L'Estuaire, vol. 25 (1)

Éditorial -- Sainte-Luce: refuge d'un incorruptible -- Le "Vocabulaire micmac" de Joseph Hamel. L'histoire d'une cueillette de données linguistiques. Partie 2: qui est Joseph Hamel? -- La famille Desrosiers dans la région de Rimouski au XVIIIe siècle. Partie 1: implantation dans la seigneurie de Rimouski -- Les trésors du grenier -- L'année des Français -- Un grand marin gaspésien. Le capitaine Paul M. Fournier -- Matane dans les relations de voyage de Champlain: un 375e anniversaire -- La naissance d'une petite paroisse au coeur de La Mitis: le cas de Sainte-Flavie -- Nouvelles brèves -- Des livres à lire

Un ancien lac au pied de l’<i>oppidum</i> de Gergovie (Puy-de-Dôme) : interactions sociétés-milieux dans le bassin de Sarliève à l’Holocène

International audienceZiel der seit 1997 im Becken von Sarliève, am Fuß des Oppidums von Gergovia (Puy-de-Dôme) durchgeführten Studien ist es, die wechselseitigen Beziehungen zwischen Mensch und Umwelt über einen langen Zeitraum aus einem systemischen und interdisziplinären Blickwinkel zu betrachten. Die Untersuchungen beziehen sich auf ein Niederschlagsgebiet mittlerer Größe in einer Region von eminenter geschichtlicher Bedeutung. Drei Untersuchungsachsen wurden definiert: •die Analyse der Entwicklung der Umwelt im Bereich dieses Niederschlagsgebietes in Hinsicht auf seine unterschiedlichen biophysikalischen Komponenten; •die Analyse der Geschichte der Flächennutzung und der Bewirtschaftung des Beckens durch die sich ablösenden Bevölkerungsgruppen; •die Analyse der durch den Menschen hervorgerufenen Umweltbelastung (Pflanzendecke, hydrosedimentäre Kräfte). Die Ergebnisse dieser Forschungen liefern die Elemente für die Erstellung eines sozialökologischen Modells, das das von 1970-1980 für die Grande Limagne ausgearbeitete Modell ablöst. Eine Abfolge von Agrarzyklen ist deutlich erkennbar. Diese stehen im Zusammenhang mit Phasen starker menschlicher Einflussnahme, die für das Mittelneolithikum, die Früh-und Spätbronzezeit, die ältere Eisenzeit, die späte Latène-und frühe Kaiserzeit, das Mittelalter und die Neuzeit erkannt wurden. Diese Zyklen sind eng verknüpft nicht nur mit der Entwicklung der Pflanzen und der Sedimentierungsdynamik, sondern auch mit den Schwankungen des Wasserstandes. In der Bronzezeit und im Mittelalter werden Transgressionsphasen mit besonders umfangreichen und einengenden Auswirkungen nachgewiesen. Der niedrige Pegel des Paläosees in der jüngeren Eisenzeit und der frühen Kaiserzeit begünstigt dagegen die Besiedlung der Uferregionen und sogar der Sohle des Beckens, das um die Zeitenwende durch ein Entwässerungssystem vollständig trocken gelegt wird. In der ersten Hälfte des 2. Jh. v. Chr. wird mit der starken Intensivierung der Siedlungstätigkeit in sämtlichen topographischen Kontexten eine deutliche quantitative Schwelle überschritten. Die Ergebnisse der archäologischen und paläoökologischen Untersuchungen lassen die methodische Erschließung der fruchtbarsten Böden im Zusammenhang mit einem stetigen wirtschaftlichen und demographischen Wachstum erkennen, das mit dem Bau großer als “zentrale Plätze“ interpretierter Siedlungen (La Grande Borne in Aulnat, Oppida von Corent, Gergovia und Gondole) zusammenfällt. In den ersten beiden Jahrhunderten unseres Zeitalters setzt sich diese Tendenz im Rahmen der Ökonomie der villae, die sich infolge der Gründung von Augustonemetum, der neuen Hauptstadt der avernischen civitas herausbildet, mit der von den Geländeformen unabhängigen Ausweitung der landwirtschaftlichen Nutzung auf das gesamte Becken fort. In der Spätantike und im frühen Mittelalter gewinnt der Sumpf in einem feuchteren Klima wieder an Boden, besonders durch die grundlegenden Veränderungen in der Art und Weise das Gebiet zu nutzen. Die mittelalterlichen Texte und die neuzeitliche Ikonographie bezeugen die Existenz eines Sees, der zu Beginn des 17. Jh. schließlich endgültig trockengelegt wird.The aim of the researches conducted since 1997 in the basin of Sarliève, at the foot of the oppidum of Gergovia (Puy-de-Dôme), is to detect in a systemic and interdisciplinary perspective the longlasting interactions societies/environment on the scale of a mediumsized basin located in a major area from an historical point of view. Three axes have been defined : * the characterization of the evolution of the environment on the scale of the basin inside its various biophysical components ; * the characterization of the history of land occcupation and of the exploitation of environment by successive populations settled in the basin ; * the characterization of the impact of human pressure on the environment (plant cover, hydro-sedimentary dynamics). Results provide elements of a new socioenvironmental model after the model completed in Limagne in the 1970'-1980'. A succession of land cycles has been detected and connected to phases of strong human pressure identified for Middle Neolithic, Early and Late Bronze Age, Early Iron Age, Early Empire, Middle Age and Modern period. These cycles are tightly connected with vegetation evolution and sedimentary dynamics but also with vertical variations of the lake level. Some phases of encroachment, particularly wide and constraining, have been revealed for Bronze Age and Middle Age. The low level of the lake during the Late Iron Age and the Early Empire in the other hand is favourable to the occupation of the edges and even at the bottom of the basin which is entirely drained due to a draining system at the turn of our era. A definite quantitative step, during the first half of the 2nd century BC, is represented by the high densification of the populated area in all kinds of physical units. Archaeological and environmental datas reveal a methodic exploitation of the most fertile lands in a context of continuous economic and demographic environment which coincides with the birth of towns identified as "central places" (such as la Grande Borne at Aulnat and the oppida of Corent at Veyre-Monton, Gergovia at La Roche-Blanche and Gondole at Le Cendre). This tendency goes on during the first two centuries AD, with the generalization of agrosystem to the whole basin, for any kind of relief, in the context of economic estates growing since the foundation of Augustonemetum, the new capital of the Arverni. The return of marsh in Late Antiquity and Early Middle Age is due to a more humid climate and to deep changes in the methods of environmental management. A real lake is attested by medieval sources and modern iconography and is definitely dried out at the beginning of the 17th century.Les recherches conduites depuis 1997 dans le bassin de Sarliève, au pied de l'oppidum de Gergovie (Puy-de-Dôme), visent à appréhender, dans une perspective systémique et interdisciplinaire, les interactions sociétés-milieux dans la longue durée, à l'échelle d'un bassin-versant de taille moyenne localisé dans une zone de première importance sur le plan historique. Trois axes de recherche ont été définis : * la caractérisation de l'évolution du milieu à l'échelle du bassin-versant dans ses différentes composantes biophysiques ; * la caractérisation de l'histoire de l'occupation du sol et de l'exploitation du milieu par les populations successives établies dans le bassin ; * la caractérisation de l'impact de la pression anthropique sur le milieu (couverture végétale, dynamiques hydrosédimentaires). Les résultats obtenus fournissent les éléments d'un modèle socio-environnemental qui renouvelle celui élaboré pour la Grande Limagne dans les années 1970-1980. Une succession de cycles agraires est clairement mise en évidence. Ceux-ci sont liés à des phases de forte pression humaine identifiées au Néolithique moyen, au Bronze ancien, au Bronze final, au premier âge du Fer, à La Tène finale, au Haut-Empire, au Moyen Âge et à l'époque moderne. Ces cycles sont étroitement corrélés avec l'évolution de la végétation et la dynamique sédimentaire, mais également avec les variations verticales du plan d'eau. Des phases de transgression particulièrement amples et contraignantes sont mises en évidence durant l'âge du Bronze et le Moyen Âge. Le bas niveau du paléolac durant le second âge du Fer et le Haut-Empire est, en revanche, propice à l'occupation des bordures et même du fond de la cuvette, qui est complètement asséchée grâce à un système de drainage aménagé aux environs du changement d'ère. Un seuil quantitatif très net est franchi dans la première moitié du IIe s. av. J.-C., avec la forte densification de l'habitat dans tous les types d'unités physiques. Les données archéologiques et paléoenvironnementales traduisent la mise en valeur méthodique des sols les plus fertiles, dans un contexte de croissance économique et démographique continue qui coïncide avec l'apparition de vastes agglomérations interprétées comme des " places centrales " (agglomération de la Grande Borne à Aulnat, oppida de Corent à Veyre-Monton, Gergovie à La Roche-Blanche et Gondole au Cendre). Cette tendance se poursuit durant les deux premiers siècles de notre ère, avec la généralisation de l'agrosystème à l'ensemble du bassin, quels que soient les types de reliefs, dans le cadre de l'économie domaniale qui se développe à la suite de la fondation d'Augustonemetum, nouvelle capitale de la cité arverne. La fin de l'Antiquité et le haut Moyen Âge voient le retour du marais à la faveur d'un climat plus humide et, surtout, de profonds changements dans les modalités de gestion du milieu. Un véritable lac est attesté par les textes médiévaux et par l'iconographie moderne. Il est définitivement asséché au début du XVIIe s

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t

A transcriptomic analysis of human centromeric and pericentric sequences in normal and tumor cells

Although there is now evidence that the expression of centromeric (CT) and pericentric (PCT) sequences are key players in major genomic functions, their transcriptional status in human cells is still poorly known. The main reason for this lack of data is the complexity and high level of polymorphism of these repeated sequences, which hampers straightforward analyses by available transcriptomic approaches. Here a transcriptomic macro-array dedicated to the analysis of CT and PCT expression is developed and validated in heat-shocked (HS) HeLa cells. For the first time, the expression status of CT and PCT sequences is analyzed in a series of normal and cancer human cells and tissues demonstrating that they are repressed in all normal tissues except in the testis, where PCT transcripts are found. Moreover, PCT sequences are specifically expressed in HS cells in a Heat-Shock Factor 1 (HSF1)-dependent fashion, and we show here that another independent pathway, involving DNA hypo-methylation, can also trigger their expression. Interestingly, CT and PCT were found illegitimately expressed in somatic cancer samples, whereas PCT were repressed in testis cancer, suggesting that the expression of CT and PCT sequences may represent a good indicator of epigenetic deregulations occurring in response to environmental changes or in cell transformation

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil

New Antibody-Free Mass Spectrometry-Based Quantification Reveals That C9ORF72 Long Protein Isoform Is Reduced in the Frontal Cortex of Hexanucleotide-Repeat Expansion Carriers

Frontotemporal dementia (FTD) is a fatal neurodegenerative disease characterized by behavioral and language disorders. The main genetic cause of FTD is an intronic hexanucleotide repeat expansion (G4C2)n in the C9ORF72 gene. A loss of function of the C9ORF72 protein associated with the allele-specific reduction of C9ORF72 expression is postulated to contribute to the disease pathogenesis. To better understand the contribution of the loss of function to the disease mechanism, we need to determine precisely the level of reduction in C9ORF72 long and short isoforms in brain tissue from patients with C9ORF72 mutations. In this study, we developed a sensitive and robust mass spectrometry (MS) method for quantifying C9ORF72 isoform levels in human brain tissue without requiring antibody or affinity reagent. An optimized workflow based on surfactant-aided protein extraction and pellet digestion was established for optimal recovery of the two isoforms in brain samples. Signature peptides, common or specific to the isoforms, were targeted in brain extracts by multiplex MS through the parallel reaction monitoring mode on a Quadrupole–Orbitrap high resolution mass spectrometer. The assay was successfully validated and subsequently applied to frontal cortex brain samples from a cohort of FTD patients with C9ORF72 mutations and neurologically normal controls without mutations. We showed that the C9ORF72 short isoform in the frontal cortices is below detection threshold in all tested individuals and the C9ORF72 long isoform is significantly decreased in C9ORF72 mutation carriers

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea–specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops

A targeted next-generation sequencing assay for the molecular diagnosis of genetic disorders with orodental involvement.

BACKGROUND: Orodental diseases include several clinically and genetically heterogeneous disorders that can present in isolation or as part of a genetic syndrome. Due to the vast number of genes implicated in these disorders, establishing a molecular diagnosis can be challenging. We aimed to develop a targeted next-generation sequencing (NGS) assay to diagnose mutations and potentially identify novel genes mutated in this group of disorders. METHODS: We designed an NGS gene panel that targets 585 known and candidate genes in orodental disease. We screened a cohort of 101 unrelated patients without a molecular diagnosis referred to the Reference Centre for Oro-Dental Manifestations of Rare Diseases, Strasbourg, France, for a variety of orodental disorders including isolated and syndromic amelogenesis imperfecta (AI), isolated and syndromic selective tooth agenesis (STHAG), isolated and syndromic dentinogenesis imperfecta, isolated dentin dysplasia, otodental dysplasia and primary failure of tooth eruption. RESULTS: We discovered 21 novel pathogenic variants and identified the causative mutation in 39 unrelated patients in known genes (overall diagnostic rate: 39%). Among the largest subcohorts of patients with isolated AI (50 unrelated patients) and isolated STHAG (21 unrelated patients), we had a definitive diagnosis in 14 (27%) and 15 cases (71%), respectively. Surprisingly, COL17A1 mutations accounted for the majority of autosomal-dominant AI cases. CONCLUSIONS: We have developed a novel targeted NGS assay for the efficient molecular diagnosis of a wide variety of orodental diseases. Furthermore, our panel will contribute to better understanding the contribution of these genes to orodental disease. TRIAL REGISTRATION NUMBERS: NCT01746121 and NCT02397824.journal articleresearch support, non-u.s. gov't2016 Feb2015 10 26importe

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