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      Oligodendrocyte-lineage cell exocytosis and L-type prostaglandin D synthase promote oligodendrocyte development and myelination

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          Abstract

          In the developing central nervous system, oligodendrocyte precursor cells (OPCs) differentiate into oligodendrocytes, which form myelin around axons. Oligodendrocytes and myelin are essential for the function of the central nervous system, as evidenced by the severe neurological symptoms that arise in demyelinating diseases such as multiple sclerosis and leukodystrophy. Although many cell-intrinsic mechanisms that regulate oligodendrocyte development and myelination have been reported, it remains unclear whether interactions among oligodendrocyte-lineage cells (OPCs and oligodendrocytes) affect oligodendrocyte development and myelination. Here, we show that blocking vesicle-associated membrane protein (VAMP) 1/2/3-dependent exocytosis from oligodendrocyte-lineage cells impairs oligodendrocyte development, myelination, and motor behavior in mice. Adding oligodendrocyte-lineage cell-secreted molecules to secretion-deficient OPC cultures partially restores the morphological maturation of oligodendrocytes. Moreover, we identified L-type prostaglandin D synthase as an oligodendrocyte-lineage cell-secreted protein that promotes oligodendrocyte development and myelination in vivo. These findings reveal a novel autocrine/paracrine loop model for the regulation of oligodendrocyte and myelin development.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            STAR: ultrafast universal RNA-seq aligner.

            Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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              NIH Image to ImageJ: 25 years of image analysis

              For the past twenty five years the NIH family of imaging software, NIH Image and ImageJ have been pioneers as open tools for scientific image analysis. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
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                Author and article information

                Contributors
                Role: Reviewing Editor
                Role: Senior Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                13 February 2023
                2023
                : 12
                : e77441
                Affiliations
                [1 ] Department of Psychiatry and Biobehavioral Sciences, Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles ( https://ror.org/046rm7j60) Los Angeles United States
                [2 ] Division of Neuroscience, IRCCS, San Raffaele Hospital ( https://ror.org/039zxt351) Milan Italy
                [3 ] Department of Pathobiochemistry, Osaka Medical and Pharmaceutical University Osaka Japan
                [4 ] Hirono Satellite, Isotope Science Center, The University of Tokyo ( https://ror.org/057zh3y96) Fukushima Japan
                [5 ] Department of Molecular Biology, University of Texas Southwestern Medical Center ( https://ror.org/05byvp690) Dallas United States
                [6 ] Brain Research Institute, University of California, Los Angeles ( https://ror.org/046rm7j60) Los Angeles United States
                [7 ] Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles ( https://ror.org/046rm7j60) Los Angeles United States
                [8 ] Molecular Biology Institute, University of California, Los Angeles ( https://ror.org/046rm7j60) Los Angeles United States
                Vollum Institute, Oregon Health & Science University ( https://ror.org/009avj582) United States
                New York University ( https://ror.org/0190ak572) United States
                Vollum Institute, Oregon Health & Science University ( https://ror.org/009avj582) United States
                Author information
                https://orcid.org/0000-0001-8510-0032
                https://orcid.org/0000-0002-6531-9544
                https://orcid.org/0000-0002-1546-5930
                Article
                77441
                10.7554/eLife.77441
                9946447
                36779701
                406aabe6-dda0-4c81-8d7b-829cad9f7076
                © 2023, Pan et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 29 January 2022
                : 12 February 2023
                Funding
                Funded by: UCLA Brain Research Institute;
                Award ID: Knaub Postdoctoral Fellowship
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: R00NS089780
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000049, National Institute on Aging;
                Award ID: R03AG065772
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000071, National Institute of Child Health and Human Development;
                Award ID: P50HD103557
                Award Recipient :
                Funded by: National Center for Advancing Translational Science UCLA CTSI Grant;
                Award ID: UL1TR001881
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000888, W. M. Keck Foundation;
                Award ID: W. M. Keck Foundation junior faculty award
                Award Recipient :
                Funded by: UCLA Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research;
                Award ID: Innovation Award
                Award Recipient :
                Funded by: Wendy Ablon Foundation;
                Award ID: Ablon Scholar Award
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000065, National Institute of Neurological Disorders and Stroke;
                Award ID: R01NS109025
                Award Recipient :
                Funded by: Friends of the Semel Institute for Neuroscience & Human Behavior;
                Award ID: Friends scholar award
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Developmental Biology
                Neuroscience
                Custom metadata
                Oligodendrocyte-lineage cells secrete L-type prostaglandin synthase in an autocrine loop to promote oligodendrocyte development and myelination.

                Life sciences
                oligodendrocyte precursor cells,oligodendrocytes,myelin,development,exocytosis,l-type prostaglandin d synthase,mouse

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