Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i

Particle detection and tracking in fluorescence time-lapse imaging: a contrario approach

This paper proposes a probabilistic approach for the detection and the tracking of particles in fluorescent time-lapse imaging. In the presence of a very noised and poor-quality data, particles and trajectories can be characterized by an a contrario model, that estimates the probability of observing the structures of interest in random data. This approach, first introduced in the modeling of human visual perception and then successfully applied in many image processing tasks, leads to algorithms that neither require a previous learning stage, nor a tedious parameter tuning and are very robust to noise. Comparative evaluations against a well-established baseline show that the proposed approach outperforms the state of the art.Comment: Published in Journal of Machine Vision and Application

3-D Magnetotelluric Investigations for geothermal exploration in Martinique (Lesser Antilles). Characteristic Deep Resistivity Structures, and Shallow Resistivity Distribution Matching Heliborne TEM Results

Within the framework of a global French program oriented towards the development of renewable energies, Martinique Island (Lesser Antilles, France) has been extensively investigated (from 2012 to 2013) through an integrated multi-methods approach, with the aim to define precisely the potential geothermal ressources, previously highlighted (Sanjuan et al., 2003). Amongst the common investigation methods deployed, we carried out three magnetotelluric (MT) surveys located above three of the most promising geothermal fields of Martinique, namely the Anses d'Arlet, the Montagne Pel{\'e}e and the Pitons du Carbet prospects. A total of about 100 MT stations were acquired showing single or multi-dimensional behaviors and static shift effects. After processing data with remote reference, 3-D MT inversions of the four complex elements of MT impedance tensor without pre-static-shift correction, have been performed for each sector, providing three 3-D resistivity models down to about 12 to 30 km depth. The sea coast effect has been taken into account in the 3-D inversion through generation of a 3-D resistivity model including the bathymetry around Martinique from the coast up to a distance of 200 km. The forward response of the model is used to calculate coast effect coefficients that are applied to the calculated MT response during the 3-D inversion process for comparison with the observed data. 3-D resistivity models of each sector, which are inherited from different geological history, show 3-D resistivity distribution and specificities related to its volcanological history. In particular, the geothermal field related to the Montagne Pel{\'e}e strato-volcano, is characterized by a quasi ubiquitous conductive layer and quite monotonic typical resistivity distribution making interpretation difficult in terms of geothermal targets. At the opposite, the resistivity distribution of Anse d'Arlet area is radically different and geothermal target is thought to be connected to a not so deep resistive intrusion elongated along a main structural axis. Beside these interesting deep structures, we demonstrate, after analyzing the results of the recent heliborne TEM survey covering the whole Martinique, that surface resistivity distribution obtained from 3-D inversion reproduce faithfully the resistivity distribution observed by TEM. In spite of a very different sampling scale, this comparison illustrates the ability of 3-D MT inversion to take into account and reproduce static shift effects in the sub-surface resistivity distribution.Comment: Wordl Geothermal Congress 2015, Apr 2015, Melbourne, Australi

Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect

Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3d individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion- aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of "soft" intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli.Comment: PLoS Computational Biology (2013

Cine and tagged cardiovascular magnetic resonance imaging in normal rat at 1.5 T: a rest and stress study

BACKGROUND: The purpose of this study was to measure regional contractile function in the normal rat using cardiac cine and tagged cardiovascular magnetic resonance (CMR) during incremental low doses of dobutamine and at rest. METHODS: Five rats were investigated for invasive left ventricle pressure measurements and five additional rats were imaged on a clinical 1.5 T MR system using a cine sequence (11-20 phases per cycle, 0.28/0.28/2 mm) and a C-SPAMM tag sequence (18-25 phases per cycle, 0.63/1.79/3 mm, tag spacing 1.25 mm). For each slice, wall thickening (WT) and circumferential strains (CS) were calculated at rest and at stress (2.5, 5 and 10 microg/min/kg of dobutamine). RESULTS: Good cine and tagged images were obtained in all the rats even at higher heart rate (300-440 bpm). Ejection fraction and left ventricular (LV) end-systolic volume showed significant changes after each dobutamine perfusion dose (p < 0.001). Tagged CMR had the capacity to resolve the CS transmural gradient and showed a significant increase of both WT and CS at stress compared to rest. Intra and interobserver study showed less variability for the tagged technique. In rats in which a LV catheter was placed, dobutamine produced a significant increase of heart rate, LV dP/dtmax and LV pressure significantly already at the lowest infusion dose. CONCLUSION: Robust cardiac cine and tagging CMR measurements can be obtained in the rat under incremental dobutamine stress using a clinical 1.5 T MR scanner

Field-induced compensation of magnetic exchange as the origin of superconductivity above \texorpdfstring{40\,T}{40~T} in \texorpdfstring{\UTe}{UTe2}

The potential spin-triplet heavy-fermion superconductor \UTe exhibits signatures of multiple distinct superconducting phases. For field aligned along the $b$ axis, a metamagnetic transition occurs at $\mu_0$\Hm$\approx35\,$T. It is associated with magnetic fluctuations that may be beneficial for the field-enhanced superconductivity surviving up to \Hm. Once the field is tilted away from the $b$ towards the $c$ axis, a reentrant superconducting phase emerges just above \Hm. In order to better understand this remarkably field-resistant superconducting phase, we conducted magnetic-torque and magnetotransport measurements in pulsed magnetic fields. We determine the record-breaking upper critical field of $\mu_0$\Hc$\approx 73\,$T and its evolution with angle. Furthermore, the normal-state Hall effect experiences a drastic suppression indicative of a reduced band polarization above \Hm in the angular range around $30^\circ$ caused by a partial compensation between the applied field and an exchange field. This promotes the Jaccarino-Peter effect as a possible mechanism for the reentrant superconductivity above \Hm.Comment: Main text: 27 pages, 4 figure, supplement: 10 pages, 5 figure

50 ans d’histoire du livre

En 1958, Albin Michel publie L’Apparition du livre, dans la collection L’Évolution de l’humanité créée par Henri Berr. Cet ouvrage, rédigé par Lucien Febvre et Henri-Jean Martin, n’est pas le seul à traiter de la question de l’imprimerie, de la civilisation du livre, mais il innove dans sa tentative d’écrire et de penser une histoire sociale, politique et économique. Le sous-titre : « le livre, ce ferment » élargissait l’horizon et ne se limitait pas au livre « cette marchandise ». La publication de L’Apparition du livre marque aussi l’arrivée d’un jeune bibliothécaire, Henri-Jean Martin, en poste à la Bibliothèque nationale : il n’a, à cette date, que 34 ans. L’ouvrage eut à ses débuts un écho commercial limité : il deviendra un ouvrage de référence, trois fois réédité ; et surtout, Henri-Jean Martin a poursuivi cette voie féconde de recherche pluridisciplinaire, propre aussi aux années 1970. L’Enssib a organisé en 2008 un colloque pour le cinquantenaire de cette publication. Ce sont les textes retravaillés, donnés à cette occasion, dont nous proposons la lecture. Il n’est pas surprenant que nous retrouvions ici les grands noms de l’historiographie et de la pensée contemporaine, de Roger Chartier à Christian Jacob

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

The relevance of biological materials and processes to computing—aliasbioputing—has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating

Plague Circulation and Population Genetics of the Reservoir Rattus rattus: The Influence of Topographic Relief on the Distribution of the Disease within the Madagascan Focus.

International audienceBACKGROUND: Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. METHODOLOGYPRINCIPAL FINDINGS: We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150-200 km(2) within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. CONCLUSIONSSIGNIFICANCE: Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations

Placental Growth Factor Contributes to Micro-Vascular Abnormalization and Blood-Retinal Barrier Breakdown in Diabetic Retinopathy

OBJECTIVE: There are controversies regarding the pro-angiogenic activity of placental growth factor (PGF) in diabetic retinopathy (DR). For a better understanding of its role on the retina, we have evaluated the effect of a sustained PGF over-expression in rat ocular media, using ciliary muscle electrotransfer (ET) of a plasmid encoding rat PGF-1 (pVAX2-rPGF-1). MATERIALS AND METHODS: pVAX2-rPGF-1 ET in the ciliary muscle (200 V/cm) was achieved in non diabetic and diabetic rat eyes. Control eyes received saline or naked plasmid ET. Clinical follow up was carried out over three months using slit lamp examination and fluorescein angiography. After the control of rPGF-1 expression, PGF-induced effects on retinal vasculature and on the blood-external barrier were evaluated respectively by lectin and occludin staining on flat-mounts. Ocular structures were visualized through histological analysis. RESULTS: After fifteen days of rPGF-1 over-expression in normal eyes, tortuous and dilated capillaries were observed. At one month, microaneurysms and moderate vascular sprouts were detected in mid retinal periphery in vivo and on retinal flat-mounts. At later stages, retinal pigmented epithelial cells demonstrated morphological abnormalities and junction ruptures. In diabetic retinas, PGF expression rose between 2 and 5 months, and, one month after ET, rPGF-1 over-expression induced glial activation and proliferation. CONCLUSION: This is the first demonstration that sustained intraocular PGF production induces vascular and retinal changes similar to those observed in the early stages of diabetic retinopathy. PGF and its receptor Flt-1 may therefore be looked upon as a potential regulatory target at this stage of the disease