The Experts below are selected from a list of 252 Experts worldwide ranked by ideXlab platform
Binh P. Nguyen - One of the best experts on this subject based on the ideXlab platform.
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Superpixel-based segmentation of Muscle Fibers in multi-channel microscopy
BMC Systems Biology, 2016Co-Authors: Binh P. Nguyen, Hans Heemskerk, Peter T. C. So, Lisa Tucker-kelloggAbstract:Background Confetti fluorescence and other multi-color genetic labelling strategies are useful for observing stem cell regeneration and for other problems of cell lineage tracing. One difficulty of such strategies is segmenting the cell boundaries, which is a very different problem from segmenting color images from the real world. This paper addresses the difficulties and presents a superpixel-based framework for segmentation of regenerated Muscle Fibers in mice. Results We propose to integrate an edge detector into a superpixel algorithm and customize the method for multi-channel images. The enhanced superpixel method outperforms the original and another advanced superpixel algorithm in terms of both boundary recall and under-segmentation error. Our framework was applied to cross-section and lateral section images of regenerated Muscle Fibers from confetti-fluorescent mice. Compared with “ground-truth” segmentations, our framework yielded median Dice similarity coefficients of 0.92 and higher. Conclusion Our segmentation framework is flexible and provides very good segmentations of multi-color Muscle Fibers. We anticipate our methods will be useful for segmenting a variety of tissues in confetti fluorecent mice and in mice with similar multi-color labels.
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superpixel based segmentation of Muscle Fibers in multi channel microscopy
BMC Systems Biology, 2016Co-Authors: Binh P. Nguyen, Hans Heemskerk, Lisa TuckerkelloggAbstract:Background Confetti fluorescence and other multi-color genetic labelling strategies are useful for observing stem cell regeneration and for other problems of cell lineage tracing. One difficulty of such strategies is segmenting the cell boundaries, which is a very different problem from segmenting color images from the real world. This paper addresses the difficulties and presents a superpixel-based framework for segmentation of regenerated Muscle Fibers in mice.
Bert Blaauw - One of the best experts on this subject based on the ideXlab platform.
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high throughput proteomics fiber typing profit for comprehensive characterization of single skeletal Muscle Fibers
Skeletal Muscle, 2020Co-Authors: Sebastian Kallabis, Lena Abraham, Stefan Muller, Verena Dzialas, Clara Turk, Janica Lea Wiederstein, Theresa Bock, Hendrik Nolte, Leonardo Nogara, Bert BlaauwAbstract:Skeletal Muscles are composed of a heterogeneous collection of fiber types with different physiological adaption in response to a stimulus and disease-related conditions. Each fiber has a specific molecular expression of myosin heavy chain molecules (MyHC). So far, MyHCs are currently the best marker proteins for characterization of individual fiber types, and several proteome profiling studies have helped to dissect the molecular signature of whole Muscles and individual Fibers. Herein, we describe a mass spectrometric workflow to measure skeletal Muscle fiber type-specific proteomes. To bypass the limited quantities of protein in single Fibers, we developed a Proteomics high-throughput fiber typing (ProFiT) approach enabling profiling of MyHC in single Fibers. Aliquots of protein extracts from separated Muscle Fibers were subjected to capillary LC-MS gradients to profile MyHC isoforms in a 96-well format. Muscle Fibers with the same MyHC protein expression were pooled and subjected to proteomic, pulsed-SILAC, and phosphoproteomic analysis. Our fiber type-specific quantitative proteome analysis confirmed the distribution of fiber types in the soleus Muscle, substantiates metabolic adaptions in oxidative and glycolytic Fibers, and highlighted significant differences between the proteomes of type IIb Fibers from different Muscle groups, including a differential expression of desmin and actinin-3. A detailed map of the Lys-6 incorporation rates in Muscle Fibers showed an increased turnover of slow Fibers compared to fast Fibers. In addition, labeling of mitochondrial respiratory chain complexes revealed a broad range of Lys-6 incorporation rates, depending on the localization of the subunits within distinct complexes. Overall, the ProFiT approach provides a versatile tool to rapidly characterize Muscle Fibers and obtain fiber-specific proteomes for different Muscle groups.
Lisa Tuckerkellogg - One of the best experts on this subject based on the ideXlab platform.
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superpixel based segmentation of Muscle Fibers in multi channel microscopy
BMC Systems Biology, 2016Co-Authors: Binh P. Nguyen, Hans Heemskerk, Lisa TuckerkelloggAbstract:Background Confetti fluorescence and other multi-color genetic labelling strategies are useful for observing stem cell regeneration and for other problems of cell lineage tracing. One difficulty of such strategies is segmenting the cell boundaries, which is a very different problem from segmenting color images from the real world. This paper addresses the difficulties and presents a superpixel-based framework for segmentation of regenerated Muscle Fibers in mice.
Stefano Schiaffino - One of the best experts on this subject based on the ideXlab platform.
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Calcineurin controls nerve activity-dependent specification of slow skeletal Muscle Fibers but not Muscle growth
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Antonio L. Serrano, Elisa Calabria, Patrizia Coniglio, Giorgia Pallafacchina, T. Lømo, Mauro Murgia, Stefano SchiaffinoAbstract:Nerve activity can induce long-lasting, transcription-dependent changes in skeletal Muscle Fibers and thus affect Muscle growth and fiber-type specificity. Calcineurin signaling has been implicated in the transcriptional regulation of slow Muscle fiber genes in culture, but the functional role of calcineurin in vivo has not been unambiguously demonstrated. Here, we report that the up-regulation of slow myosin heavy chain (MyHC) and a MyHC-slow promoter induced by slow motor neurons in regenerating rat soleus Muscle is prevented by the calcineurin inhibitors cyclosporin A (CsA), FK506, and the calcineurin inhibitory protein domain from cain/cabin-1. In contrast, calcineurin inhibitors do not block the increase in fiber size induced by nerve activity in regenerating Muscle. The activation of MyHC-slow induced by direct electro-stimulation of denervated regenerating Muscle with a continuous low frequency impulse pattern is blocked by CsA, showing that calcineurin function in Muscle Fibers and not in motor neurons is responsible for nerve-dependent specification of slow Muscle Fibers. Calcineurin is also involved in the maintenance of the slow Muscle fiber gene program because in the adult soleus Muscle, cain causes a switch from MyHC-slow to fast-type MyHC-2X and MyHC-2B gene expression, and the activity of the MyHC-slow promoter is inhibited by CsA and FK506.
Yasuhisa Endo - One of the best experts on this subject based on the ideXlab platform.
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galanin immunoreactive nerve terminals innervating the striated Muscle Fibers of the rat esophagus
Neuroscience Letters, 1995Co-Authors: Hirofumi Kuramoto, Yasuhisa EndoAbstract:Abstract Galanin (GAL) immunohistochemistry combined with acetylcholinesterase (AChE) histochemistry was applied to demonstrate the innervation of the rat esophageal Muscle coats. GAL immunoreactivity was found in a number of nerve cell bodies in the myenteric ganglia and in numerous varicose and non-varicose nerve Fibers in the myenteric plexus and around blood vessels. Many GAL-positive varicose Fibers ran in the internodal strands and along the striated Muscle Fibers. They often ramified and terminated on the Muscle Fibers to form arborizing structures, which were most abundant in the thoracic portion of the esophagus. Such GAL-positive terminals were localized in most (87.7%) of AChE-reactive motor endplates on the esophageal striated Muscles. Left supranodose vagotomy caused a significant decrease of the GAL-arborizing terminals on the striated Muscles of the esophagus. This suggests that they are terminals of efferent Fibers in the vagus nerve.
