accepted in most of the literature on the subject. We show that this interpretation is largely a result of the use of categories for the analysis of public funding that are not really suited to the French case. We thus develop two new categories: joint laboratories as a distinct organisational structure between public research organisations and universities; and human resources funding as a description of the specific allocation mode of CNRS (Centre National de la Recherche Scientifique) to the joint laboratories, which we consider as more similar to project funding than to core funding. We then show that the French system has changed fundamentally in the last two decades, moving towards a system much nearer to other European countries than normally assumed, albeit following a distinct evolutionary trajectory based on the gradual restructuring of existing instruments. In methodological terms, this underlines the importance of adapting the categories for the analysis of funding systems to the specificities of each national contex

Comparing the evolution of national research policies: What patterns of change?

This article presents a comparative analysis of the evolution of national research policies during the past three decades in six European countries (Austria, Italy, France, Netherlands, Norway and Switzerland), with a special focus on the changes of public project funding schemes. It systematically uses indicators on the volume of funding attributed by each instrument and agency, which have been developed in a project of the European network of excellence PRIME. A common model is identified in these countries, where project funding is the second main channel of public funding of research, but also there are considerable variations among them in the share of instruments and agencies, and in beneficiaries. There are three interesting commonalities: a strong increase of project funding volumes; a differentiation of instruments; and a general shift towards instruments oriented to thematic priorities. They also show that individual countries appear to follow quite distinct paths in the organisation setting of funding agencies, and that national differences in funding portfolios persist through tim

Variola virus in a 300-year-old Siberian mummy.

International audienceNo abstract available

Detection of the A189G mtDNA heteroplasmic mutation in relation to age in modern and ancient bones.

International audienceThe aim of this study was to demonstrate the presence of the A189G age-related point mutation on DNA extracted from bone. For this, a peptide nucleic acid (PNA)/DNA sequencing method which can determine an age threshold for the appearance of the mutation was used. Initially, work was done in muscle tissue in order to evaluate the sensitivity of the technique and afterwards in bone samples from the same individuals. This method was also applied to ancient bones from six well-preserved skeletal remains. The mutation was invariably found in muscle, and at a rate of up to 20% in individuals over 60 years old. In modern bones, the mutation was detected in individuals aged 38 years old or more, at a rate of up to 1%, but its occurrence was not systematic (only four out of ten of the individuals over 50 years old carried the heteroplasmy). For ancient bones, the mutation was also found in the oldest individuals according to osteologic markers. The study of this type of age-related mutation and a more complete understanding of its manifestation has potentially useful applications. Combined with traditional age markers, it could improve identification accuracy in forensic cases or in anthropological studies of ancient populations

Hétérogénéité des ascendances mésolithiques et steppiques dans des génomes d’individus du Néolithique et du Campaniforme du territoire français

Les transitions archéologiques se caractérisent notamment par d’importants changements démographiques et sociétaux, qui peuvent avoir des répercussions à l’échelle du génome des individus. Ainsi, la transition du Néolithique à l’âge du Bronze s’est accompagnée de contributions génomiques massives d’éleveurs originaires des steppes pontico-caspiennes aux populations locales, ces dernières résultant d’interactions complexes entre chasseurs-cueilleurs indigènes et agriculteurs d’ascendance anato..

Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %)

Focus : Les pathogènes du passé, une connaissance en devenir. : In 9. La paléogénomique, pour une lecture du passé au présent.

Focus/Chapitre/LivreEn Sibérie, les températures frôlent les -60° C. Un climat idéal pour conserver les corps, l'ADN et les traces de certaines microbes

Molecular identification of bacteria by total sequence screening: Determining the cause of death in ancient human subjects

Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17th to the 19th century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity ≥95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17th century to the early 18th century. © 2011 Thèves et al