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      The manganese transporter SLC39A8 links alkaline ceramidase 1 to inflammatory bowel disease

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          Abstract

          The metal ion transporter SLC39A8 is associated with physiological traits and diseases, including blood manganese (Mn) levels and inflammatory bowel diseases (IBD). The mechanisms by which SLC39A8 controls Mn homeostasis and epithelial integrity remain elusive. Here, we generate Slc39a8 intestinal epithelial cell-specific-knockout ( Slc39a8-IEC KO) mice, which display markedly decreased Mn levels in blood and most organs. Radiotracer studies reveal impaired intestinal absorption of dietary Mn in Slc39a8-IEC KO mice. SLC39A8 is localized to the apical membrane and mediates 54Mn uptake in intestinal organoid monolayer cultures. Unbiased transcriptomic analysis identifies alkaline ceramidase 1 (ACER1), a key enzyme in sphingolipid metabolism, as a potential therapeutic target for SLC39A8-associated IBDs. Importantly, treatment with an ACER1 inhibitor attenuates colitis in Slc39a8-IEC KO mice by remedying barrier dysfunction. Our results highlight the essential roles of SLC39A8 in intestinal Mn absorption and epithelial integrity and offer a therapeutic target for IBD associated with impaired Mn homeostasis.

          Abstract

          The metal transporter SLC39A8 is linked to blood manganese (Mn) levels and inflammatory bowel diseases (IBD). Here, the authors show that loss of SLC39A8 impairs intestinal Mn absorption and epithelial integrity, suggesting potential therapeutic strategies targeting alkaline ceramidase 1 for IBD patients with SLC39A8 deficiency.

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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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            Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies.

            Inflammatory bowel disease is a global disease in the 21st century. We aimed to assess the changing incidence and prevalence of inflammatory bowel disease around the world.
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              A RAPID METHOD OF TOTAL LIPID EXTRACTION AND PURIFICATION

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                Author and article information

                Contributors
                youngseo@umich.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                5 June 2024
                5 June 2024
                2024
                : 15
                : 4775
                Affiliations
                [1 ]Department of Nutritional Sciences, University of Michigan School of Public Health, ( https://ror.org/00jmfr291) Ann Arbor, MI USA
                [2 ]GRID grid.214458.e, ISNI 0000000086837370, Department of Pathology, , University of Michigan Medical School, ; Ann Arbor, MI USA
                [3 ]GRID grid.214458.e, ISNI 0000000086837370, Michigan Regional Comprehensive Metabolomics Resource Core, , University of Michigan Medical School, ; Ann Arbor, MI USA
                [4 ]GRID grid.214458.e, ISNI 0000000086837370, Division of Gastroenterology and Hepatology, Department of Internal Medicine, , University of Michigan Medical School, ; Ann Arbor, MI USA
                [5 ]GRID grid.214458.e, ISNI 0000000086837370, Department of Molecular and Integrative Physiology, , University of Michigan Medical School, ; Ann Arbor, MI USA
                [6 ]GRID grid.214458.e, ISNI 0000000086837370, Department of Human Genetics, , University of Michigan Medical School, ; Ann Arbor, MI USA
                Author information
                http://orcid.org/0000-0002-0437-4785
                http://orcid.org/0000-0002-2618-5870
                http://orcid.org/0000-0003-2280-7422
                http://orcid.org/0000-0003-3884-0665
                Article
                49049
                10.1038/s41467-024-49049-8
                11153611
                38839750
                8137928b-12c2-4267-a261-132a05a87c66
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 25 February 2022
                : 17 May 2024
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000062, U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases);
                Award ID: DK034933
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000065, U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS);
                Award ID: R21NS112974
                Award ID: R01NS116008
                Award ID: R01NS089896
                Award Recipient :
                Funded by: U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)
                Funded by: U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)
                Categories
                Article
                Custom metadata
                © Springer Nature Limited 2024

                Uncategorized
                homeostasis,ulcerative colitis,metals,crohn's disease
                Uncategorized
                homeostasis, ulcerative colitis, metals, crohn's disease

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