TIMD4 Rs6882076 SNP Is Associated with Decreased Levels Of
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Investigation of Functional Genes at Homologous Loci Identified Based
Journal of Atherosclerosis and Thrombosis Vol.22, No.5 455 Original Article Investigation of Functional Genes at Homologous Loci Identified Based on Genome-wide Association Studies of Blood Lipids via High-fat Diet Intervention in Rats using an in vivo Approach Koichi Akiyama, Yi-Qiang Liang, Masato Isono and Norihiro Kato Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan Aim: It is challenging to identify causal (or target) genes at individual loci detected using genome- wide association studies (GWAS). In order to follow up GWAS loci, we investigated functional genes at homologous loci identified using human lipid GWAS that responded to a high-fat, high-choles- terol diet (HFD) intervention in an animal model. Methods: The HFD intervention was carried out for four weeks in male rats of the spontaneously hypertensive rat strain. The liver and adipose tissues were subsequently excised for analyses of changes in the gene expression as compared to that observed in rats fed normal rat chow (n=8 per group). From 98 lipid-associated loci reported in previous GWAS, 280 genes with rat orthologs were initially selected as targets for the two-staged analysis involving screening with DNA microarray and validation with quantitative PCR (qPCR). Consequently, genes showing a differential expression due to HFD were examined for changes in the expression induced by atorvastatin, which was indepen- dently administered to the rats. Results: Using the HFD intervention in the rats, seven known (Abca1, Abcg5, Abcg8, Lpl, Nr1h3, Pcsk9 and Pltp) and three novel (Madd, Stac3 and Timd4) genes were identified as potential signifi- cant targets, with an additional list of 23 suggestive genes. -
Systems and Chemical Biology Approaches to Study Cell Function and Response to Toxins
Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences Presented by MSc. Yingying Jiang born in Shandong, China Oral-examination: Systems and chemical biology approaches to study cell function and response to toxins Referees: Prof. Dr. Rob Russell Prof. Dr. Stefan Wölfl CONTRIBUTIONS The chapter III of this thesis was submitted for publishing under the title “Drug mechanism predominates over toxicity mechanisms in drug induced gene expression” by Yingying Jiang, Tobias C. Fuchs, Kristina Erdeljan, Bojana Lazerevic, Philip Hewitt, Gordana Apic & Robert B. Russell. For chapter III, text phrases, selected tables, figures are based on this submitted manuscript that has been originally written by myself. i ABSTRACT Toxicity is one of the main causes of failure during drug discovery, and of withdrawal once drugs reached the market. Prediction of potential toxicities in the early stage of drug development has thus become of great interest to reduce such costly failures. Since toxicity results from chemical perturbation of biological systems, we combined biological and chemical strategies to help understand and ultimately predict drug toxicities. First, we proposed a systematic strategy to predict and understand the mechanistic interpretation of drug toxicities based on chemical fragments. Fragments frequently found in chemicals with certain toxicities were defined as structural alerts for use in prediction. Some of the predictions were supported with mechanistic interpretation by integrating fragment- chemical, chemical-protein, protein-protein interactions and gene expression data. Next, we systematically deciphered the mechanisms of drug actions and toxicities by analyzing the associations of drugs’ chemical features, biological features and their gene expression profiles from the TG-GATEs database. -
Recombinant T-Cell Immunoglobulin and Mucin Domain Containing Protein 4 (TIMD4)
RPH854Hu01 100µg Recombinant T-Cell Immunoglobulin And Mucin Domain Containing Protein 4 (TIMD4) Organism Species: Homo sapiens (Human) Instruction manual FOR RESEARCH USE ONLY NOT FOR USE IN CLINICAL DIAGNOSTIC PROCEDURES 12th Edition (Revised in Aug, 2016) 1 / 4 [ PROPERTIES ] Source: Prokaryotic expression Host: E.coli Residues: Glu25~Gln314 Tags: N-terminal His Tag Subcellular Location: Secreted Purity: > 95% Traits: Freeze-dried powder Buffer formulation: 100mMNaHCO3, 500mMNaCl, pH8.3, containing 0.01% SKL, 5% Trehalose. Original Concentration: 100µg/mL Applications: Positive Control; Immunogen; SDS-PAGE; WB. (May be suitable for use in other assays to be determined by the end user.) Predicted isoelectric point: Predicted Molecular Mass: 35.0kDa Accurate Molecular Mass: 40kDa as determined by SDS-PAGE reducing conditions. Phenomenon explanation: The possible reasons that the actual band size differs from the predicted are as follows: 1.Splice variants: Alternative splicing may create different sized proteins from the same gene. 2. Relative charge: The composition of amino acids may affects the charge of the protein. 3. Post-translational modification: Phosphorylation, glycosylation, methylation etc. 4. Post-translation cleavage: Many proteins are synthesized as pro-proteins, and then cleaved to give the active form. 5. Polymerization of the target protein: Dimerization, multimerization etc. [ USAGE ] Reconstitute in 100mM NaHCO3, 500mM NaCl (pH8.3) to a concentration of 0.1-1.0 mg/mL. Do not vortex. 2 / 4 [ STORAGE AND STABILITY ] Storage: Avoid repeated freeze/thaw cycles. Store at 2-8ºC for one month. Aliquot and store at -80ºC for 12 months. Stability Test: The thermal stability is described by the loss rate. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
Cellular Entry and Uncoating of Naked and Quasi-Enveloped Human
RESEARCH ARTICLE Cellular entry and uncoating of naked and quasi-enveloped human hepatoviruses Efraı´nE Rivera-Serrano1,2, Olga Gonza´ lez-Lo´ pez1,2, Anshuman Das2, Stanley M Lemon2,3* 1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States; 2Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, United States; 3Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, United States Abstract Many ‘non-enveloped’ viruses, including hepatitis A virus (HAV), are released non- lytically from infected cells as infectious, quasi-enveloped virions cloaked in host membranes. Quasi-enveloped HAV (eHAV) mediates stealthy cell-to-cell spread within the liver, whereas stable naked virions shed in feces are optimized for environmental transmission. eHAV lacks virus- encoded surface proteins, and how it enters cells is unknown. We show both virion types enter by clathrin- and dynamin-dependent endocytosis, facilitated by integrin b1, and traffic through early and late endosomes. Uncoating of naked virions occurs in late endosomes, whereas eHAV undergoes ALIX-dependent trafficking to lysosomes where the quasi-envelope is enzymatically degraded and uncoating ensues coincident with breaching of endolysosomal membranes. Neither virion requires PLA2G16, a phospholipase essential for entry of other picornaviruses. Thus naked and quasi-enveloped virions enter via similar endocytic pathways, but uncoat in different compartments and release their genomes to the cytosol in a manner mechanistically distinct from other Picornaviridae. DOI: https://doi.org/10.7554/eLife.43983.001 *For correspondence: [email protected] Competing interests: The Introduction authors declare that no The presence or absence of an external lipid envelope has featured strongly in the systematic classi- competing interests exist. -
Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A. -
1 Self-Maintaining Gut Macrophages Are Essential for Intestinal
Self-maintaining Gut Macrophages Are Essential for Intestinal Homeostasis De Schepper Sebastiaan1*, Verheijden Simon1*†, Aguilera-Lizarraga Javi1, Viola Maria Francesca1, Boesmans Werend2, Stakenborg Nathalie1, Voytyuk Iryna3, Smidt Inga3, Boeckx Bram4,5, Dierckx de Casterlé Isabelle6, Baekelandt Veerle7, Gonzalez Dominguez Erika1, Mack Matthias8, Depoortere Inge9, De Strooper Bart3, Sprangers Ben4, Himmelreich Uwe10, Soenen Stefaan10, Guilliams Martin11, Vanden Berghe Pieter2, Jones Elizabeth12, Lambrechts Diether5,6, Boeckxstaens Guy1 1Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, University of Leuven, Leuven, Belgium. 2Laboratory for Enteric Neuroscience, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, University of Leuven, Leuven, Belgium. 3VIB – KU Leuven Center for Brain and Disease Research, Leuven, Belgium. 4VIB Center for Cancer Biology, Leuven, Belgium. 5Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium. 6Laboratory of Experimental Transplantation, Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium. 7Research Group for Neurobiology and Gene Therapy, Department of Neurosciences, University of Leuven, Leuven, Belgium. 8Department of Internal Medicine – Nephrology, University Hospital Regensburg, Regensburg, Germany. 9Gut Peptide Research Lab, Translational -
Self-Renewing Resident Cardiac Macrophages Limit Adverse Remodeling Following Myocardial Infarction
JOURNAL CLUB 3/19/19 SAHIL MAHAJAN ARTICLES https://doi.org/10.1038/s41590-018-0272-2 Corrected: Publisher Correction Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction Sarah A. Dick1,2,11, Jillian A. Macklin 1,2,3,4,11, Sara Nejat 1,11, Abdul Momen1, Xavier Clemente-Casares1, Marwan G. Althagafi1,4, Jinmiao Chen 5,6, Crystal Kantores 1, Siyavash Hosseinzadeh1,4, Laura Aronoff1,4, Anthony Wong 1,7, Rysa Zaman 1,7, Iulia Barbu1,7, Rickvinder Besla1,4, Kory J. Lavine8, Babak Razani8,9, Florent Ginhoux 5,6, Mansoor Husain1,2,3,4,10, Myron I. Cybulsky1,4,10, Clinton S. Robbins1,4,7,10 and Slava Epelman 1,2,3,4,7,10* Macrophages promote both injury and repair after myocardial infarction, but discriminating functions within mixed populations remains challenging. Here we used fate mapping, parabiosis and single-cell transcriptomics to demonstrate that at steady state, TIMD4+LYVE1+MHC-IIloCCR2− resident cardiac macrophages self-renew with negligible blood monocyte input. Monocytes par- tially replaced resident TIMD4–LYVE1–MHC-IIhiCCR2− macrophages and fully replaced TIMD4−LYVE1−MHC-IIhiCCR2+ macro- phages, revealing a hierarchy of monocyte contribution to functionally distinct macrophage subsets. Ischemic injury reduced TIMD4+ and TIMD4– resident macrophage abundance, whereas CCR2+ monocyte-derived macrophages adopted multiple cell fates within infarcted tissue, including those nearly indistinguishable from resident macrophages. Recruited macrophages did not express TIMD4, highlighting the ability of TIMD4 to track a subset of resident macrophages in the absence of fate map- ping. Despite this similarity, inducible depletion of resident macrophages using a Cx3cr1-based system led to impaired cardiac function and promoted adverse remodeling primarily within the peri-infarct zone, revealing a nonredundant, cardioprotective role of resident cardiac macrophages. -
Pinaud-2021-Frontimmunol-New.P
New insights into biomphalysin gene family diversification in the vector snail Biomphalaria glabrata Silvain Pinaud, Guillaume Tetreau, Pierre Poteaux, Richard Galinier, Cristian Chaparro, Damien Lassalle, Anaïs Portet, Elodie Simphor, Benjamin Gourbal, David Duval To cite this version: Silvain Pinaud, Guillaume Tetreau, Pierre Poteaux, Richard Galinier, Cristian Chaparro, et al.. New insights into biomphalysin gene family diversification in the vector snail Biomphalaria glabrata. Fron- tiers in Immunology, Frontiers, 2021, 12, 10.3389/fimmu.2021.635131. hal-03219003 HAL Id: hal-03219003 https://hal.archives-ouvertes.fr/hal-03219003 Submitted on 6 May 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ORIGINAL RESEARCH published: 01 April 2021 doi: 10.3389/fimmu.2021.635131 New Insights Into Biomphalysin Gene Family Diversification in the Vector Edited by: Roberta Lima Caldeira, Snail Biomphalaria glabrata Oswaldo Cruz Foundation (Fiocruz), Brazil Silvain Pinaud 1,2†‡, Guillaume Tetreau 1,2‡, Pierre Poteaux 1,2, Richard Galinier 1,2, Reviewed by: Cristian Chaparro 1,2, Damien Lassalle 1,2, Anaïs Portet 1,2†, Elodie Simphor 1,2, Coenraad Adema, Benjamin Gourbal 1,2 and David Duval 1,2* University of New Mexico, United States 1 IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France, 2 CNRS, IFREMER, University of Maria G. -
Mammalian NPC1 Genes May Undergo Positive Selection And
Al-Daghri et al. BMC Medicine 2012, 10:140 http://www.biomedcentral.com/1741-7015/10/140 RESEARCHARTICLE Open Access Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes Nasser M Al-Daghri1,2,3*, Rachele Cagliani4, Diego Forni4, Majed S Alokail1,2,3, Uberto Pozzoli4, Khalid M Alkharfy1,2,3,5, Shaun Sabico1,2,3, Mario Clerici6,7† and Manuela Sironi4† Abstract Background: The NPC1 gene encodes a protein involved in intracellular lipid trafficking; its second endosomal loop (loop 2) is a receptor for filoviruses. A polymorphism (His215Arg) in NPC1 was associated with obesity in Europeans. Adaptations to diet and pathogens represented powerful selective forces; thus, we analyzed the evolutionary history of the gene and exploited this information for the identification of variants/residues of functional importance in human disease. Methods: We performed phylogenetic analysis, population genetic tests, and genotype-phenotype analysis in a population from Saudi Arabia. Results: Maximum-likelihood ratio tests indicated the action of positive selection on loop 2 and identified three residues as selection targets; these were confirmed by an independent random effects likelihood (REL) analysis. No selection signature was detected in present-day human populations, but analysis of nonsynonymous polymorphisms showed that a variant (Ile642Met, rs1788799) in the sterol sensing domain affects a highly conserved position. This variant and the previously described His215Arg polymorphism were tested for association with obesity and type 2 diabetes (T2D) in a cohort from Saudi Arabia. Whereas no association with obesity was detected, 642Met allele was found to predispose to T2D. A significant interaction was noted with sex (P = 0.041), and stratification on the basis of gender indicated that the association is driven by men (P = 0.0021, OR = 1.5). -
Methylation Epigenetic Landscape of Cpg DNA Defining CD4 T Cell Memory By
The Journal of Immunology Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation H. Kiyomi Komori, Traver Hart, Sarah A. LaMere, Pamela V. Chew, and Daniel R. Salomon Memory T cells are primed for rapid responses to Ag; however, the molecular mechanisms responsible for priming remain incom- pletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpGs) mapped by deep sequencing of T cell activation in human naive and memory CD4 T cells. Four hundred sixty-six CpGs (132 genes) displayed differential methylation between naive and memory cells. Twenty-one genes exhibited both differential methylation and gene expression before activation, linking pro- moter DNA methylation states to gene regulation; 6 of 21 genes encode proteins closely studied in T cells, whereas 15 genes represent novel targets for further study. Eighty-four genes demonstrated differential methylation between memory and naive cells that cor- related to differential gene expression following activation, of which 39 exhibited reduced methylation in memory cells coupled with increased gene expression upon activation compared with naive cells. These reveal a class of primed genes more rapidly expressed in memory compared with naive cells and putatively regulated by DNA methylation. These findings define a DNA methylation sig- nature unique to memory CD4 T cells that correlates with activation-induced gene expression. The Journal of Immunology, 2015, 194: 1565–1579. ifferentiation into fast-acting memory cells following Ag have a demethylated IL-4 gene promoter (10), do not express IFN-g, recognition is a central tenet of T cell immunology. -
Innate and Adaptive Immune Functions of Peyer's Patch
Innate and Adaptive Immune Functions of Peyer’s Patch Monocyte-Derived Cells Article Innate and Adaptive Immune Functions of Peyer’s Patch Monocyte-Derived Cells Johnny Bonnardel, Clément da Silva, Sandrine Henri, Samira Tamoutounour, Lionel Chasson, Frederic Montañana-Sanchis, Jean-Pierre Gorvel, Hugues Lelouard To cite this version: Johnny Bonnardel, Clément da Silva, Sandrine Henri, Samira Tamoutounour, Lionel Chasson, et al.. Innate and Adaptive Immune Functions of Peyer’s Patch Monocyte-Derived Cells Article Innate and Adaptive Immune Functions of Peyer’s Patch Monocyte-Derived Cells. Cell Reports, Elsevier Inc, 2015, pp.770-784. 10.1016/j.celrep.2015.03.067. hal-01212685 HAL Id: hal-01212685 https://hal-amu.archives-ouvertes.fr/hal-01212685 Submitted on 7 Oct 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Article Innate and Adaptive Immune Functions of Peyer’s Patch Monocyte-Derived Cells Graphical Abstract Authors Johnny Bonnardel, Cle´ ment Da Silva, ..., Jean-Pierre Gorvel, Hugues Lelouard Correspondence [email protected] In Brief Bonnardel et al. provide a comprehensive analysis of the phenotype, distribution, ontogeny, lifespan, function, and transcriptional profile of Peyer’s patch (PP) mononuclear phagocyte system.