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  • 1
    Publication Date: 2013-11-15
    Description: Gut commensal microbes shape the mucosal immune system by regulating the differentiation and expansion of several types of T cell. Clostridia, a dominant class of commensal microbe, can induce colonic regulatory T (Treg) cells, which have a central role in the suppression of inflammatory and allergic responses. However, the molecular mechanisms by which commensal microbes induce colonic Treg cells have been unclear. Here we show that a large bowel microbial fermentation product, butyrate, induces the differentiation of colonic Treg cells in mice. A comparative NMR-based metabolome analysis suggests that the luminal concentrations of short-chain fatty acids positively correlates with the number of Treg cells in the colon. Among short-chain fatty acids, butyrate induced the differentiation of Treg cells in vitro and in vivo, and ameliorated the development of colitis induced by adoptive transfer of CD4(+) CD45RB(hi) T cells in Rag1(-/-) mice. Treatment of naive T cells under the Treg-cell-polarizing conditions with butyrate enhanced histone H3 acetylation in the promoter and conserved non-coding sequence regions of the Foxp3 locus, suggesting a possible mechanism for how microbial-derived butyrate regulates the differentiation of Treg cells. Our findings provide new insight into the mechanisms by which host-microbe interactions establish immunological homeostasis in the gut.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Furusawa, Yukihiro -- Obata, Yuuki -- Fukuda, Shinji -- Endo, Takaho A -- Nakato, Gaku -- Takahashi, Daisuke -- Nakanishi, Yumiko -- Uetake, Chikako -- Kato, Keiko -- Kato, Tamotsu -- Takahashi, Masumi -- Fukuda, Noriko N -- Murakami, Shinnosuke -- Miyauchi, Eiji -- Hino, Shingo -- Atarashi, Koji -- Onawa, Satoshi -- Fujimura, Yumiko -- Lockett, Trevor -- Clarke, Julie M -- Topping, David L -- Tomita, Masaru -- Hori, Shohei -- Ohara, Osamu -- Morita, Tatsuya -- Koseki, Haruhiko -- Kikuchi, Jun -- Honda, Kenya -- Hase, Koji -- Ohno, Hiroshi -- England -- Nature. 2013 Dec 19;504(7480):446-50. doi: 10.1038/nature12721. Epub 2013 Nov 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230-0045, Japan [2] The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan [3]. ; 1] RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230-0045, Japan [2] The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan [3] Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan [4]. ; 1] RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230-0045, Japan [2] Institute for Advanced Biosciences, Keio University, Yamagata 997-0052, Japan [3]. ; RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230-0045, Japan. ; Institute for Advanced Biosciences, Keio University, Yamagata 997-0052, Japan. ; 1] RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230-0045, Japan [2] Graduate School of Medical Life Science, Yokohama City University, Kanagawa 230-0045, Japan. ; Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan. ; 1] RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230-0045, Japan [2] PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan. ; The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan. ; Preventative Health National Research Flagship, CSIRO Food and Nutritional Sciences, South Australia 5000, Australia. ; 1] RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230-0045, Japan [2] Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan [3] Graduate School of Medical Life Science, Yokohama City University, Kanagawa 230-0045, Japan. ; 1] Graduate School of Medical Life Science, Yokohama City University, Kanagawa 230-0045, Japan [2] RIKEN Center for Sustainable Resource Science, Kanagawa 230-0045, Japan. ; 1] RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230-0045, Japan [2] CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan. ; 1] RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Kanagawa 230-0045, Japan [2] The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan [3] PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan [4].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24226770" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation/drug effects ; Adoptive Transfer ; Animals ; Butyrates/analysis/*metabolism/pharmacology ; *Cell Differentiation/drug effects ; Colitis/drug therapy/pathology ; Colon/cytology/*immunology/metabolism/*microbiology ; Conserved Sequence ; Female ; *Fermentation ; Forkhead Transcription Factors/genetics ; Germ-Free Life ; Histones/metabolism ; Homeostasis/drug effects ; Intestinal Mucosa/cytology/immunology ; Lymphocyte Count ; Magnetic Resonance Spectroscopy ; Male ; Metabolome ; Mice ; Promoter Regions, Genetic/drug effects ; *Symbiosis ; T-Lymphocytes, Regulatory/*cytology/drug effects/immunology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2017-07-06
    Description: Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis -regulatory mutations. Here we propose a simple method to decompose cis -regulatory ( i.e. , allelic genotype), genomic imprinting [ i.e. , parent-of-origin (PO)], and maternal [ i.e. , maternal genotype (MG)] effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 3
    Publication Date: 2016-10-12
    Description: Author(s): J. J. T. Wagenaar, A. M. J. den Haan, J. M. de Voogd, L. Bossoni, T. A. de Jong, M. de Wit, K. M. Bastiaans, D. J. Thoen, A. Endo, T. M. Klapwijk, J. Zaanen, and T. H. Oosterkamp The nuclear spin-lattice relaxation time T 1 is an important probe of the electronic properties of solids, but here traditional NMR methods struggle due to weak signals, so advanced tools like magnetic resonance force microscopy (MRFM) are needed. The authors extend high-resolution MRFM to measure T 1 at a temperature of 42 mK, a 100-fold improvement, with a 1000-fold increase in volume sensitivity. This opens up the possibility to measure the magnetic properties of oxide interfaces, topological insulators, high- T c superconductors, and other strongly correlated electron systems. [Phys. Rev. Applied 6, 014007] Published Fri Jul 15, 2016
    Electronic ISSN: 2331-7019
    Topics: Physics
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  • 4
    Publication Date: 2004-04-08
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 5
    Publication Date: 2009-06-15
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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