Processus de Cox marqué dirigé par un environnement prédit : application à la répartition spatiale de juvéniles en forêt tropicale humide

International audienceUn des points faibles des modèles de dynamique forestière spatialement explicites est la modélisation du recrutement. Un inventaire détaillé du peuplement et des conditions environnementales a permis de mettre en évidence les effets de ces deux facteurs sur la densité locale de juvéniles. Mais en pratique, la collecte de telles données est coûteuse et ne peut être réalisée à grande échelle : seule une partie des juvéniles est échantillonnée et l'environnement n'est connu que partiellement. L'objectif est ici de proposer une approche pour prédire la répartition spatiale et le génotype des juvéniles sur la base d'un échantillonnage raisonnable des juvéniles, des adultes et de l'environnement. La position des juvéniles est considérée comme la réalisation d'un processus ponctuel marqué, les marques étant constituées par les génotypes. L'intensité du processus traduit les mécanismes de dispersion à l'origine de l'organisation spatiale et de la diversité génétique des juvéniles. L'intensité dépend de la survie des graines, qui dépend elle-même des conditions environnementales. Il est donc nécessaire de prédire l'environnement sur toute la zone d'étude. L'environnement, représenté par un champ aléatoire multivarié, est prédit grâce à un modèle hiérarchique spatial capable de traiter simultanément des variables de nature différente. Contrairement aux modèles existants où les variables environnementales sont considérées comme connues, le modèle de recrutement proposé prend en compte les erreurs liées à la prédiction de l'environnement. La méthode est appliquée à la prédiction du recrutement des juvéniles en forêt tropicale (Guyane française)

Ours, hommes, hyènes : qui a occupé la grotte de Bourdette (Sainte-Colombe-en-Bruilhois, Lot-et-Garonne, France) ?

À côté d’abondants indices d’occupation par l’Ours des cavernes (ossements, griffades, bauges), la grotte de Bourdette a livré les restes d’une vingtaine d’autres espèces ainsi que quelques vestiges lithiques. Une telle association de vestiges est a priori incompatible avec un fonctionnement seul de la grotte comme tanière d’Ours. Pour parvenir à distinguer les différentes occupations de Bourdette, et pour en établir la chronologie, une approche interdisciplinaire est ici développée en incluant l’étude taphonomique des restes osseux, l’analyse typotechnologique des pièces lithiques et la confrontation des différents éléments de chronologie disponibles (biochronologie, datations radiocarbone, attribution chronoculturelle des industries lithiques). À Bourdette se sont succédé ours et hyènes qui ont utilisé la grotte comme tanière et repaire, les dernières y ayant ramené les ossements de leurs proies (essentiellement bovinés et chevaux). Les vestiges lithiques semblent eux provenir de remaniements depuis le plateau, sans qu’aucune réelle occupation humaine du site ne puisse être démontrée. Les éléments de biochronologie et les datations radiocarbone disponibles s’accordent pour placer les occupations du site aux alentours de 40 ka cal. BP. La présence d’ossements d’Ours rongés par les hyènes permet d’affirmer qu’au moins une partie des occupations de la grotte par les ours et les hyènes a été pseudo-contemporaine. À Bourdette, les os sont particulièrement émoussés, possiblement à la suite des circulations ursines (« charriage à sec ») : cette atteinte est si omniprésente qu’elle a considérablement restreint l’étude taphonomique, obligeant à reconsidérer les critères classiquement utilisés en taphonomie osseuse.In Bourdette, if evidences of cave bear occupation are omnipresent (in the form of bones, claw marks and beds), the cave also delivered remains of more than a dozen other species as well as some lithic artifacts. Such a combination of different materials cannot be fully explained by the sole function of the cave as a bear den. In order to distinguish the different types of occupations in Bourdette and to establish their chronology, this paper proposes an interdisciplinary study that brings together data from faunal taphonomy, lithic typotechnology, biochronology and radiocarbon dating. Both Cave bear and Hyena used Bourdette as a den, the latter bringing remains of its preys in the cave (mostly Bovines and Horse). The presence of lithic artifacts in Bourdette seems only to be the result of post-depositional transport, so that men probably never occupied the cave themselves. Biochronological data and radiocarbon dates both date the deposits around 40 ka cal. BP. Some bear bones were gnawed by hyenas, thus indicating that occupations of the cave by the two carnivores were, at least in part, broadly contemporaneous. The intensity of polishing is particularly intense on Bourdette bones, probably due to bear circulations in the cave (“charriage à sec”), to the point that procedures used commonly in bone taphonomy were severely undermined

Mineral precipitation-induced porosity reduction and its effect on transport parameters in diffusion-controlled porous media

Background: In geochemically perturbed systems where porewater and mineral assemblages are unequilibrated the processes of mineral precipitation and dissolution may change important transport properties such as porosity and pore diffusion coefficients. These reactions might alter the sealing capabilities of the rock by complete pore-scale precipitation (cementation) of the system or by opening new migration pathways through mineral dissolution. In actual 1D continuum reactive transport codes the coupling of transport and porosity is generally accomplished through the empirical Archie\u27s law. There is very little reported data on systems with changing porosity under well controlled conditions to constrain model input parameters. In this study celestite (SrSO4) was precipitated in the pore space of a compacted sand column under diffusion controlled conditions and the effect on the fluid migration properties was investigated by means of three complementary experimental approaches: (1) tritiated water (HTO) tracer through diffusion, (2) computed micro-tomography (μ-CT) imaging and (3) post-mortem analysis of the precipitate (selective dissolution, SEM/EDX). Results: The through-diffusion experiments reached steady state after 15days, at which point celestite precipitation ceased and the non-reactive HTO flux became constant. The pore space in the precipitation zone remained fully connected using a 6μm μ-CT spatial resolution with 25% porosity reduction in the approx. 0.35mm thick dense precipitation zone. The porosity and transport parameters prior to pore-scale precipitation were in good agreement with a porosity of 0.42±0.09 (HTO) and 0.40±0.03 (μ-CT), as was the mass of SrSO4 precipitate estimated by μ-CT at 25±5mg and selective dissolution 21.7±0.4mg, respectively. However, using this data as input parameters the 1D single continuum reactive transport model was not able to accurately reproduce both the celestite precipitation front and the remaining connected porosity. The model assumed there was a direct linkage of porosity to the effective diffusivity using only one cementation value over the whole porosity range of the system investigated. Conclusions: The 1D single continuous model either underestimated the remaining connected porosity in the precipitation zone, or overestimated the amount of precipitate. These findings support the need to implement a modified, extended Archie\u27s law to the reactive transport model and show that pore-scale precipitation transforms a system (following Archie\u27s simple power law with only micropores present) towards a system similar to clays with micro- and nanoporosity. © 2015 Chagneau et al

A densification mechanism to model the mechanical effect of methane hydrates in sandy sediments

Recent pore‐scale observations and geomechanical investigations suggest the lack of true cohesion in methane hydrate‐bearing sediments (MHBSs) and propose that their mechanical behavior is governed by kinematic constrictions at pore‐scale. This paper presents a constitutive model for MHBS, which does not rely on physical bonding between hydrate crystals and sediment grains but on the densification effect that pore invasion with hydrate has on the sediment mechanical properties. The Hydrate‐CASM extends the critical state model Clay and Sand Model (CASM) by implementing the subloading surface model and introducing the densification mechanism. The model suggests that the decrease of the sediment available void volume during hydrate formation stiffens its structure and has a similar mechanical effect as the increase of sediment density. In particular, the model attributes stress‐strain changes observed in MHBS to the variations in sediment available void volume with hydrate saturation and its consequent effect on isotropic yield stress and swelling line slope. The model performance is examined against published experimental data from drained triaxial tests performed at different confining stress and with distinct hydrate saturation and morphology. Overall, the simulations capture the influence of hydrate saturation in both the magnitude and trend of the stiffness, shear strength, and volumetric response of synthetic MHBS. The results are validated against those obtained from previous mechanical models for MHBS that examine the same experimental data. The Hydrate‐CASM performs similarly to previous models, but its formulation only requires one hydrate‐related empirical parameter to express changes in the sediment elastic stiffness with hydrate saturation

In vivo Bioluminescence Imaging of Ca(2+) Signalling in the Brain of Drosophila

Many different cells' signalling pathways are universally regulated by Ca(2+) concentration [Ca(2+)] rises that have highly variable amplitudes and kinetic properties. Optical imaging can provide the means to characterise both the temporal and spatial aspects of Ca(2+) signals involved in neurophysiological functions. New methods for in vivo imaging of Ca(2+) signalling in the brain of Drosophila are required for probing the different dynamic aspects of this system. In studies here, whole brain Ca(2+) imaging was performed on transgenic flies with targeted expression of the bioluminescent Ca(2+) reporter GFP-aequorin (GA) in different neural structures. A photon counting based technique was used to undertake continuous recordings of cytosolic [Ca(2+)] over hours. Time integrals for reconstructing images and analysis of the data were selected offline according to the signal intensity. This approach allowed a unique Ca(2+) response associated with cholinergic transmission to be identified by whole brain imaging of specific neural structures. Notably, [Ca(2+)] transients in the Mushroom Bodies (MBs) following nicotine stimulation were accompanied by a delayed secondary [Ca(2+)] rise (up to 15 min. later) in the MB lobes. The delayed response was sensitive to thapsigargin, suggesting a role for intra-cellular Ca(2+) stores. Moreover, it was reduced in dunce mutant flies, which are impaired in learning and memory. Bioluminescence imaging is therefore useful for studying Ca(2+) signalling pathways and for functional mapping of neurophysiological processes in the fly brain

Defense Against Cannibalism: The SdpI Family of Bacterial Immunity/Signal Transduction Proteins

The SdpI family consists of putative bacterial toxin immunity and signal transduction proteins. One member of the family in Bacillus subtilis, SdpI, provides immunity to cells from cannibalism in times of nutrient limitation. SdpI family members are transmembrane proteins with 3, 4, 5, 6, 7, 8, or 12 putative transmembrane α-helical segments (TMSs). These varied topologies appear to be genuine rather than artifacts due to sequencing or annotation errors. The basic and most frequently occurring element of the SdpI family has 6 TMSs. Homologues of all topological types were aligned to determine the homologous TMSs and loop regions, and the positive-inside rule was used to determine sidedness. The two most conserved motifs were identified between TMSs 1 and 2 and TMSs 4 and 5 of the 6 TMS proteins. These showed significant sequence similarity, leading us to suggest that the primordial precursor of these proteins was a 3 TMS–encoding genetic element that underwent intragenic duplication. Various deletional and fusional events, as well as intragenic duplications and inversions, may have yielded SdpI homologues with topologies of varying numbers and positions of TMSs. We propose a specific evolutionary pathway that could have given rise to these distantly related bacterial immunity proteins. We further show that genes encoding SdpI homologues often appear in operons with genes for homologues of SdpR, SdpI’s autorepressor. Our analyses allow us to propose structure–function relationships that may be applicable to most family members

Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus

Acetobacter species have been used for brewing traditional vinegar and are known to have genetic instability. To clarify the mutability, Acetobacter pasteurianus NBRC 3283, which forms a multi-phenotype cell complex, was subjected to genome DNA sequencing. The genome analysis revealed that there are more than 280 transposons and five genes with hyper-mutable tandem repeats as common features in the genome consisting of a 2.9-Mb chromosome and six plasmids. There were three single nucleotide mutations and five transposon insertions in 32 isolates from the cell complex. The A. pasteurianus hyper-mutability was applied for breeding a temperature-resistant strain grown at an unviable high-temperature (42°C). The genomic DNA sequence of a heritable mutant showing temperature resistance was analyzed by mutation mapping, illustrating that a 92-kb deletion and three single nucleotide mutations occurred in the genome during the adaptation. Alpha-proteobacteria including A. pasteurianus consists of many intracellular symbionts and parasites, and their genomes show increased evolution rates and intensive genome reduction. However, A. pasteurianus is assumed to be a free-living bacterium, it may have the potentiality to evolve to fit in natural niches of seasonal fruits and flowers with other organisms, such as yeasts and lactic acid bacteria

Etude de la colibactine dans les infections urinaires

Urinary tract infections (UTIs) are among the most common community-acquired or nosocomial bacterial infections. They are most often caused by uropathogenic Escherichia coli (UPECs). We assembled a collection of UPECs from 223 patients suffering from community-acquired UTIs in order to understand the role and impact of potential virulence factors of UPECs that have been little studied until now. In particular, we showed that 43% of UPECs carried a pathogenicity island, the pks island. It encodes a machinery for the synthesis of various secondary metabolites including a genotoxin, colibactin. In commensal intestinal E. coli, colibactin is suspected of promoting colorectal cancer. My aim was to study the impact and role of the pks island and its metabolites in the pathophysiology of UTIs. We have shown that the pks biosynthesis machinery is active in humans during UTI. For the first time, we found a marker metabolite for colibactin production in more than half of the urine of patients with pks+ UPEC UTIs. These clinical isolates of pks+ UPECs are genotoxic in vitro. By reproducing UTI in a mouse model, we demonstrated the expression of the pks machinery in intracellular bacterial communities formed in bladder cells and demonstrated the presence of DNA damage in urothelial cells related to colibactin production. This damage occurs even in KRT14+ progenitor cells of the bladder. This study suggests that UTIs may have longer-term consequences for the host, particularly in bladder cancer. In perspective, it seems also appropriate to question the current recommendation of no treatment for asymptomatic bacteriuria, which can persist for months or even years even though they are caused by strains that frequently carry the pks island and are genotoxic.Les infections urinaires (UTI) sont parmi les infections bactériennes communautaires ou nosocomiales les plus fréquentes. Elles sont le plus souvent causées par des Escherichia coli uropathogènes (UPEC). Nous avons constitué une collection d’UPEC issus de 223 patients souffrants d’UTI communautaires afin de comprendre le rôle et l’impact de potentiels facteurs de virulence des UPEC jusque-là peu étudiés. En particulier nous avons montré que 43% des UPEC portaient un îlot de pathogénicité, l’îlot pks. Il code pour une machinerie de synthèse de différents métabolites secondaires dont une génotoxine, la colibactine. Chez les E. coli commensales intestinales, la colibactine est suspectée de promouvoir le cancer colorectal. Mon objectif a été d’étudier l’impact et le rôle de l’îlot pks et de ses métabolites dans la physiopathologie des UTI. Nous avons montré que la machinerie de biosynthèse pks était active chez l’Homme durant l’UTI. Nous avons ainsi retrouvé pour la première fois un métabolite témoin de la production de la colibactine dans plus de la moitié des urines des patients atteints d’une UTI à UPEC pks+. Ces isolats cliniques d’UPEC pks+ sont génotoxiques in vitro. En reproduisant une UTI en modèle murin, nous avons démontré l’expression de la machinerie pks dans les communautés bactériennes intracellulaires formées dans les cellules vésicales et nous avons mis en évidence la présence de dommages à l’ADN dans les cellules urothéliales liés à la production de colibactine. Ces dommages surviennent y compris dans des cellules KRT14+ progénitrices de la vessie. Cette étude suggère que les UTI pourraient par ce biais avoir des conséquences à plus long terme sur l’hôte, en particulier dans le cancer de la vessie. En perspective, il convient également de questionner l'actuelle recommandation d'absence de traitement des bactériuries asymptomatiques, qui peuvent ainsi persister des mois voire des années alors qu’elles sont causées par des souches fréquemment porteuses de l’îlot pks et génotoxiques