Deep Learning Improves Macromolecule Identification in 3D Cellular Cryo-Electron Tomograms

International audienceCryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and reconstruction artifacts, as well as the presence of many molecular species in the crowded volumes. Here, we present DeepFinder, a computational procedure that uses artificial neural networks to simultaneously localize multiple classes of macromolecules. Once trained, the inference stage of DeepFinder is faster than template matching and performs better than other competitive deep learning methods at identifying macromolecules of various sizes in both synthetic and experimental datasets. On cellular cryo-ET data, DeepFinder localized membrane-bound and cytosolic ribosomes (~3.2 MDa), Rubisco (~560 kDa soluble complex), and photosystem II (~550 kDa membrane complex) with an accuracy comparable to expert-supervised ground truth annotations. DeepFinder is therefore a promising algorithm for the semi-automated analysis of a wide range of molecular targets in cellular tomograms

The BLLAST field experiment: Boundary-Layer late afternoon and sunset turbulence

Due to the major role of the sun in heating the earth's surface, the atmospheric planetary boundary layer over land is inherently marked by a diurnal cycle. The afternoon transition, the period of the day that connects the daytime dry convective boundary layer to the night-time stable boundary layer, still has a number of unanswered scientific questions. This phase of the diurnal cycle is challenging from both modelling and observational perspectives: it is transitory, most of the forcings are small or null and the turbulence regime changes from fully convective, close to homogeneous and isotropic, toward a more heterogeneous and intermittent state. These issues motivated the BLLAST (Boundary-Layer Late Afternoon and Sunset Turbulence) field campaign that was conducted from 14 June to 8 July 2011 in southern France, in an area of complex and heterogeneous terrain. A wide range of instrumented platforms including full-size aircraft, remotely piloted aircraft systems, remote-sensing instruments, radiosoundings, tethered balloons, surface flux stations and various meteorological towers were deployed over different surface types. The boundary layer, from the earth's surface to the free troposphere, was probed during the entire day, with a focus and intense observation periods that were conducted from midday until sunset. The BLLAST field campaign also provided an opportunity to test innovative measurement systems, such as new miniaturized sensors, and a new technique for frequent radiosoundings of the low troposphere. Twelve fair weather days displaying various meteorological conditions were extensively documented during the field experiment. The boundary-layer growth varied from one day to another depending on many contributions including stability, advection, subsidence, the state of the previous day's residual layer, as well as local, meso- or synoptic scale conditions. Ground-based measurements combined with tethered-balloon and airborne observations captured the turbulence decay from the surface throughout the whole boundary layer and documented the evolution of the turbulence characteristic length scales during the transition period. Closely integrated with the field experiment, numerical studies are now underway with a complete hierarchy of models to support the data interpretation and improve the model representations.publishedVersio

Cyclodextrin Fundamentals, Reactivity and Analysis

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The History of Cyclodextrins

International audienceThis book presents the historical development of Cyclodextrins by scientists who have made outstanding contribution to the field. Cyclodextrins are safe, cage-like molecules that have found major applications in many industrial sectors such as medicine, food, agriculture, environment and chemistry

Deep Eutectic Solvents for Medicine, Gas Solubilization and Extraction of Natural Substances

International audienceInitially considered as a sub-class of ionic liquids, eutectic mixtures are formed by mixtures of low cost, often biodegradable Lewis or Bronsted acids and bases. Eutectic mixtures have gathered a growing scientific interest by the academic and industrial communities as they are interesting for many applications ranging from metal processing to biomass treatment or pharmaceuticals. This volume gathers contributions by some of the most active research groups in the world using eutectic mixtures for applications in separation, extraction or pharmaceutical and medical applications. The different contributions aim at a large overview of the field for these particular applications by reviewing literature data and presenting ground breaking research in the different fields

Easy DNA modeling and more with GraphiteLifeExplorer.

The GraphiteLifeExplorer tool enables biologists to reconstruct 3D cellular complexes built from proteins and DNA molecules. Models of DNA molecules can be drawn in an intuitive way and assembled to proteins or others globular structures. Real time navigation and immersion offer a unique view to the reconstructed biological machinery

130 years of cyclodextrin discovery for health, food, agriculture, and the industry: a review

International audienceCyclodextrins are a group of cyclic oligosaccharides obtained by enzymatic degradation of starch. They are remarkable macrocyclic molecules that have led major theoretical and practical advances in chemistry, biology, biochemistry, health science, and agriculture. Their molecular structure is composed of a hydrophobic cavity that can encapsulate other compounds to form inclusion complexes through host-guest interactions. This unique feature is at the origin of many applications. Cyclodextrins and their derivatives have a wide variety of practical applications in almost all sectors of the industry, including pharmacy, medicine, foods, cosmetics, chromatography, catalysis, biotechnology, and the textile industry. Villiers published the first reference to cyclodextrins in 1891, and since then, these molecules have continued to fascinate academia and industry. Currently, more than 2000 publications on cyclodextrins are published each year. On the occasion of the 130th anniversary of their discovery, in this review, we present an historical overview of the development and applications of cyclodextrins. First, we present the discovery and first chemical studies on cyclodextrins. Then, the main results obtained during the 1911-1970 exploration period are discussed. A third part presents the historical landmarks in the development of cyclodextrins from 1970 to the present day

Wastewater technology attenuates the toxicity of shisha smoking

International audienceShisha smoking is rapidly gaining popularity, especially among the youths, yet knowledge on its toxic effects is limited. While the waterpipe device through which the smoke is bubbling should remove particles and toxic compounds, shisha smoking is still inducing cancers and several acute and chronic diseases. A possible solution to decrease smoke toxicity would be to trap most toxic smoke compounds in the water phase by adding adsorbents, solubilizers and complexing agents such as activated charcoal, cyclodextrins, biomicelles, liposomes and bionanocomposites. Here we discuss flavored tobacco, smoke toxicity, the Low Tox Nargileh, and materials that can be added to the water bowl to decrease toxicity. Further research on the trapping of shisha smoke may also lead to application in various industrial sectors involving smoke emissions

Rhodium-Catalyzed Hydroformylation Promoted by Modified Cyclodextrins: Current Scope and Future Developments

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3D model export.

<p>Upper left image: This 3D scene has been made in GraphiteLifeExplorer and exported (upper right image) in Maya thanks to Molecular Maya (<a href="http://www.molecularmovies.com/toolkit/" target="_blank">http://www.molecularmovies.com/toolkit/</a>) and (lower images) in the Blender 3D tool thanks to the ePMV plugin <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053609#pone.0053609-Johnson1" target="_blank">[31]</a>. In Blender, a script written by L. Autin (Scripps) superimposes an inverse kinematic armature to the linkers. This mechanical articulation greatly helps and facilitates the animation of the proteins from a first position (right figure) to a second position (left figure): thanks to the IK chain, moving the pink and green domains results in a reconformation of the linkers, pushed or pulled like a chain, in the deformation of the geometry (the tubes representing the linkers) attached to the linkers, and in the displacement of the CTD domain (green-blue/yellow). The model can serve as an interactive data-constrained thinking tool to help a lab contemplate plausible dynamics for this system. Note that the inverse kinematic joints of such an armature can be set at each alpha-carbon of any backbone if the linkers is no more a tube but an aminoacid based linker modeled with tools like Phyre2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053609#pone.0053609-Kelley1" target="_blank">[32]</a> and be combined with physics solvers hosted in the high-end 3D packages.</p