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ANALYTICAL SCIENCES NOVEMBER 2020, VOL. 36 1 2020 © The Japan Society for Analytical Chemistry Supporting Information Fig. S1 Detailed MS/MS data of myoglobin. 17 2 ANALYTICAL SCIENCES NOVEMBER 2020, VOL. 36 Table S1 : The protein names (antigens) identified by pH 2.0 solution in the eluted-fraction. These proteins were identified one or more out of six analyses. Accession Description P08908 5-hydroxytryptamine receptor 1A OS=Homo sapiens GN=HTR1A PE=1 SV=3 - [5HT1A_HUMAN] Q9NRR6 72 kDa inositol polyphosphate 5-phosphatase OS=Homo sapiens GN=INPP5E PE=1 SV=2 - [INP5E_HUMAN] P82987 ADAMTS-like protein 3 OS=Homo sapiens GN=ADAMTSL3 PE=2 SV=4 - [ATL3_HUMAN] Q9Y6K8 Adenylate kinase isoenzyme 5 OS=Homo sapiens GN=AK5 PE=1 SV=2 - [KAD5_HUMAN] P02763 Alpha-1-acid glycoprotein 1 OS=Homo sapiens GN=ORM1 PE=1 SV=1 - [A1AG1_HUMAN] P19652 Alpha-1-acid glycoprotein 2 OS=Homo sapiens GN=ORM2 PE=1 SV=2 - [A1AG2_HUMAN] P01011 Alpha-1-antichymotrypsin OS=Homo sapiens GN=SERPINA3 PE=1 SV=2 - [AACT_HUMAN] P01009 Alpha-1-antitrypsin OS=Homo sapiens GN=SERPINA1 PE=1 SV=3 - [A1AT_HUMAN] P04217 Alpha-1B-glycoprotein OS=Homo sapiens GN=A1BG PE=1 SV=4 - [A1BG_HUMAN] P08697 Alpha-2-antiplasmin OS=Homo sapiens GN=SERPINF2 PE=1 SV=3 - [A2AP_HUMAN] P02765 Alpha-2-HS-glycoprotein OS=Homo sapiens GN=AHSG PE=1 SV=1 - [FETUA_HUMAN] P01023 Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 - [A2MG_HUMAN] P01019 Angiotensinogen OS=Homo sapiens GN=AGT PE=1 SV=1 - [ANGT_HUMAN] Q9NQ90 Anoctamin-2 OS=Homo sapiens GN=ANO2 PE=1 SV=2 - [ANO2_HUMAN] P01008 Antithrombin-III -
Genetic Screens in Isogenic Mammalian Cell Lines Without Single Cell Cloning
ARTICLE https://doi.org/10.1038/s41467-020-14620-6 OPEN Genetic screens in isogenic mammalian cell lines without single cell cloning Peter C. DeWeirdt1,2, Annabel K. Sangree1,2, Ruth E. Hanna1,2, Kendall R. Sanson1,2, Mudra Hegde 1, Christine Strand 1, Nicole S. Persky1 & John G. Doench 1* Isogenic pairs of cell lines, which differ by a single genetic modification, are powerful tools for understanding gene function. Generating such pairs of mammalian cells, however, is labor- 1234567890():,; intensive, time-consuming, and, in some cell types, essentially impossible. Here, we present an approach to create isogenic pairs of cells that avoids single cell cloning, and screen these pairs with genome-wide CRISPR-Cas9 libraries to generate genetic interaction maps. We query the anti-apoptotic genes BCL2L1 and MCL1, and the DNA damage repair gene PARP1, identifying both expected and uncharacterized buffering and synthetic lethal interactions. Additionally, we compare acute CRISPR-based knockout, single cell clones, and small- molecule inhibition. We observe that, while the approaches provide largely overlapping information, differences emerge, highlighting an important consideration when employing genetic screens to identify and characterize potential drug targets. We anticipate that this methodology will be broadly useful to comprehensively study gene function across many contexts. 1 Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA. 2These authors contributed equally: Peter C. DeWeirdt, -
Release Β ATP-Induced IL-1 and Canonical Nicotinic Agonists Inhibit Phosphocholine-Modified Macromolecules
Phosphocholine-Modified Macromolecules and Canonical Nicotinic Agonists Inhibit ATP-Induced IL-1β Release This information is current as Andreas Hecker, Mira Küllmar, Sigrid Wilker, Katrin of September 24, 2021. Richter, Anna Zakrzewicz, Srebrena Atanasova, Verena Mathes, Thomas Timm, Sabrina Lerner, Jochen Klein, Andreas Kaufmann, Stefan Bauer, Winfried Padberg, Wolfgang Kummer, Sabina Janciauskiene, Martin Fronius, Elke K. H. Schweda, Günter Lochnit and Veronika Grau Downloaded from J Immunol 2015; 195:2325-2334; Prepublished online 22 July 2015; doi: 10.4049/jimmunol.1400974 http://www.jimmunol.org/content/195/5/2325 http://www.jimmunol.org/ Supplementary http://www.jimmunol.org/content/suppl/2015/07/22/jimmunol.140097 Material 4.DCSupplemental References This article cites 42 articles, 11 of which you can access for free at: http://www.jimmunol.org/content/195/5/2325.full#ref-list-1 by guest on September 24, 2021 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2015 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. -
Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis
Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2010 Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis Ryan Fassnacht Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Physiology Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/2246 This Thesis is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Ryan C. Fassnacht 2010 All Rights Reserved Molecular Mechanisms Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. by Ryan Christopher Fassnacht, B.S. Hampden Sydney University, 2005 M.S. Virginia Commonwealth University, 2010 Director: Valeria Mas, Ph.D., Associate Professor of Surgery and Pathology Division of Transplant Department of Surgery Virginia Commonwealth University Richmond, Virginia July 9, 2010 Acknowledgement The Author wishes to thank his family and close friends for their support. He would also like to thank the members of the molecular transplant team for their help and advice. This project would not have been possible with out the help of Dr. Valeria Mas and her endearing -
List of Genes Used in Cell Type Enrichment Analysis
List of genes used in cell type enrichment analysis Metagene Cell type Immunity ADAM28 Activated B cell Adaptive CD180 Activated B cell Adaptive CD79B Activated B cell Adaptive BLK Activated B cell Adaptive CD19 Activated B cell Adaptive MS4A1 Activated B cell Adaptive TNFRSF17 Activated B cell Adaptive IGHM Activated B cell Adaptive GNG7 Activated B cell Adaptive MICAL3 Activated B cell Adaptive SPIB Activated B cell Adaptive HLA-DOB Activated B cell Adaptive IGKC Activated B cell Adaptive PNOC Activated B cell Adaptive FCRL2 Activated B cell Adaptive BACH2 Activated B cell Adaptive CR2 Activated B cell Adaptive TCL1A Activated B cell Adaptive AKNA Activated B cell Adaptive ARHGAP25 Activated B cell Adaptive CCL21 Activated B cell Adaptive CD27 Activated B cell Adaptive CD38 Activated B cell Adaptive CLEC17A Activated B cell Adaptive CLEC9A Activated B cell Adaptive CLECL1 Activated B cell Adaptive AIM2 Activated CD4 T cell Adaptive BIRC3 Activated CD4 T cell Adaptive BRIP1 Activated CD4 T cell Adaptive CCL20 Activated CD4 T cell Adaptive CCL4 Activated CD4 T cell Adaptive CCL5 Activated CD4 T cell Adaptive CCNB1 Activated CD4 T cell Adaptive CCR7 Activated CD4 T cell Adaptive DUSP2 Activated CD4 T cell Adaptive ESCO2 Activated CD4 T cell Adaptive ETS1 Activated CD4 T cell Adaptive EXO1 Activated CD4 T cell Adaptive EXOC6 Activated CD4 T cell Adaptive IARS Activated CD4 T cell Adaptive ITK Activated CD4 T cell Adaptive KIF11 Activated CD4 T cell Adaptive KNTC1 Activated CD4 T cell Adaptive NUF2 Activated CD4 T cell Adaptive PRC1 Activated -
Markers of T Cell Senescence in Humans
International Journal of Molecular Sciences Review Markers of T Cell Senescence in Humans Weili Xu 1,2 and Anis Larbi 1,2,3,4,5,* 1 Biology of Aging Program and Immunomonitoring Platform, Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Biopolis, Singapore 138648, Singapore; [email protected] 2 School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore 3 Department of Microbiology, National University of Singapore, Singapore 117597, Singapore 4 Department of Geriatrics, Faculty of Medicine, University of Sherbrooke, Sherbrooke, QC J1K 2R1, Canada 5 Faculty of Sciences, University ElManar, Tunis 1068, Tunisia * Correspondence: [email protected]; Tel.: +65-6407-0412 Received: 31 May 2017; Accepted: 26 July 2017; Published: 10 August 2017 Abstract: Many countries are facing the aging of their population, and many more will face a similar obstacle in the near future, which could be a burden to many healthcare systems. Increased susceptibility to infections, cardiovascular and neurodegenerative disease, cancer as well as reduced efficacy of vaccination are important matters for researchers in the field of aging. As older adults show higher prevalence for a variety of diseases, this also implies higher risk of complications, including nosocomial infections, slower recovery and sequels that may reduce the autonomy and overall quality of life of older adults. The age-related effects on the immune system termed as “immunosenescence” can be exemplified by the reported hypo-responsiveness to influenza vaccination of the elderly. T cells, which belong to the adaptive arm of the immune system, have been extensively studied and the knowledge gathered enables a better understanding of how the immune system may be affected after acute/chronic infections and how this matters in the long run. -
Recent Advances of M6a Methylation Modification in Esophageal Squamous Cell Carcinoma
Zhang et al. Cancer Cell Int (2021) 21:421 https://doi.org/10.1186/s12935-021-02132-2 Cancer Cell International REVIEW Open Access Recent advances of m6A methylation modifcation in esophageal squamous cell carcinoma Xiaoqing Zhang1†, Ning Lu1†, Li Wang2†, Yixuan Wang1, Minna Li1, Ying Zhou3, Manli Cui1*, Mingxin Zhang1,3* and Lingmin Zhang4* Abstract In recent years, with the development of RNA sequencing technology and bioinformatics methods, the epigenetic modifcation of RNA based on N6-methyladenosine (m6A) has gradually become a research hotspot in the feld of bioscience. m6A is the most abundant internal modifcation in eukaryotic messenger RNAs (mRNAs). m6A methylation modifcation can dynamically and reversibly regulate RNA transport, localization, translation and degradation through the interaction of methyltransferase, demethylase and reading protein. m6A methylation can regulate the expression of proto-oncogenes and tumor suppressor genes at the epigenetic modifcation level to afect tumor occurrence and metastasis. The morbidity and mortality of esophageal cancer (EC) are still high worldwide. Esophageal squamous cell carcinoma (ESCC) is the most common tissue subtype of EC. This article reviews the related concepts, biological functions and recent advances of m6A methylation in ESCC, and looks forward to the prospect of m6A methylation as a new diagnostic biomarker and potential therapeutic target for ESCC. Keywords: N6-methyladenosine, Methylation, Esophageal squamous cell carcinoma Introduction surgical resection, combined radiotherapy and chemo- Esophageal cancer (EC) is one of the most invasive malig- therapy have improved the prognosis of patients with nant tumors of digestive tract in the world, and its mor- ESCC, the 5-year overall survival rate is still very low [5], bidity and mortality are still high in China [1]. -
Cognition and Steroidogenesis in the Rhesus Macaque
Cognition and Steroidogenesis in the Rhesus Macaque Krystina G Sorwell A DISSERTATION Presented to the Department of Behavioral Neuroscience and the Oregon Health & Science University School of Medicine in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2013 School of Medicine Oregon Health & Science University CERTIFICATE OF APPROVAL This is to certify that the PhD dissertation of Krystina Gerette Sorwell has been approved Henryk Urbanski Mentor/Advisor Steven Kohama Member Kathleen Grant Member Cynthia Bethea Member Deb Finn Member 1 For Lily 2 TABLE OF CONTENTS Acknowledgments ......................................................................................................................................................... 4 List of Figures and Tables ............................................................................................................................................. 7 List of Abbreviations ................................................................................................................................................... 10 Abstract........................................................................................................................................................................ 13 Introduction ................................................................................................................................................................. 15 Part A: Central steroidogenesis and cognition ............................................................................................................ -
Human Β‑1,3‑Glucuronyltransferase 1/B3GAT1 Antibody Monoclonal Mouse Igg2a Clone # 1002707 Catalog Number: MAB8560
Human β‑1,3‑Glucuronyltransferase 1/B3GAT1 Antibody Monoclonal Mouse IgG2A Clone # 1002707 Catalog Number: MAB8560 DESCRIPTION Species Reactivity Human Specificity Detects human β-1,3-Glucuronyltransferase 1/B3GAT1 in direct ELISAs. Source Monoclonal Mouse IgG2A Clone # 1002707 Purification Protein A or G purified from hybridoma culture supernatant Immunogen Chinese Hamster Ovary cell line, CHO-derived human β‑1,3‑Glucuronyltransferase 1/B3GAT1 His25-Ile334 Accession # Q9P2W7 Formulation Lyophilized from a 0.2 μm filtered solution in PBS with Trehalose. See Certificate of Analysis for details. *Small pack size (-SP) is supplied either lyophilized or as a 0.2 μm filtered solution in PBS. APPLICATIONS Please Note: Optimal dilutions should be determined by each laboratory for each application. General Protocols are available in the Technical Information section on our website. Recommended Sample Concentration Immunohistochemistry 5-25 µg/mL See Below DATA Immunohistochemistry β-1,3-Glucuronyltransferase 1/B3GAT1 in Human Brain. β-1,3-Glucuronyltransferase 1/B3GAT1 was detected in immersion fixed paraffin-embedded sections of human brain (cortex) using Mouse Anti-Human β-1,3- Glucuronyltransferase 1/B3GAT1 Monoclonal Antibody (Catalog # MAB8560) at 5 µg/mL for 1 hour at room temperature followed by incubation with the Anti-Mouse IgG VisUCyte™ HRP Polymer Antibody (Catalog # VC001). Before incubation with the primary antibody, tissue was subjected to heat-induced epitope retrieval using Antigen Retrieval Reagent-Basic (Catalog # CTS013). Tissue was stained using DAB (brown) and counterstained with hematoxylin (blue). Specific staining was localized to cytoplasm in neurons. View our protocol for IHC Staining with VisUCyte HRP Polymer Detection Reagents. PREPARATION AND STORAGE Reconstitution Reconstitute at 0.5 mg/mL in sterile PBS. -
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. -
To Study Mutant P53 Gain of Function, Various Tumor-Derived P53 Mutants
Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science By Shama K Khokhar M.Sc., Bilaspur University, 2004 B.Sc., Bhopal University, 2002 2007 1 COPYRIGHT SHAMA K KHOKHAR 2007 2 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES Date of Defense: 12-03-07 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MY SUPERVISION BY SHAMA KHAN KHOKHAR ENTITLED Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science Madhavi P. Kadakia, Ph.D. Thesis Director Daniel Organisciak , Ph.D. Department Chair Committee on Final Examination Madhavi P. Kadakia, Ph.D. Steven J. Berberich, Ph.D. Michael Leffak, Ph.D. Joseph F. Thomas, Jr., Ph.D. Dean, School of Graduate Studies 3 Abstract Khokhar, Shama K. M.S., Department of Biochemistry and Molecular Biology, Wright State University, 2007 Differential effect of TAp63γ mutants on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. p63, a member of the p53 gene family, known to play a role in development, has more recently also been implicated in cancer progression. Mice lacking p63 exhibit severe developmental defects such as limb truncations, abnormal skin, and absence of hair follicles, teeth, and mammary glands. Germline missense mutations of p63 have been shown to be responsible for several human developmental syndromes including SHFM, EEC and ADULT syndromes and are associated with anomalies in the development of organs of epithelial origin. -
Understanding the Role of the Chromosome 15Q25.1 in COPD Through Epigenetics and Transcriptomics
European Journal of Human Genetics (2018) 26:709–722 https://doi.org/10.1038/s41431-017-0089-8 ARTICLE Understanding the role of the chromosome 15q25.1 in COPD through epigenetics and transcriptomics 1 1,2 1,3,4 5,6 5,6 Ivana Nedeljkovic ● Elena Carnero-Montoro ● Lies Lahousse ● Diana A. van der Plaat ● Kim de Jong ● 5,6 5,7 6 8 9 10 Judith M. Vonk ● Cleo C. van Diemen ● Alen Faiz ● Maarten van den Berge ● Ma’en Obeidat ● Yohan Bossé ● 11 1,12 12 1 David C. Nickle ● BIOS Consortium ● Andre G. Uitterlinden ● Joyce J. B. van Meurs ● Bruno C. H. Stricker ● 1,4,13 6,8 5,6 1 1 Guy G. Brusselle ● Dirkje S. Postma ● H. Marike Boezen ● Cornelia M. van Duijn ● Najaf Amin Received: 14 March 2017 / Revised: 6 November 2017 / Accepted: 19 December 2017 / Published online: 8 February 2018 © The Author(s) 2018. This article is published with open access Abstract Chronic obstructive pulmonary disease (COPD) is a major health burden in adults and cigarette smoking is considered the most important environmental risk factor of COPD. Chromosome 15q25.1 locus is associated with both COPD and smoking. Our study aims at understanding the mechanism underlying the association of chromosome 15q25.1 with COPD through epigenetic and transcriptional variation in a population-based setting. To assess if COPD-associated variants in 1234567890();,: 15q25.1 are methylation quantitative trait loci, epigenome-wide association analysis of four genetic variants, previously associated with COPD (P < 5 × 10−8) in the 15q25.1 locus (rs12914385:C>T-CHRNA3, rs8034191:T>C-HYKK, rs13180: C>T-IREB2 and rs8042238:C>T-IREB2), was performed in the Rotterdam study (n = 1489).