A Patch-Based Method for Repetitive and Transient Event Detection in Fluorescence Imaging

Automatic detection and characterization of molecular behavior in large data sets obtained by fast imaging in advanced light microscopy become key issues to decipher the dynamic architectures and their coordination in the living cell. Automatic quantification of the number of sudden and transient events observed in fluorescence microscopy is discussed in this paper. We propose a calibrated method based on the comparison of image patches expected to distinguish sudden appearing/vanishing fluorescent spots from other motion behaviors such as lateral movements. We analyze the performances of two statistical control procedures and compare the proposed approach to a frame difference approach using the same controls on a benchmark of synthetic image sequences. We have then selected a molecular model related to membrane trafficking and considered real image sequences obtained in cells stably expressing an endocytic-recycling trans-membrane protein, the Langerin-YFP, for validation. With this model, we targeted the efficient detection of fast and transient local fluorescence concentration arising in image sequences from a data base provided by two different microscopy modalities, wide field (WF) video microscopy using maximum intensity projection along the axial direction and total internal reflection fluorescence microscopy. Finally, the proposed detection method is briefly used to statistically explore the effect of several perturbations on the rate of transient events detected on the pilot biological model

Les caractères du détritisme paléogène aux abords du Massif du Pelvoux (Alpes externes méridionales)

Mémoire HS n° 13 - Géologie Alpine : Le détritisme dans le Sud-Est de la France - Colloque Association des Géologues du Sud-est - Grenoble 11-12 décembre 1986Aux abords du Pelvoux, la sédimentation tertiaire montre des apports détritiques importants. La nature et la répartition du flux terrigène sont contrôlées par la nature du substratum qui subit la transgression nummulitique ainsi que par le jeu d ' accidents synsédimentaires. Partout, la base de la série, ainsi que son couronnement par les couches détritiques terminales (Grès de Saint-Disdier ; Grès du Champsaur et Olistostrome) attestent de ce détritisme. Néanmoins le SE et l'E du Pelvoux montrent souvent un détritisme plus important, soit que la totalité de la série -ou presque- se trouve représentée par les seuls Grès du Champsaur, soit que le détritisme grossier (à olistolites souvent) envahisse la série paléogène sur pratiquement toute sa hauteur

The Tropical Seagrass Halophila stipulacea: Reviewing What We Know From Its Native and Invasive Habitats, Alongside Identifying Knowledge Gaps

Halophila stipulacea is a small tropical seagrass, native to the Red Sea, Persian Gulf, and the Indian Ocean. It invaded the Mediterranean Sea 150 years ago as a Lessepsian migrant, but so far has remained in insulated, small populations across this basin. Surprisingly, in 2002 it was reported in the Caribbean Sea, where within less than two decades it spread to most of the Caribbean Island nations and reaching the South American continent. Unlike its invasion of Mediterranean, in the Caribbean H. stipulacea creates large, continuous populations in many areas. Reports from the Caribbean demonstrated the invasiveness of H. stipulacea by showing that it displaces local Caribbean seagrass species. The motivation for this review comes from the necessity to unify the existing knowledge on several aspects of this species in its native and invasive habitats, identify knowledge gaps and develop a critical strategy to understand its invasive capacity and implement an effective monitoring and conservation plan to mitigate its potential spread outside its native ranges. We systematically reviewed 164 studies related to H. stipulacea to create the "Halophila stipulacea database." This allowed us to evaluate the current biological, ecological, physiological, biochemical, and molecular knowledge of H. stipulacea in its native and invasive ranges. Here we (i) discuss the possible environmental conditions and plant mechanisms involved in its invasiveness, (ii) assess the impact of H. stipulacea on native seagrasses and ecosystem functions in the invaded regions, (iii) predict the ability of this species to invade European and transoceanic coastal waters, (iv) identify knowledge gaps that should be addressed to better understand the biology and ecology of this species both in its native and non-native habitats, which would improve our ability to predict H. stipulacea's potential to expand into new areas in the future. Considering the predicted climate change scenarios and exponential human pressures on coastal areas, we stress the need for coordinated global monitoring and mapping efforts that will record changes in H. stipulacea and its associated communities over time, across its native, invasive and prospective distributional ranges. This will require the involvement of biologists, ecologists, economists, modelers, managers, and local stakeholder

The Tumor Necrosis Factor Alpha and Interleukin 6 Auto-paracrine Signaling Loop Controls Mycobacterium avium Infection via Induction of IRF1/IRG1 in Human Primary Macrophages

Macrophages sense and respond to pathogens by induction of antimicrobial and inflammatory programs to alert other immune cells and eliminate the infectious threat. We have previously identified the transcription factor IRF1 to be consistently activated in macrophages during Mycobacterium avium infection, but its precise role during infection is not clear. Here, we show that tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6) autocrine/paracrine signaling contributes to controlling the intracellular growth of M. avium in human primary macrophages through activation of IRF1 nuclear translocation and expression of IRG1, a mitochondrial enzyme that produces the antimicrobial metabolite itaconate. Small interfering RNA (siRNA)-mediated knockdown of IRF1 or IRG1 increased the mycobacterial load, whereas exogenously provided itaconate was bacteriostatic at high concentrations. While the overall level of endogenous itaconate was low in M. avium-infected macrophages, the repositioning of mitochondria to M. avium phagosomes suggests a mechanism by which itaconate can be delivered directly to M. avium phagosomes in sufficient quantities to inhibit growth. Using mRNA hybridization, we further show that uninfected bystander cells actively contribute to the resolution of infection by producing IL-6 and TNF-α, which, via paracrine signaling, activate IRF1/IRG1 and strengthen the antimicrobial activity of infected macrophages. This mechanism contributes to the understanding of why patients on anti-inflammatory treatment, e.g., with tocilizumab or infliximab, can be more susceptible to mycobacterial disease

Persistent mycobacteria evade an antibacterial program mediated by phagolysosomal TLR7/8/MyD88 in human primary macrophages.

Pathogenic mycobacteria reside in macrophages where they avoid lysosomal targeting and degradation through poorly understood mechanisms proposed to involve arrest of phagosomal maturation at an early endosomal stage. A clear understanding of how this relates to host defenses elicited from various intracellular compartments is also missing and can only be studied using techniques allowing single cell and subcellular analyses. Using confocal imaging of human primary macrophages infected with Mycobacterium avium (Mav) we show evidence that Mav phagosomes are not arrested at an early endosomal stage, but mature to a (LAMP1+/LAMP2+/CD63+) late endosomal/phagolysosomal stage where inflammatory signaling and Mav growth restriction is initiated through a mechanism involving Toll-like receptors (TLR) 7 and 8, the adaptor MyD88 and transcription factors NF-κB and IRF-1. Furthermore, a fraction of the mycobacteria re-establish in a less hostile compartment (LAMP1-/LAMP2-/CD63-) where they not only evade destruction, but also recognition by TLRs, growth restriction and inflammatory host responses that could be detrimental for intracellular survival and establishment of chronic infections

Advanced microcopy to study tracking and spatiotemporal organization of intracellular membranes

International audienceThe study of membrane plasticity and the role of molecular "machines" in the control of biogenesis of the endo-cellular membranes have highlighted the crucial role of the "Rab" GTPases family as organizing centers of functional molecular platforms in membrane sub-domains. Yet, to understand the regulation and coordination of these molecular assemblies, which are responsible for cellular dynamic architectures, a more global vision, the development and the correlation of approaches at different spatial and temporal scales are needed. Focused biological models will be presented and will serve as guidelines that consider the mosaic of "Rabs domains" in particular at the plasma membrane within the context of recycling and exocytosis processes of fluorescently labeled cargos. In these In Vivo biological contexts, approaches aimed to measure and understand the multi-specific nature of these complexes have been developed. Our overall target is to model and assess the functional coordination between the different molecular machineries involved in the biogenesis of membrane sub-domains and their regulation. However, considering the "fickle" nature of such dynamic architectures, the current performance of image acquisition systems and the analytical tools at our disposal, many technological challenges must be overcome. Moreover, to extract maximum information on the same sample, the development of an adapted microscopy, correlating different modalities, is needed. Last but not least, accurate image descriptors, allowing automatic detection and classification of molecular behaviors in space and time, are indispensable

Advanced microcopy to study tracking and spatiotemporal organization of intracellular membranes

International audienceThe study of membrane plasticity and the role of molecular "machines" in the control of biogenesis of the endo-cellular membranes have highlighted the crucial role of the "Rab" GTPases family as organizing centers of functional molecular platforms in membrane sub-domains. Yet, to understand the regulation and coordination of these molecular assemblies, which are responsible for cellular dynamic architectures, a more global vision, the development and the correlation of approaches at different spatial and temporal scales are needed. Focused biological models will be presented and will serve as guidelines that consider the mosaic of "Rabs domains" in particular at the plasma membrane within the context of recycling and exocytosis processes of fluorescently labeled cargos. In these In Vivo biological contexts, approaches aimed to measure and understand the multi-specific nature of these complexes have been developed. Our overall target is to model and assess the functional coordination between the different molecular machineries involved in the biogenesis of membrane sub-domains and their regulation. However, considering the "fickle" nature of such dynamic architectures, the current performance of image acquisition systems and the analytical tools at our disposal, many technological challenges must be overcome. Moreover, to extract maximum information on the same sample, the development of an adapted microscopy, correlating different modalities, is needed. Last but not least, accurate image descriptors, allowing automatic detection and classification of molecular behaviors in space and time, are indispensable