74,066 research outputs found

    On Top of the Alveolar Epithelium: Surfactant and the Glycocalyx

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    Gas exchange in the lung takes place via the air-blood barrier in the septal walls of alveoli. The tissue elements that oxygen molecules have to cross are the alveolar epithelium, the interstitium and the capillary endothelium. The epithelium that lines the alveolar surface is covered by a thin and continuous liquid lining layer. Pulmonary surfactant acts at this air-liquid interface. By virtue of its biophysical and immunomodulatory functions, surfactant keeps alveoli open, dry and clean. What needs to be added to this picture is the glycocalyx of the alveolar epithelium. Here, we briefly review what is known about this glycocalyx and how it can be visualized using electron microscopy. The application of colloidal thorium dioxide as a staining agent reveals differences in the staining pattern between type I and type II alveolar epithelial cells and shows close associations of the glycocalyx with intraalveolar surfactant subtypes such as tubular myelin. These morphological findings indicate that specific spatial interactions between components of the surfactant system and those of the alveolar epithelial glycocalyx exist which may contribute to the maintenance of alveolar homeostasis, in particular to alveolar micromechanics, to the functional integrity of the air-blood barrier, to the regulation of the thickness and viscosity of the alveolar lining layer, and to the defence against inhaled pathogens. Exploring the alveolar epithelial glycocalyx in conjunction with the surfactant system opens novel physiological perspectives of potential clinical relevance for future research

    4D visualization of embryonic, structural crystallization by single-pulse microscopy

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    In many physical and biological systems the transition from an amorphous to ordered native structure involves complex energy landscapes, and understanding such transformations requires not only their thermodynamics but also the structural dynamics during the process. Here, we extend our 4D visualization method with electron imaging to include the study of irreversible processes with a single pulse in the same ultrafast electron microscope (UEM) as used before in the single-electron mode for the study of reversible processes. With this augmentation, we report on the transformation of amorphous to crystalline structure with silicon as an example. A single heating pulse was used to initiate crystallization from the amorphous phase while a single packet of electrons imaged selectively in space the transformation as the structure continuously changes with time. From the evolution of crystallinity in real time and the changes in morphology, for nanosecond and femtosecond pulse heating, we describe two types of processes, one that occurs at early time and involves a nondiffusive motion and another that takes place on a longer time scale. Similar mechanisms of two distinct time scales may perhaps be important in biomolecular folding

    Electron Cryomicroscopy: From Molecules to Cells

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    Today's biomolecular electron microscopy uses essentially three different imaging modalities: (i) electron crystallography, (ii) single particle analysis and (iii) electron tomography. Ideally, these imaging modalities are applied to frozen-hydrated samples to ensure an optimum preservation of the structures under scrutiny. Electron crystallography requires the existence of two-dimensional crystals. In principle, electron crystallography is a high-resolution technique and it has indeed been demonstrated in a number of cases that near-atomic resolution can be attained. Single-particle analysis is particularly suited for structural studies of large macromolecular complexes. The amount of material needed is minute and some degree of heterogeneity is tolerable since image classification can be used for further 'purification in silico'. In principle, single particle analysis can attain high-resolution but, in practice, this often remains an elusive goal. However, since medium resolution structures can be obtained relatively easily, it often provides an excellent basis for hybrid approaches in which high-resolution structures of components are integrated into the medium resolution structures of the holocomplexes. Electron tomography can be applied to non-repetitive structures. Most supramolecuar structures inside cells fall into this category. In order to obtain three-dimensional structures of objects with unique topologies it is necessary to obtain different views by physical tilting. The challenge is to obtain large numbers of projection images covering as wide a tilt range as possible and, at the same time, to minimize the cumulative electron dose. Cryoelectron tomography provides medium resolution three-dimensional images of a wide range of biological structures from isolated supramolecular assemblies to organelles and cells. It allows the visualization of molecular machines in their functional environment (in situ) and the mapping of entire molecular landscapes

    3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

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    Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

    Nanodiamond landmarks for subcellular multimodal optical and electron imaging.

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    There is a growing need for biolabels that can be used in both optical and electron microscopies, are non-cytotoxic, and do not photobleach. Such biolabels could enable targeted nanoscale imaging of sub-cellular structures, and help to establish correlations between conjugation-delivered biomolecules and function. Here we demonstrate a sub-cellular multi-modal imaging methodology that enables localization of inert particulate probes, consisting of nanodiamonds having fluorescent nitrogen-vacancy centers. These are functionalized to target specific structures, and are observable by both optical and electron microscopies. Nanodiamonds targeted to the nuclear pore complex are rapidly localized in electron-microscopy diffraction mode to enable "zooming-in" to regions of interest for detailed structural investigations. Optical microscopies reveal nanodiamonds for in-vitro tracking or uptake-confirmation. The approach is general, works down to the single nanodiamond level, and can leverage the unique capabilities of nanodiamonds, such as biocompatibility, sensitive magnetometry, and gene and drug delivery

    Building Near-Real-Time Processing Pipelines with the Spark-MPI Platform

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    Advances in detectors and computational technologies provide new opportunities for applied research and the fundamental sciences. Concurrently, dramatic increases in the three Vs (Volume, Velocity, and Variety) of experimental data and the scale of computational tasks produced the demand for new real-time processing systems at experimental facilities. Recently, this demand was addressed by the Spark-MPI approach connecting the Spark data-intensive platform with the MPI high-performance framework. In contrast with existing data management and analytics systems, Spark introduced a new middleware based on resilient distributed datasets (RDDs), which decoupled various data sources from high-level processing algorithms. The RDD middleware significantly advanced the scope of data-intensive applications, spreading from SQL queries to machine learning to graph processing. Spark-MPI further extended the Spark ecosystem with the MPI applications using the Process Management Interface. The paper explores this integrated platform within the context of online ptychographic and tomographic reconstruction pipelines.Comment: New York Scientific Data Summit, August 6-9, 201
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