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Find video protocols related to scientific articles indexed in Pubmed.
Ultramicroscopy: light-sheet-based microscopy for imaging centimeter-sized objects with micrometer resolution.
Cold Spring Harb Protoc
PUBLISHED: 08-03-2013
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Ultramicroscopy (UM) is a powerful imaging technique that achieves precise and accurate three-dimensional (3D) reconstructions of intact macroscopic specimens with micrometer resolution. It was developed for specimens in the size range of ?1-15 mm, such as whole mouse brains, mouse embryos, mouse organs, and Drosophila melanogaster. In UM, the specimen is illuminated perpendicular to the observation pathway by two thin counterpropagating sheets of laser light. UM is closely related to a growing family of comparable microscopy approaches based on light sheet illumination developed in recent years. This article presents an overview of light-sheet-based microscopy and describes the underlying physics of light sheet generation. The assembly of an "ultramicroscope" for investigating fixed chemically cleared tissue is described in detail, and the functions of the essential components, such as mechanics, camera, and objectives, are discussed. Finally, practical applications of UM for studying mouse organs, mouse embryos, and Drosophila adults are described.
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Immunostaining, dehydration, and clearing of mouse embryos for ultramicroscopy.
Cold Spring Harb Protoc
PUBLISHED: 08-03-2013
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This protocol describes the preparation of mouse embryos for ultramicroscopy (UM), a powerful imaging technique that achieves precise and accurate three-dimensional (3D) reconstructions of intact macroscopic specimens with micrometer resolution. In UM, a specimen in the size range of ?1-15 mm is illuminated perpendicular to the observation pathway by two thin counterpropagating sheets of laser light. In combination with fluorescein isothiocyanate (FITC) immunostaining, UM allows visualization of somatic motor and sensorial nerve fibers in whole mouse embryos. Even the fine branches of the sensomotoric fibers can be visualized over a distance of up to several millimeters. In this protocol, mouse embryos are fixed and immunostained in preparation for UM. Because UM requires the excitation light sheet to travel throughout the entire horizontal width of the specimen, specimens usually have to be rendered transparent before microscope inspection. Here, the embryos are dehydrated in ethanol and then cleared in a solution of benzyl alcohol and benzyl benzoate.
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Dehydration and clearing of whole mouse brains and dissected hippocampi for ultramicroscopy.
Cold Spring Harb Protoc
PUBLISHED: 07-03-2013
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This protocol describes the preparation of whole mouse brains and dissected hippocampi for ultramicroscopy (UM), a powerful imaging technique that achieves precise and accurate three-dimensional (3D) reconstructions of intact macroscopic specimens with micrometer resolution. In UM, a specimen in the size range of ?1-15 mm is illuminated perpendicular to the observation pathway by two thin counterpropagating sheets of laser light. Thus, specimens for UM need to be sufficiently transparent, which requires chemical clearing in most cases. In this protocol, mouse brains and hippocampi are carefully dissected and dehydrated, and then cleared in a solution of benzyl benzoate and benzyl alcohol.
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Dehydration and clearing of adult Drosophila for ultramicroscopy.
Cold Spring Harb Protoc
PUBLISHED: 07-03-2013
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This protocol describes the preparation of adult flies for ultramicroscopy (UM), a powerful imaging technique that achieves precise and accurate three-dimensional (3D) reconstructions of intact macroscopic specimens with micrometer resolution. In UM, a specimen in the size range of ?1-15 mm is illuminated perpendicular to the observation pathway by two thin counterpropagating sheets of laser light. Thus, specimens for UM need to be sufficiently transparent, which requires chemical clearing in most cases. In this protocol, Drosophila melanogaster adults are fixed, dehydrated in ethanol, and then cleared in a solution of benzyl alcohol and benzyl benzoate.
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Prdm6 is essential for cardiovascular development in vivo.
PLoS ONE
PUBLISHED: 01-01-2013
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Members of the PRDM protein family have been shown to play important roles during embryonic development. Previous in vitro and in situ analyses indicated a function of Prdm6 in cells of the vascular system. To reveal physiological functions of Prdm6, we generated conditional Prdm6-deficient mice. Complete deletion of Prdm6 results in embryonic lethality due to cardiovascular defects associated with aberrations in vascular patterning. However, smooth muscle cells could be regularly differentiated from Prdm6-deficient embryonic stem cells and vascular smooth muscle cells were present and proliferated normally in Prdm6-deficient embryos. Conditional deletion of Prdm6 in the smooth muscle cell lineage using a SM22-Cre driver line resulted in perinatal lethality due to hemorrhage in the lungs. We thus identified Prdm6 as a factor that is essential for the physiological control of cardiovascular development.
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Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury.
Nat. Med.
PUBLISHED: 05-26-2011
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Studying regeneration in the central nervous system (CNS) is hampered by current histological and imaging techniques because they provide only partial information about axonal and glial reactions. Here we developed a tetrahydrofuran-based clearing procedure that renders fixed and unsectioned adult CNS tissue transparent and fully penetrable for optical imaging. In large spinal cord segments, we imaged fluorescently labeled cells by ultramicroscopy and two-photon microscopy without the need for histological sectioning. We found that more than a year after injury growth-competent axons regenerated abundantly through the injury site. A few growth-incompetent axons could also regenerate when they bypassed the lesion. Moreover, we accurately determined quantitative changes of glial cells after spinal cord injury. Thus, clearing CNS tissue enables an unambiguous evaluation of axon regeneration and glial reactions. Our clearing procedure also renders other organs transparent, which makes this approach useful for a large number of preclinical paradigms.
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Spalt mediates an evolutionarily conserved switch to fibrillar muscle fate in insects.
Nature
PUBLISHED: 05-26-2011
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Flying insects oscillate their wings at high frequencies of up to 1,000 Hz and produce large mechanical forces of 80 W per kilogram of muscle. They utilize a pair of perpendicularly oriented indirect flight muscles that contain fibrillar, stretch-activated myofibres. In contrast, all other, more slowly contracting, insect body muscles have a tubular muscle morphology. Here we identify the transcription factor Spalt major (Salm) as a master regulator of fibrillar flight muscle fate in Drosophila. salm is necessary and sufficient to induce fibrillar muscle fate. salm switches the entire transcriptional program from tubular to fibrillar fate by regulating the expression and splicing of key sarcomeric components specific to each muscle type. Spalt function is conserved in insects evolutionarily separated by 280 million years. We propose that Spalt proteins switch myofibres from tubular to fibrillar fate during development, a function potentially conserved in the vertebrate heart--a stretch-activated muscle sharing features with insect flight muscle.
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Image contrast enhancement in confocal ultramicroscopy.
Opt Lett
PUBLISHED: 07-29-2010
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Ultramicroscopy allows for the 3D reconstruction of centimeter sized samples with a spatial resolution of several micrometers. Nevertheless, in poorly cleared or very large specimens the images may suffer from blurring and low contrast levels. To address these problems, ultramicroscopy was combined with the principle of confocal microscopy using a slowly rotating Nipkow disk. This configuration was tested by comparing images from mouse hippocampal neurons and mouse liver blood vessels recorded in confocal and conventional mode. It was found that confocality minimizes the background noise and considerably improves the signal-to-noise ratio when applied to ultramicroscopy.
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Image enhancement in ultramicroscopy by improved laser light sheets.
J Biophotonics
PUBLISHED: 06-25-2010
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In the majority of implementations of light sheet microscopy, such as ultramicroscopy, the laser beam illuminating the specimen is truncated by a slit aperture before it is focused to a light sheet by a single cylindrical lens. A light sheet generated in this way can be made very thin near to the focal point, but unfortunately its Rayleigh range is severely limited. This problem can be partially solved by using a smaller slit aperture. However, this also causes a major loss in power, a severe broadening of the beam waist, and thus a significant loss of resolution along the detection axis. We developed improved light-sheet-generation optics, which provide longer Raleigh ranges, whilst retaining beam waists comparable to our standard system with one cylindrical lens. Using the modified system we achieved a marked improvement in the resolution of ultramicroscopy reconstructions of representative biological specimens.
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Regulation and functions of the lms homeobox gene during development of embryonic lateral transverse muscles and direct flight muscles in Drosophila.
PLoS ONE
PUBLISHED: 06-24-2010
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Patterning and differentiation of developing musculatures require elaborate networks of transcriptional regulation. In Drosophila, significant progress has been made into identifying the regulators of muscle development and defining their interactive networks. One major family of transcription factors involved in these processes consists of homeodomain proteins. In flies, several members of this family serve as muscle identity genes to specify the fates of individual muscles, or groups thereof, during embryonic and/or adult muscle development. Herein, we report on the expression and function of a new Drosophila homeobox gene during both embryonic and adult muscle development.
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Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy.
Front Syst Neurosci
PUBLISHED: 01-13-2010
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Genetic mutants are invaluable for understanding the development, physiology and behaviour of Drosophila. Modern molecular genetic techniques enable the rapid generation of large numbers of different mutants. To phenotype these mutants sophisticated microscopy techniques are required, ideally allowing the 3D-reconstruction of the anatomy of an adult fly from a single scan. Ultramicroscopy enables up to cm fields of view, whilst providing micron resolution. In this paper, we present ultramicroscopy reconstructions of the flight musculature, the nervous system, and the digestive tract of entire, chemically cleared, drosophila in autofluorescent light. The 3D-reconstructions thus obtained verify that the anatomy of a whole fly, including the filigree spatial organization of the direct flight muscles, can be analysed from a single ultramicroscopy reconstruction. The recording procedure, including 3D-reconstruction using standard software, takes no longer than 30 min. Additionally, image segmentation, which would allow for further quantitative analysis, was performed.
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3D-reconstruction of blood vessels by ultramicroscopy.
Organogenesis
PUBLISHED: 03-31-2009
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As recently shown, ultramicroscopy (UM) allows 3D-visualization of even large microscopic structures with microm resolution. Thus, it can be applied to anatomical studies of numerous biological and medical specimens. We reconstructed the three-dimensional architecture of tomato-lectin (Lycopersicon esculentum) stained vascular networks by UM in whole mouse organs. The topology of filigree branches of the microvasculature was visualized. Since tumors require an extensive growth of blood vessels to survive, this novel approach may open up new vistas in neurobiology and histology, particularly in cancer research.
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Three-dimensional imaging of solvent-cleared organs using 3DISCO.
Nat Protoc
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The examination of tissue histology by light microscopy is a fundamental tool for investigating the structure and function of organs under normal and disease states. Many current techniques for tissue sectioning, imaging and analysis are time-consuming, and they present major limitations for 3D tissue reconstruction. The introduction of methods to achieve the optical clearing and subsequent light-sheet laser scanning of entire transparent organs without sectioning represents a major advance in the field. We recently developed a highly reproducible and versatile clearing procedure called 3D imaging of solvent-cleared organs, or 3DISCO, which is applicable to diverse tissues including brain, spinal cord, immune organs and tumors. Here we describe a detailed protocol for performing 3DISCO and present its application to various microscopy techniques, including example results from various mouse tissues. The tissue clearing takes as little as 3 h, and imaging can be completed in ?45 min. 3DISCO is a powerful technique that offers 3D histological views of tissues in a fraction of the time and labor required to complete standard histology studies.
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Chemical clearing and dehydration of GFP expressing mouse brains.
PLoS ONE
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Generally, chemical tissue clearing is performed by a solution consisting of two parts benzyl benzoate and one part benzyl alcohol. However, prolonged exposure to this mixture markedly reduces the fluorescence of GFP expressing specimens, so that one has to compromise between clearing quality and fluorescence preservation. This can be a severe drawback when working with specimens exhibiting low GFP expression rates. Thus, we screened for a substitute and found that dibenzyl ether (phenylmethoxymethylbenzene, CAS 103-50-4) can be applied as a more GFP-friendly clearing medium. Clearing with dibenzyl ether provides improved tissue transparency and strikingly improved fluorescence intensity in GFP expressing mouse brains and other samples as mouse spinal cords, or embryos. Chemical clearing, staining, and embedding of biological samples mostly requires careful foregoing tissue dehydration. The commonly applied tissue dehydration medium is ethanol, which also can markedly impair GFP fluorescence. Screening for a substitute also for ethanol we found that tetrahydrofuran (CAS 109-99-9) is a more GFP-friendly dehydration medium than ethanol, providing better tissue transparency obtained by successive clearing. Combined, tetrahydrofuran and dibenzyl ether allow dehydration and chemical clearing of even delicate samples for UM, confocal microscopy, and other microscopy techniques.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.