Patch-Based Markov Models for Event Detection in Fluorescence Bioimaging

International audienceThe study of protein dynamics is essential for understanding the multi-molecular complexes at subcellular levels. Fluorescent Protein (XFP)-tagging and time-lapse fluorescence microscopy enable to observe molecular dynamics and interactions in live cells, unraveling the live states of the matter. Original image analysis methods are then required to process challenging 2D or 3D image sequences. Recently, tracking methods that estimate the whole trajectories of moving objects have been successfully developed. In this paper, we address rather the detection of meaningful events in spatio-temporal fluorescence image sequences, such as apparent stable "stocking areas" involved in membrane transport. We propose an original patch-based Markov modeling to detect spatial irregularities in fluorescence images with low false alarm rates. This approach has been developed for real image sequences of cells expressing XFP-tagged Rab proteins, known to regulate membrane trafficking

The CryoCapsule : Simplifying Correlative Light to Electron Microscopy

Correlating complementary multiple scale images of the same object is a straightforward means to decipher biological processes. Light microscopy and electron microscopy are the most commonly used imaging techniques, yet despite their complementarity, the experimental procedures available to correlate them are technically complex. We designed and manufactured a new device adapted to many biological specimens, the CryoCapsule, that simplifies the multiple sample preparation steps, which at present separate live cell fluorescence imaging from contextual high-resolution electron microscopy, thus opening new strategies for full correlative light to electron microscopy. We tested the biological application of this highly optimized tool on three different specimens: the in vitro Xenopus laevis mitotic spindle, melanoma cells over-expressing YFP-langerin sequestered in organized membranous subcellular organelles and a pigmented melanocytic cell in which the endosomal system was labeled with internalized fluorescent transferrin

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

Computational geometry-based scale-space and modal image decomposition application to light video-microscopy imaging

In this paper a framework for defining scale-spaces, based on the computational geometry concepts of a-shapes, is proposed. In this approach, objects (curves or surfaces) of increasing convexity are computed by selective sub-sampling, from the original shape to its convex hull. The relationships with the Empirical Mode Decomposition (EMD), the curvature motion-based scale-space and some operators from mathematical morphology, are studied. Finally, we address the problem of additive image/signal decomposition in fluorescence video-microscopy. An image sequence is mainly considered as a collection of 1D temporal signals, each pixel being associated with its temporal intensity variation

Functional and structural comparison of pyrrolnitrin- and iprodione-induced modifications in the class III histidine-kinase Bos1 of Botrytis cinerea.

Dicarboximides and phenylpyrroles are commonly used fungicides against plant pathogenic ascomycetes. Although their effect on fungal osmosensing systems has been shown in many studies, their modes-of-action still remain unclear. Laboratory- or field-mutants of fungi resistant to either or both fungicide categories generally harbour point mutations in the sensor histidine kinase of the osmotic signal transduction cascade.In the present study we compared the mechanisms of resistance to the dicarboximide iprodione and to pyrrolnitrin, a structural analogue of phenylpyrrole fungicides, in Botrytis cinerea. Pyrrolnitrin-induced mutants and iprodione-induced mutants of B. cinerea were produced in vitro. For the pyrrolnitrin-induced mutants, a high level of resistance to pyrrolnitrin was associated with a high level of resistance to iprodione. For the iprodione-induced mutants, the high level of resistance to iprodione generated variable levels of resistance to pyrrolnitrin and phenylpyrroles. All selected mutants showed hypersensitivity to high osmolarity and regardless of their resistance levels to phenylpyrroles, they showed strongly reduced fitness parameters (sporulation, mycelial growth, aggressiveness on plants) compared to the parental phenotypes. Most of the mutants presented modifications in the osmosensing class III histidine kinase affecting the HAMP domains. Site directed mutagenesis of the bos1 gene was applied to validate eight of the identified mutations. Structure modelling of the HAMP domains revealed that the replacements of hydrophobic residues within the HAMP domains generally affected their helical structure, probably abolishing signal transduction. Comparing mutant phenotypes to the HAMP structures, our study suggests that mutations perturbing helical structures of HAMP2-4 abolish signal-transduction leading to loss-of-function phenotype. The mutation of residues E529, M427, and T581, without consequences on HAMP structure, highlighted their involvement in signal transduction. E529 and M427 seem to be principally involved in osmotic signal transduction

A detection-based framework for the analysis of recycling in TIRF microscopy

International audienceEndocytosis/recycling and exocytosis are mechanisms conserved through evolution allowing cells to communicate with their external medium. In order to study these dynamic processes, the present work proposes a patch-based method for detecting recycling or exocytotic events at the Plasma membrane in fast TIRF microscopy combined with the computation of normalized temporal representations of those events. Evaluation, performed on TIRF sequences showing Transferrin receptor (TfR) recycling, validates a high detection rate fully compatible with an automatic data extraction and analysis of the plasma membrane recycling process

Conditional random fields for object and background estimation in fluorescence video-microscopy

International audienceThis paper describes an original method to detect XFP-tagged pro- teins in time-lapse microscopy. Non-local measurements able to capture spatial intensity variations are incorporated within a Con- ditional Random Field (CRF) framework to localize the objects of interest. The minimization of the related energy is performed by a min-cut/max-flow algorithm. Furthermore, we estimate the slowly varying background at each time step. The difference between the current image and the estimated background provides new and re- liable measurements for object detection. Experimental results on simulated and real data demonstrate the performance of the proposed method

A quantitative approach for space-time membrane trafficking orientation

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