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      A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis

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      Nature Communications
      Nature Publishing Group UK
      Microbiome, Translational research

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          Abstract

          Idiopathic pulmonary fibrosis (IPF) is a chronic and fatal disease of unknown etiology; however, apoptosis of lung alveolar epithelial cells plays a role in disease progression. This intractable disease is associated with increased abundance of Staphylococcus and Streptococcus in the lungs, yet their roles in disease pathogenesis remain elusive. Here, we report that Staphylococcus nepalensis releases corisin, a peptide conserved in diverse staphylococci, to induce apoptosis of lung epithelial cells. The disease in mice exhibits acute exacerbation after intrapulmonary instillation of corisin or after lung infection with corisin-harboring S. nepalensis compared to untreated mice or mice infected with bacteria lacking corisin. Correspondingly, the lung corisin levels are significantly increased in human IPF patients with acute exacerbation compared to patients without disease exacerbation. Our results suggest that bacteria shedding corisin are involved in acute exacerbation of IPF, yielding insights to the molecular basis for the elevation of staphylococci in pulmonary fibrosis.

          Abstract

          Idiopathic pulmonary fibrosis is associated with increased abundance of Staphylococcus and Streptococcus in the lungs. Here, the authors identify a Staphylococcus nepalensis-derived peptide, named corisin, to induce apoptosis of lung epithelial cells and exacerbation of pulmonary fibrosis in mice.

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          Idiopathic pulmonary fibrosis.

          Idiopathic pulmonary fibrosis is a prototype of chronic, progressive, and fibrotic lung disease. Healthy tissue is replaced by altered extracellular matrix and alveolar architecture is destroyed, which leads to decreased lung compliance, disrupted gas exchange, and ultimately respiratory failure and death. In less than a decade, understanding of the pathogenesis and management of this disease has been transformed, and two disease-modifying therapies have been approved, worldwide. In this Seminar, we summarise the presentation, pathophysiology, diagnosis, and treatment options available for patients with idiopathic pulmonary fibrosis. This disease has improved understanding of the mechanisms of lung fibrosis, and offers hope that similar approaches will transform the management of patients with other progressive fibrotic lung diseases.
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            BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

            Abstract Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.
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              Exposure of phosphatidylserine on the surface of apoptotic lymphocytes triggers specific recognition and removal by macrophages.

              During normal tissue remodeling, macrophages remove unwanted cells, including those that have undergone programmed cell death, or apoptosis. This widespread process extends to the deletion of thymocytes (negative selection), in which cells expressing inappropriate Ag receptors undergo apoptosis, and are phagocytosed by thymic macrophages. Although phagocytosis of effete leukocytes by macrophages has been known since the time of Metchnikoff, only recently has it been recognized that apoptosis leads to surface changes that allow recognition and removal of these cells before they are lysed. Our data suggest that macrophages specifically recognize phosphatidylserine that is exposed on the surface of lymphocytes during the development of apoptosis. Macrophage phagocytosis of apoptotic lymphocytes was inhibited, in a dose-dependent manner, by liposomes containing phosphatidyl-L-serine, but not by liposomes containing other anionic phospholipids, including phosphatidyl-D-serine. Phagocytosis of apoptotic lymphocytes was also inhibited by the L isoforms of compounds structurally related to phosphatidylserine, including glycerophosphorylserine and phosphoserine. The membranes of apoptotic lymphocytes bound increased amounts of merocyanine 540 dye relative to those of normal cells, indicating that their membrane lipids were more loosely packed, consistent with a loss of membrane phospholipid asymmetry. Apoptotic lymphocytes were shown to express phosphatidylserine (PS) externally, because PS on their surfaces was accessible to derivatization by fluorescamine, and because apoptotic cells expressed procoagulant activity. These observations suggest that apoptotic lymphocytes lose membrane phospholipid asymmetry and expose phosphatidylserine on the outer leaflet of the plasma membrane. Macrophages then phagocytose apoptotic lymphocytes after specific recognition of the exposed PS.
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                Author and article information

                Contributors
                icann@illinois.edu
                gabazza@doc.medic.mie-u.ac.jp
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                24 March 2020
                24 March 2020
                2020
                : 11
                : 1539
                Affiliations
                [1 ]ISNI 0000 0004 0372 555X, GRID grid.260026.0, Department of Immunology, , Mie University Faculty and Graduate School of Medicine, ; Edobashi 2-174, Tsu, Mie 514-8507 Japan
                [2 ]ISNI 0000 0004 0372 555X, GRID grid.260026.0, Center for Intractable Diseases, , Mie University, ; Edobashi 2-174, Tsu, Mie 514-8507 Japan
                [3 ]ISNI 0000 0004 1936 9991, GRID grid.35403.31, Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering), , University of Illinois at Urbana–Champaign, ; Urbana, IL USA
                [4 ]ISNI 0000 0004 0372 555X, GRID grid.260026.0, Department of Pulmonary and Critical Care Medicine, , Mie University Faculty and Graduate School of Medicine, ; Edobashi 2-174, Tsu, Mie 514-8507 Japan
                [5 ]ISNI 0000 0004 0372 555X, GRID grid.260026.0, Department of Diabetes and Endocrinology, , Mie University Faculty and Graduate School of Medicine, ; Edobashi 2-174, Tsu, Mie 514-8507 Japan
                [6 ]Respiratory Center, Matsusaka Municipal Hospital, Tonomachi 1550, Matsusaka, Mie 515-8544 Japan
                [7 ]ISNI 0000 0004 1936 9991, GRID grid.35403.31, The School of Molecular and Cellular Biology, , University of Illinois at Urbana–Champaign, ; Urbana, IL USA
                [8 ]ISNI 0000 0004 1936 9991, GRID grid.35403.31, Department of Animal Science, , University of Illinois at Urbana–Champaign, ; Urbana, IL USA
                [9 ]ISNI 0000 0004 1936 9991, GRID grid.35403.31, W.M. Keck Center for Functional and Comparative Genomics, , University of Illinois at Urbana–Champaign, ; Urbana, IL USA
                [10 ]ISNI 0000 0004 0372 555X, GRID grid.260026.0, Department of Neural Regeneration and Cell Communication, , Mie University Graduate School of Medicine, ; Tsu, Mie 14101 Japan
                [11 ]BioComo Incorporation, Komono, Mie 510-1233 Japan
                [12 ]ISNI 0000 0004 0372 555X, GRID grid.260026.0, Department of Microbiology and Molecular Genetics, , Mie University Graduate School of Medicine, ; Tsu, Mie 514-8507 Japan
                [13 ]ISNI 0000 0004 1772 6756, GRID grid.417192.8, Department of Respiratory Medicine and Allergy, Tosei General Hospital, ; 160 Nishioiwake-cho, Seto, Aichi 489-8642 Japan
                [14 ]ISNI 0000 0001 0656 4913, GRID grid.263536.7, Research Institute of Green Science and Technology, Graduate School of Agriculture, , Shizuoka University, ; 836 Ohya, Suruga-ku, Shizuoka, 422-8529 Japan
                [15 ]ISNI 0000 0001 0656 4913, GRID grid.263536.7, Green Chemistry Research Division, Research Institute of Green Science and Technology, , Shizuoka University, ; 836 Ohya, Suruga-ku, Shizuoka, 422-8529 Japan
                [16 ]ISNI 0000 0004 1936 9991, GRID grid.35403.31, Division of Nutritional Sciences, University of Illinois at Urbana–Champaign, ; Urbana, IL USA
                [17 ]ISNI 0000 0004 1936 9991, GRID grid.35403.31, Department of Microbiology, , University of Illinois at Urbana–Champaign, ; Urbana, IL USA
                Author information
                http://orcid.org/0000-0001-7937-474X
                http://orcid.org/0000-0002-7749-5844
                http://orcid.org/0000-0002-0037-7049
                http://orcid.org/0000-0001-5782-4981
                Article
                15344
                10.1038/s41467-020-15344-3
                7093394
                32210242
                53202130-e152-49c4-b24c-73e65ddbad95
                © The Author(s) 2020

                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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 6 June 2019
                : 3 March 2020
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                microbiome,translational research
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                microbiome, translational research

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