Supplementary Material Toxicological Impacts and Likely Protein Targets Of
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Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas
Supplementary Online Content Thaivalappil S, Bauman N, Saieg A, Movius E, Brown KJ, Preciado D. Propranolol-mediated attenuation of MMP-9 excretion in infants with hemangiomas. JAMA Otolaryngol Head Neck Surg. doi:10.1001/jamaoto.2013.4773 eTable. List of All of the Proteins Identified by Proteomics This supplementary material has been provided by the authors to give readers additional information about their work. © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable. List of All of the Proteins Identified by Proteomics Protein Name Prop 12 mo/4 Pred 12 mo/4 Δ Prop to Pred mo mo Myeloperoxidase OS=Homo sapiens GN=MPO 26.00 143.00 ‐117.00 Lactotransferrin OS=Homo sapiens GN=LTF 114.00 205.50 ‐91.50 Matrix metalloproteinase‐9 OS=Homo sapiens GN=MMP9 5.00 36.00 ‐31.00 Neutrophil elastase OS=Homo sapiens GN=ELANE 24.00 48.00 ‐24.00 Bleomycin hydrolase OS=Homo sapiens GN=BLMH 3.00 25.00 ‐22.00 CAP7_HUMAN Azurocidin OS=Homo sapiens GN=AZU1 PE=1 SV=3 4.00 26.00 ‐22.00 S10A8_HUMAN Protein S100‐A8 OS=Homo sapiens GN=S100A8 PE=1 14.67 30.50 ‐15.83 SV=1 IL1F9_HUMAN Interleukin‐1 family member 9 OS=Homo sapiens 1.00 15.00 ‐14.00 GN=IL1F9 PE=1 SV=1 MUC5B_HUMAN Mucin‐5B OS=Homo sapiens GN=MUC5B PE=1 SV=3 2.00 14.00 ‐12.00 MUC4_HUMAN Mucin‐4 OS=Homo sapiens GN=MUC4 PE=1 SV=3 1.00 12.00 ‐11.00 HRG_HUMAN Histidine‐rich glycoprotein OS=Homo sapiens GN=HRG 1.00 12.00 ‐11.00 PE=1 SV=1 TKT_HUMAN Transketolase OS=Homo sapiens GN=TKT PE=1 SV=3 17.00 28.00 ‐11.00 CATG_HUMAN Cathepsin G OS=Homo -
Part One Amino Acids As Building Blocks
Part One Amino Acids as Building Blocks Amino Acids, Peptides and Proteins in Organic Chemistry. Vol.3 – Building Blocks, Catalysis and Coupling Chemistry. Edited by Andrew B. Hughes Copyright Ó 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-32102-5 j3 1 Amino Acid Biosynthesis Emily J. Parker and Andrew J. Pratt 1.1 Introduction The ribosomal synthesis of proteins utilizes a family of 20 a-amino acids that are universally coded by the translation machinery; in addition, two further a-amino acids, selenocysteine and pyrrolysine, are now believed to be incorporated into proteins via ribosomal synthesis in some organisms. More than 300 other amino acid residues have been identified in proteins, but most are of restricted distribution and produced via post-translational modification of the ubiquitous protein amino acids [1]. The ribosomally encoded a-amino acids described here ultimately derive from a-keto acids by a process corresponding to reductive amination. The most important biosynthetic distinction relates to whether appropriate carbon skeletons are pre-existing in basic metabolism or whether they have to be synthesized de novo and this division underpins the structure of this chapter. There are a small number of a-keto acids ubiquitously found in core metabolism, notably pyruvate (and a related 3-phosphoglycerate derivative from glycolysis), together with two components of the tricarboxylic acid cycle (TCA), oxaloacetate and a-ketoglutarate (a-KG). These building blocks ultimately provide the carbon skeletons for unbranched a-amino acids of three, four, and five carbons, respectively. a-Amino acids with shorter (glycine) or longer (lysine and pyrrolysine) straight chains are made by alternative pathways depending on the available raw materials. -
Novel Missense Mutation in PTPN22 in a Chinese Pedigree With
Gong et al. BMC Endocrine Disorders (2018) 18:76 https://doi.org/10.1186/s12902-018-0305-8 RESEARCHARTICLE Open Access Novel missense mutation in PTPN22 in a Chinese pedigree with Hashimoto’s thyroiditis Licheng Gong1†, Beihong Liu2,3†, Jing Wang4, Hong Pan3, Anhui Qi2,3, Siyang Zhang2,3, Jinyi Wu1, Ping Yang1* and Binbin Wang3,4,5* Abstract Background: Hashimoto’s thyroiditis is a complex autoimmune thyroid disease, the onset of which is associated with environmental exposures and specific susceptibility genes. Its incidence in females is higher than its incidence in males. Thus far, although some susceptibility loci have been elaborated, including PTPN22, FOXP3, and CD25, the aetiology and pathogenesis of Hashimoto’s thyroiditis remains unclear. Methods: Four affected members from a Chinese family with Hashimoto’s thyroiditis were selected for whole-exome sequencing. Missense, nonsense, frameshift, or splicing-site variants shared by all affected members were identified after frequency filtering against public and internal exome databases. Segregation analysis was performed by Sanger sequencing among all members with available DNA. Results: We identified a missense mutation in PTPN22 (NM_015967.5; c. 77A > G; p.Asn26Ser) using whole-exome sequencing. PTPN22 is a known susceptibility gene associated with increased risks of multiple autoimmune diseases. Cosegregation analysis confirmed that all patients in this family, all of whom were female, carried the mutation. All public and private databases showed that the missense mutation was extremely rare. Conclusions: We found a missense mutation in PTPN22 in a Chinese HT pedigree using whole-exome sequencing. Our study, for the first time, linked a rare variant of PTPN22 to Hashimoto’s thyroiditis, providing further evidence of the disease-causing or susceptibility role of PTPN22 in autoimmune thyroid disease. -
Insights Into Diphthamide, Key Diphtheria Toxin Effector
Toxins 2013, 5, 958-968; doi:10.3390/toxins5050958 OPEN ACCESS toxins ISSN 2072-6651 www.mdpi.com/journal/toxins Brief Report Insights into Diphthamide, Key Diphtheria Toxin Effector Wael Abdel-Fattah 1,†, Viktor Scheidt 1,†, Shanow Uthman 2, Michael J. R. Stark 3 and Raffael Schaffrath 1,2,* 1 Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel D-34132, Germany; E-Mails: [email protected] (W.A.-F.); [email protected] (V.S.) 2 Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; E-Mail: [email protected] 3 Centre for Gene Regulation & Expression, University of Dundee, Dundee, DD1 5EH, Scotland; E-Mail: [email protected] † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +49-561-804-4175; Fax: +49-561-804-4337. Received: 14 March 2013; in revised form: 17 April 2013 / Accepted: 26 April 2013 / Published: 3 May 2013 Abstract: Diphtheria toxin (DT) inhibits eukaryotic translation elongation factor 2 (eEF2) by ADP-ribosylation in a fashion that requires diphthamide, a modified histidine residue on eEF2. In budding yeast, diphthamide formation involves seven genes, DPH1-DPH7. In an effort to further study diphthamide synthesis and interrelation among the Dph proteins, we found, by expression in E. coli and co-immune precipitation in yeast, that Dph1 and Dph2 interact and that they form a complex with Dph3. Protein-protein interaction mapping shows that Dph1-Dph3 complex formation can be dissected by progressive DPH1 gene truncations. This identifies N- and C-terminal domains on Dph1 that are crucial for diphthamide synthesis, DT action and cytotoxicity of sordarin, another microbial eEF2 inhibitor. -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
Symphytum Officinale) Hairy Roots by Rnai Silencing of Homospermidine Synthase
Published online: 2019-08-26 Original Papers Reduction of Pyrrolizidine Alkaloid Levels in Comfrey (Symphytum officinale) Hairy Roots by RNAi Silencing of Homospermidine Synthase Authors Lars H. Kruse 1, 3, Thomas Stegemann1, Julia Jensen-Kroll 1, Annika Engelhardt 1, Anne-Maria Wesseling 1, Annemarie Lippert 2, Jutta Ludwig-Müller 2,DietrichOber1 Affiliations ABSTRACT 1 Botanisches Institut, Kiel University, Kiel, Germany Comfrey is a medicinal plant, extracts of which are tradition- 2 Institut für Botanik, Technische Universität Dresden, ally used for the treatment of painful inflammatory muscle Dresden, Germany and joint problems, because the plant contains allantoin and 3 Plant Biology Section, School of Integrative Plant Science, rosmarinic acid. However, its medicinal use is limited because Cornell University, USA of its toxic pyrrolizidine alkaloid (PA) content. PAs encompass more than 400 different compounds that have been identified Key words from various plant lineages. To date, only the first pathway- Symphytum officinale, alkaloid extraction, transgenic tissue specific enzyme, homospermidine synthase (HSS), has been culture, transcript quantification, Boraginaceae characterized. HSS catalyzes the formation of homospermi- dine, which is exclusively incorporated into PAs. HSS has been received May 6, 2019 recruited several times independently in various plant line- revised August 5, 2019 ages during evolution by duplication of the gene encoding de- accepted August 15, 2019 oxyhypusine synthase (DHS), an enzyme of primary metabo- Bibliography lism. Here, we describe the establishment of RNAi knockdown DOI https://doi.org/10.1055/a-0998-5125 hairy root mutants of HSS in Symphytum officinale. A knock- – Published online August 26, 2019 | Planta Med 2019; 85: down of HSS by 60 80% resulted in a significant reduction of 1177–1186 © Georg Thieme Verlag KG Stuttgart · New York | homospermidine by ~ 86% and of the major PA components ‑ ‑ ISSN 0032‑0943 7 acetylintermedine N-oxide and 3 acetylmyoscorpine N-ox- ide by approximately 60%. -
Symbiotic Adaptations in the Fungal Cultivar of Leaf-Cutting Ants
ARTICLE Received 15 Apr 2014 | Accepted 24 Oct 2014 | Published 1 Dec 2014 DOI: 10.1038/ncomms6675 Symbiotic adaptations in the fungal cultivar of leaf-cutting ants Henrik H. De Fine Licht1,w, Jacobus J. Boomsma2 & Anders Tunlid1 Centuries of artificial selection have dramatically improved the yield of human agriculture; however, strong directional selection also occurs in natural symbiotic interactions. Fungus- growing attine ants cultivate basidiomycete fungi for food. One cultivar lineage has evolved inflated hyphal tips (gongylidia) that grow in bundles called staphylae, to specifically feed the ants. Here we show extensive regulation and molecular signals of adaptive evolution in gene trancripts associated with gongylidia biosynthesis, morphogenesis and enzymatic plant cell wall degradation in the leaf-cutting ant cultivar Leucoagaricus gongylophorus. Comparative analysis of staphylae growth morphology and transcriptome-wide expressional and nucleotide divergence indicate that gongylidia provide leaf-cutting ants with essential amino acids and plant-degrading enzymes, and that they may have done so for 20–25 million years without much evolutionary change. These molecular traits and signatures of selection imply that staphylae are highly advanced coevolutionary organs that play pivotal roles in the mutualism between leaf-cutting ants and their fungal cultivars. 1 Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden. 2 Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark. w Present Address: Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark. Correspondence and requests for materials should be addressed to H.H.D.F.L. -
Production of Muconic Acid in Plants T ⁎ Aymerick Eudesa,B, , Roland Berthomieua,C, Zhangying Haoa,B, Nanxia Zhaoa,D, ⁎ Veronica Teixeira Benitesa,E, Edward E.K
Metabolic Engineering 46 (2018) 13–19 Contents lists available at ScienceDirect Metabolic Engineering journal homepage: www.elsevier.com/locate/meteng Production of muconic acid in plants T ⁎ Aymerick Eudesa,b, , Roland Berthomieua,c, Zhangying Haoa,b, Nanxia Zhaoa,d, ⁎ Veronica Teixeira Benitesa,e, Edward E.K. Baidooa,e, Dominique Loquéa,b,f,g, a Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA b Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA c Ecole Polytechnique, Université Paris-Saclay, Palaiseau 91120, France d Department of Bioengineering, Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA e Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA f Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA g Université Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France ARTICLE INFO ABSTRACT Keywords: Muconic acid (MA) is a dicarboxylic acid used for the production of industrially relevant chemicals such as Muconic acid adipic acid, terephthalic acid, and caprolactam. Because the synthesis of these polymer precursors generates Salicylic acid toxic intermediates by utilizing petroleum-derived chemicals and corrosive catalysts, the development of al- Catechol ternative strategies for the bio-based production of MA has garnered significant interest. Plants produce organic Shikimate carbon skeletons by harvesting carbon dioxide and energy from the sun, and therefore represent advantageous Plastid hosts for engineered metabolic pathways towards the manufacturing of chemicals. -
(12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown Et Al
US 20030082511A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown et al. (43) Pub. Date: May 1, 2003 (54) IDENTIFICATION OF MODULATORY Publication Classification MOLECULES USING INDUCIBLE PROMOTERS (51) Int. Cl." ............................... C12O 1/00; C12O 1/68 (52) U.S. Cl. ..................................................... 435/4; 435/6 (76) Inventors: Steven J. Brown, San Diego, CA (US); Damien J. Dunnington, San Diego, CA (US); Imran Clark, San Diego, CA (57) ABSTRACT (US) Correspondence Address: Methods for identifying an ion channel modulator, a target David B. Waller & Associates membrane receptor modulator molecule, and other modula 5677 Oberlin Drive tory molecules are disclosed, as well as cells and vectors for Suit 214 use in those methods. A polynucleotide encoding target is San Diego, CA 92121 (US) provided in a cell under control of an inducible promoter, and candidate modulatory molecules are contacted with the (21) Appl. No.: 09/965,201 cell after induction of the promoter to ascertain whether a change in a measurable physiological parameter occurs as a (22) Filed: Sep. 25, 2001 result of the candidate modulatory molecule. Patent Application Publication May 1, 2003 Sheet 1 of 8 US 2003/0082511 A1 KCNC1 cDNA F.G. 1 Patent Application Publication May 1, 2003 Sheet 2 of 8 US 2003/0082511 A1 49 - -9 G C EH H EH N t R M h so as se W M M MP N FIG.2 Patent Application Publication May 1, 2003 Sheet 3 of 8 US 2003/0082511 A1 FG. 3 Patent Application Publication May 1, 2003 Sheet 4 of 8 US 2003/0082511 A1 KCNC1 ITREXCHO KC 150 mM KC 2000000 so 100 mM induced Uninduced Steady state O 100 200 300 400 500 600 700 Time (seconds) FIG. -
In TCR-Stimulated Thymocytes Induction of Chromosomal DNA Degradation Caspase-Activated Deoxyribonuclease in the Possible Involv
Possible Involvement of Cyclophilin B and Caspase-Activated Deoxyribonuclease in the Induction of Chromosomal DNA Degradation in TCR-Stimulated Thymocytes This information is current as of September 28, 2021. Takuya Nagata, Hiroyuki Kishi, Qing Li Liu, Tomoyasu Yoshino, Tadashi Matsuda, Zhe Xiong Jin, Kimie Murayama, Kazuhiro Tsukada and Atsushi Muraguchi J Immunol 2000; 165:4281-4289; ; doi: 10.4049/jimmunol.165.8.4281 Downloaded from http://www.jimmunol.org/content/165/8/4281 References This article cites 42 articles, 23 of which you can access for free at: http://www.jimmunol.org/ http://www.jimmunol.org/content/165/8/4281.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on September 28, 2021 • 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 © 2000 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Possible Involvement of Cyclophilin B and Caspase-Activated Deoxyribonuclease in the Induction of Chromosomal DNA Degradation in TCR-Stimulated Thymocytes1 Takuya Nagata,* Hiroyuki Kishi,* Qing Li Liu,* Tomoyasu Yoshino,* Tadashi Matsuda,* Zhe Xiong Jin,* Kimie Murayama,‡ Kazuhiro Tsukada,† and Atsushi Muraguchi2* TCR engagement of immature CD4؉CD8؉ thymocytes induces clonal maturation (positive selection) as well as clonal deletion (negative selection) in the thymus. -
Curcumin Alters Gene Expression-Associated DNA Damage, Cell Cycle, Cell Survival and Cell Migration and Invasion in NCI-H460 Human Lung Cancer Cells in Vitro
ONCOLOGY REPORTS 34: 1853-1874, 2015 Curcumin alters gene expression-associated DNA damage, cell cycle, cell survival and cell migration and invasion in NCI-H460 human lung cancer cells in vitro I-TSANG CHIANG1,2, WEI-SHU WANG3, HSIN-CHUNG LIU4, SU-TSO YANG5, NOU-YING TANG6 and JING-GUNG CHUNG4,7 1Department of Radiation Oncology, National Yang‑Ming University Hospital, Yilan 260; 2Department of Radiological Technology, Central Taiwan University of Science and Technology, Taichung 40601; 3Department of Internal Medicine, National Yang‑Ming University Hospital, Yilan 260; 4Department of Biological Science and Technology, China Medical University, Taichung 404; 5Department of Radiology, China Medical University Hospital, Taichung 404; 6Graduate Institute of Chinese Medicine, China Medical University, Taichung 404; 7Department of Biotechnology, Asia University, Taichung 404, Taiwan, R.O.C. Received March 31, 2015; Accepted June 26, 2015 DOI: 10.3892/or.2015.4159 Abstract. Lung cancer is the most common cause of cancer CARD6, ID1 and ID2 genes, associated with cell survival and mortality and new cases are on the increase worldwide. the BRMS1L, associated with cell migration and invasion. However, the treatment of lung cancer remains unsatisfactory. Additionally, 59 downregulated genes exhibited a >4-fold Curcumin has been shown to induce cell death in many human change, including the DDIT3 gene, associated with DNA cancer cells, including human lung cancer cells. However, the damage; while 97 genes had a >3- to 4-fold change including the effects of curcumin on genetic mechanisms associated with DDIT4 gene, associated with DNA damage; the CCPG1 gene, these actions remain unclear. Curcumin (2 µM) was added associated with cell cycle and 321 genes with a >2- to 3-fold to NCI-H460 human lung cancer cells and the cells were including the GADD45A and CGREF1 genes, associated with incubated for 24 h. -
Cleavage and Nuclear Translocation of the Caspase 3 Substrate Rho GDP-Dissociation Inhibitor, D4-GDI, During Apoptosis
Cell Death and Differentiation (1999) 6, 412 ± 419 ã 1999 Stockton Press All rights reserved 13509047/99 $12.00 http://www.stockton-press.co.uk/cdd Cleavage and nuclear translocation of the caspase 3 substrate Rho GDP-dissociation inhibitor, D4-GDI, during apoptosis 1 ,1 Ronald J Krieser and Alan Eastman* Introduction 1 Department of Pharmacology and Toxicology, Dartmouth Medical School, Apoptosis plays a central role in such processes as Hanover, New Hampshire 03755, USA development, tissue homeostasis, and thymic selection, as * corresponding author: tel: (603)-650-1501; fax: (603)-650-1129; well as pathologies ranging from neurodegenerative disease, e-mail: [email protected] autoimmune disorders, and viral infection, to cancer. Much research on apoptosis has focused on determining proteins involved in decisions of cell fate, and regulation of the Received 17.11.98; revised 15.2.99; accepted 2.3.99 execution phase of cell death involving protease and Edited by G. Salvesen endonuclease activation. A great deal of this information has been gained from the study of small organisms such as Abstract the nematode C. elegans, which has a well-defined developmental program during which specific cells die. The While investigating endonucleases potentially involved in characterization of nematodes with mutations in the cell death apoptosis, an antisera was raised to bovine deoxyribonu- process has led to identification of genes which regulate clease II, but it recognized a smaller protein of 26 kDa protein apoptosis.1 The mammalian homologs have been identified in a variety of cell lines. The 26 kDa protein underwent for many of these regulatory genes.