Exploring the Effect of Nssnps in Human YPEL3 Gene in Cellular
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Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
187093439.Pdf
CORE Metadata, citation and similar papers at core.ac.uk Provided by Apollo M BoC | ARTICLE Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions Georg H. H. Bornera, Marco Y. Heina,*, Jennifer Hirstb,*, James R. Edgarb, Matthias Manna, and Margaret S. Robinsonb aDepartment of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; bCambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom ABSTRACT We developed “fractionation profiling,” a method for rapid proteomic analysis Monitoring Editor of membrane vesicles and protein particles. The approach combines quantitative proteomics Adam Linstedt with subcellular fractionation to generate signature protein abundance distribution profiles. Carnegie Mellon University Functionally associated groups of proteins are revealed through cluster analysis. To validate Received: Jul 8, 2014 the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin- Revised: Aug 6, 2014 coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins fromDrosophila Accepted: Aug 7, 2014 S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin- coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale pro- tein interaction maps. -
Accepted By:- Signature Redacted Department of Biology Graduate Co-Chair: Michael T
EXPLORING THE FUNCTIONAL CONSERVATION OF MUSCLEBLIND (MBL) PROTEINS by MASSACH USETTS INSTITUTE Julia C. Oddo d o ECHNOLOGY B.S. Molecular, Cellular, and Developmental Biology, SE 1 7 2015 Minor Biochemistry 2011 LIB RARIES SUBMITTED TO THE DEPARTMENT OF BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTERS OF SCIENCE IN BIOLOGY AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY SEPTEMBER 2015 C 2015 Massachusetts Institute of Technology. All rights reserved. The author hereby grants to MIT permission to reproduce and to distribute publicly paper and electronic copies of this thesis document in whole or in part in any medium now known or hereafter created. Signature redacted Signature of Auth or:_ Department of Biology May 22, 2015 Certified by: Signature redacte Thesis Supervisor: Chris B. Burge Professor of Biology and Biological Engineering Director Program CSB Certified by: Signature redactec Thesis Co-Supervisor: Eric T. Wang Research Fellow Accepted by:- Signature redacted Department of Biology Graduate Co-Chair: Michael T. Hemann Associate Professor of Biology 1 EXPLORING THE FUNCTIONAL CONSERVATION OF MUSCLEBLIND (MBL) PROTEINS by Julia C. Oddo Submitted to the Department of Biology on September 8th, 2015 in Partial Fulfillment of the Requirements for the Degree of Master of Science in Biology ABSTRACT Muscleblind (Mbl) is an evolutionarily conserved family of proteins involved in many aspects of RNA metabolism, including alternative splicing. Disruption of Muscleblind in several animals lends to a variety of defects and disease, including the multi-systemic disorder Myotonic Dystrophy (DM). Though much is known about the involvement of Muscleblind in DM, there is much basic knowledge of the protein's function to be discovered. -
Large Meta-Analysis of Genome-Wide Association Studies
medRxiv preprint doi: https://doi.org/10.1101/2020.10.01.20200659; this version posted October 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Large meta-analysis of genome-wide association studies expands knowledge of the genetic etiology of Alzheimer’s disease and highlights potential translational opportunities Céline Bellenguez1,*,#, Fahri Küçükali2,3,4*, Iris Jansen5,6*, Victor Andrade7,8*, Sonia Morenau- Grau9,10,*, Najaf Amin11,12, Benjamin Grenier-Boley1, Anne Boland13, Luca Kleineidam7,8, Peter Holmans14, Pablo Garcia9,10, Rafael Campos Martin7, Adam Naj15,16, Yang Qiong17, Joshua C. Bis18, Vincent Damotte1, Sven Van der Lee5,6,19, Marcos Costa1, Julien Chapuis1, Vilmentas Giedraitis20, María Jesús Bullido10,21, Adolfo López de Munáin10,22, Jordi Pérez- Tur10,23, Pascual Sánchez-Juan10,24, Raquel Sánchez-Valle25, Victoria Álvarez26, Pau Pastor27, Miguel Medina10,28, Jasper Van Dongen2,3,4, Christine Van Broeckhoven2,3,4, Rik Vandenberghe29,30, Sebastiaan Engelborghs31,32, Gael Nicolas33, Florence Pasquier34, Olivier Hanon35, Carole Dufouil36, Claudine Berr37, Stéphanie Debette36, Jean-François Dartigues36, Gianfranco Spalletta38, Benedetta Nacmias39,40, Vincenzo Solfrezzi41, Barbara Borroni42, Lucio Tremolizzo43, Davide Seripa44, Paolo Caffarra45, Antonio Daniele46,47, Daniela Galimberti48,49, Innocenzo Rainero50, Luisa Benussi51, Alesio Squassina52, Patrizia Mecoci53, Lucilla Parnetti54, Carlo Masullo55, Beatrice Arosio56, John Hardy57, Simon Mead58, Kevin Morgan59, Clive Holmes60, Patrick Kehoe61, Bob Woods62, EADB, Charge, ADGC, Jin Sha15,16, Yi Zhao15,63, Chien-Yueh Lee15,63, Pavel P. -
WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT (51) International Patent Classification: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, C12Q 1/68 (2018.01) A61P 31/18 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/70 (2006.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2018/056167 OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (22) International Filing Date: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 16 October 2018 (16. 10.2018) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/573,025 16 October 2017 (16. 10.2017) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, ΓΕ , IS, IT, LT, LU, LV, (71) Applicant: MASSACHUSETTS INSTITUTE OF MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TECHNOLOGY [US/US]; 77 Massachusetts Avenue, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Cambridge, Massachusetts 02139 (US). -
NATURAL KILLER CELLS, HYPOXIA, and EPIGENETIC REGULATION of HEMOCHORIAL PLACENTATION by Damayanti Chakraborty Submitted to the G
NATURAL KILLER CELLS, HYPOXIA, AND EPIGENETIC REGULATION OF HEMOCHORIAL PLACENTATION BY Damayanti Chakraborty Submitted to the graduate degree program in Pathology and Laboratory Medicine and the Graduate Faculty of the University of Kansas in partial fulfillment ofthe requirements for the degree of Doctor of Philosophy. ________________________________ Chair: Michael J. Soares, Ph.D. ________________________________ Jay Vivian, Ph.D. ________________________________ Patrick Fields, Ph.D. ________________________________ Soumen Paul, Ph.D. ________________________________ Michael Wolfe, Ph.D. ________________________________ Adam J. Krieg, Ph.D. Date Defended: 04/01/2013 The Dissertation Committee for Damayanti Chakraborty certifies that this is the approved version of the following dissertation: NATURAL KILLER CELLS, HYPOXIA, AND EPIGENETIC REGULATION OF HEMOCHORIAL PLACENTATION ________________________________ Chair: Michael J. Soares, Ph.D. Date approved: 04/01/2013 ii ABSTRACT During the establishment of pregnancy, uterine stromal cells differentiate into decidual cells and recruit natural killer (NK) cells. These NK cells are characterized by low cytotoxicity and distinct cytokine production. In rodent as well as in human pregnancy, the uterine NK cells peak in number around mid-gestation after which they decline. NK cells associate with uterine spiral arteries and are implicated in pregnancy associated vascular remodeling processes and potentially in modulating trophoblast invasion. Failure of trophoblast invasion and vascular remodeling has been shown to be associated with pathological conditions like preeclampsia syndrome, hypertension in mother and/or fetal growth restriction. We hypothesize that NK cells fundamentally contribute to the organization of the placentation site. In order to study the in vivo role of NK cells during pregnancy, gestation stage- specific NK cell depletion was performed in rats using anti asialo GM1 antibodies. -
Associated 16P11.2 Deletion in Drosophila Melanogaster
ARTICLE DOI: 10.1038/s41467-018-04882-6 OPEN Pervasive genetic interactions modulate neurodevelopmental defects of the autism- associated 16p11.2 deletion in Drosophila melanogaster Janani Iyer1, Mayanglambam Dhruba Singh1, Matthew Jensen1,2, Payal Patel 1, Lucilla Pizzo1, Emily Huber1, Haley Koerselman3, Alexis T. Weiner 1, Paola Lepanto4, Komal Vadodaria1, Alexis Kubina1, Qingyu Wang 1,2, Abigail Talbert1, Sneha Yennawar1, Jose Badano 4, J. Robert Manak3,5, Melissa M. Rolls1, Arjun Krishnan6,7 & 1234567890():,; Santhosh Girirajan 1,2,8 As opposed to syndromic CNVs caused by single genes, extensive phenotypic heterogeneity in variably-expressive CNVs complicates disease gene discovery and functional evaluation. Here, we propose a complex interaction model for pathogenicity of the autism-associated 16p11.2 deletion, where CNV genes interact with each other in conserved pathways to modulate expression of the phenotype. Using multiple quantitative methods in Drosophila RNAi lines, we identify a range of neurodevelopmental phenotypes for knockdown of indi- vidual 16p11.2 homologs in different tissues. We test 565 pairwise knockdowns in the developing eye, and identify 24 interactions between pairs of 16p11.2 homologs and 46 interactions between 16p11.2 homologs and neurodevelopmental genes that suppress or enhance cell proliferation phenotypes compared to one-hit knockdowns. These interac- tions within cell proliferation pathways are also enriched in a human brain-specific network, providing translational relevance in humans. Our study indicates a role for pervasive genetic interactions within CNVs towards cellular and developmental phenotypes. 1 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. 2 Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA. -
Chromosome Abnormalities in Two Patients with Features of Autosomal Dominant Robinow Syndrome
ß 2007 Wiley-Liss, Inc. American Journal of Medical Genetics Part A 143A:1790–1795 (2007) Research Letter Chromosome Abnormalities in Two Patients With Features of Autosomal Dominant Robinow Syndrome Juliana F. Mazzeu,1 Ana Cristina Krepischi-Santos,1 Carla Rosenberg,1 Karoly Szuhai,2 Jeroen Knijnenburg,2 Janneke M.M. Weiss,3 Irina Kerkis,1 Zan Mustacchi,4 Guilherme Colin,5 Roˆmulo Mombach,6 Rita de Ca´ssia M. Pavanello,1 Paulo A. Otto,1 and Angela M. Vianna-Morgante1* 1Centro de Estudos do Genoma Humano, Departamento de Gene´tica e Biologia Evolutiva, Instituto de Biocieˆncias, Universidade de Sa˜o Paulo, Sa˜o Paulo, Brazil 2Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands 3Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands 4Hospital Infantil Darcy Vargas, Sa˜o Paulo, Brazil 5Departamento de Gene´tica Me´dica, Univille, Joinville, Brazil 6Centrinho Prefeito Luiz Gomes, Secretaria Municipal de Sau´de, Joinville, Brazil Received 13 April 2006; Accepted 13 December 2006 How to cite this article: Mazzeu JF, Krepischi-Santos AC, Rosenberg C, Szuhai K, Knijnenburg J, Weiss JMM, Kerkis I, Mustacchi Z, Colin G, Mombach R, Pavanello RM, Otto PA, Vianna-Morgante AM. 2007. Chromosome abnormalities in two patients with features of autosomal dominant Robinow syndrome. Am J Med Genet Part A 143A:1790–1795. To the Editor: Patient 1 Robinow syndrome [OMIM 180700] is characteriz- At age 3 4/12 years the girl was diagnosed as ed by fetal facies, mesomelic dwarfism, and hypo- affected by DRS (Fig. 1A). Detailed clinical examina- plastic genitalia. -
Genome-Wide Profiling of Promoter Methylation in Human
Oncogene (2006) 25, 3059–3064 & 2006 Nature Publishing Group All rights reserved 0950-9232/06 $30.00 www.nature.com/onc TECHNICAL REPORT Genome-wide profiling of promoter methylation in human I Hatada1,2, M Fukasawa1,2, M Kimura1,2, S Morita1,2, K Yamada3, T Yoshikawa3, S Yamanaka4,5, C Endo4, A Sakurada4, M Sato4, T Kondo4, A Horii5, T Ushijima6 and H Sasaki7,8 1Laboratory of Genome Science, Biosignal Genome Resource Center, Department of Molecular and Cellular Biology, Gunma University, Maebashi, Japan; 2PRESTO, Japan Science and Technology Corporation (JST), Kawaguchi, Japan; 3Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan, 4Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan; 5Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan; 6Carcinogenesis Division, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan; 7Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan and 8Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan DNA methylation in the promoter region of a gene is Microarray-based methods of comparing differences in associated with a loss of that gene’s expression and plays DNA methylation in the genome of two samples using an important role in gene silencing. The inactivation of methylation-sensitive restriction enzymes (Yan et al., tumor-suppressor genes by aberrant methylation in the 2001; Hatada et al., 2002) have two problems. The first promoter region is well recognized in carcinogenesis. is that the microarrays contain clones from libraries of However, there has been little study in this area when it CpG islands. -
Genome-Wide Methylation Study on Depression: Differential Methylation and Variable Methylation in Monozygotic Twins
OPEN Citation: Transl Psychiatry (2015) 5, e557; doi:10.1038/tp.2015.49 www.nature.com/tp ORIGINAL ARTICLE Genome-wide methylation study on depression: differential methylation and variable methylation in monozygotic twins A Córdova-Palomera1,2, M Fatjó-Vilas1,2, C Gastó2,3,4, V Navarro2,3,4, M-O Krebs5,6,7 and L Fañanás1,2 Depressive disorders have been shown to be highly influenced by environmental pathogenic factors, some of which are believed to exert stress on human brain functioning via epigenetic modifications. Previous genome-wide methylomic studies on depression have suggested that, along with differential DNA methylation, affected co-twins of monozygotic (MZ) pairs have increased DNA methylation variability, probably in line with theories of epigenetic stochasticity. Nevertheless, the potential biological roots of this variability remain largely unexplored. The current study aimed to evaluate whether DNA methylation differences within MZ twin pairs were related to differences in their psychopathological status. Data from the Illumina Infinium HumanMethylation450 Beadchip was used to evaluate peripheral blood DNA methylation of 34 twins (17 MZ pairs). Two analytical strategies were used to identify (a) differentially methylated probes (DMPs) and (b) variably methylated probes (VMPs). Most DMPs were located in genes previously related to neuropsychiatric phenotypes. Remarkably, one of these DMPs (cg01122889) was located in the WDR26 gene, the DNA sequence of which has been implicated in major depressive disorder from genome-wide association studies. Expression of WDR26 has also been proposed as a biomarker of depression in human blood. Complementarily, VMPs were located in genes such as CACNA1C, IGF2 and the p38 MAP kinase MAPK11, showing enrichment for biological processes such as glucocorticoid signaling.