DOCSLIB.ORG

Exploring the Microbiome of the Mediterranean Sponge Aplysina Aerophoba by Single-Cell and Metagenomics

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Exploring the Microbiome of the Mediterranean Sponge Aplysina Aerophoba by Single-Cell and Metagenomics Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik Doctoral thesis for a doctoral degree at the Graduate School of Life Sciences Julius-Maximilians-Universität Würzburg Section: Integrative Biology Submitted by Beate Magdalena Slaby from München Würzburg, March 2017 Submitted on: ……………………………………………………… Members of the Promotionskomitee Chairperson: Prof. Dr. Thomas Müller Primary Supervisor: Prof. Dr. Ute Hentschel Humeida Supervisor (Second): Prof. Dr. Thomas Dandekar Supervisor (Third): Prof. Dr. Frédéric Partensky Date of public defense: ……………………………………………………… Date of receipt of certificates: ……………………………………………………… ii Affidavit I hereby confirm that my thesis entitled ‘Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics’ is the result of my own work. I did not receive any help or support from commercial consultants. All sources and / or materials applied are listed and specified in the thesis. Furthermore, I confirm that this thesis has not yet been submitted as part of another examination process neither in identical nor in similar form. Place, Date Signature iii Acknowledgements I received financial support for this thesis project by a grant of the German Excellence Initiative to the Graduate School of Life Sciences of the University of Würzburg through a PhD fellowship, and from the SponGES project that has received funding from the European Union’s Horizon 2020 research and innovation program. I would like to thank: Dr. Ute Hentschel Humeida for her support and encouragement, and for providing so many extraordinary opportunities. Dr. Thomas Dandekar and Dr. Frédéric Partensky for the supervision and a number of very helpful discussions. my current and former colleagues in the Research Unit Marine Microbiology at the Division of Marine Ecology, GEOMAR Kiel, particularly Kristina, Hannes, Martin, Bettina, Tanja, Jutta, Regine, Sabrina, Giampiero, Laura, Lucía, Kathrin, Jule, Yu-Chen, Dr. Johannes Imhoff, Ignacio, and Alvaro for their support, their friendship, and making the relocation in the middle of the PhD project not only possible, but enjoyable. all my former colleagues at the Department of Botany II in Würzburg, especially Janine, Lucas, Tine, Anni, Elli, Wilma, Moni, Andrea, Natascha, Usama, Cheng, and Ann-Janine for their friendship and support. Dr. Gabriele Blum-Oehler, Jenny Braysher, Bianca Putz, and Franz-Xaver Kober of the Graduate School of Life Sciences for answering all my questions. The US Department of Energy Joint Genome Institute, and especially Dr. Tanja Woyke, Dr. Susannah Tringe, Dr. Scott Clingenpeel and Dr. Alex Copeland for their support and sharing their expertise. The Marine Biology Station Portorož and Piran, Slovenia, for the sampling possibility. Dr. Monika Bright for her support with sampling. Dr. Laura Steindler, Ilia Burgsdorf, and Dr. Thomas Hackl for great collaborations. Dr. Frank Förster for access to the server and support. The FACS and Cell Sorting Unit Würzburg for support with FACS sorting. Dr. Autun Purser for proof-reading. My family and friends for their unconditional support and encouragement, especially my parents, my brother, my ‘moving crew’ Markus and Willi, and Dom. iv Table of contents AFFIDAVIT ......................................................................................................................... III ACKNOWLEDGEMENTS ................................................................................................ IV TABLE OF CONTENTS ..................................................................................................... V LIST OF FIGURES ........................................................................................................... VII LIST OF TABLES ............................................................................................................... IX SUMMARY ........................................................................................................................... X ZUSAMMENFASSUNG ................................................................................................... XII 1 INTRODUCTION ........................................................................................................ 14 1.1 Sponges (phylum Porifera) .................................................................................. 14 1.2 Sponge-microbe symbiosis .................................................................................. 17 1.2.1 Microbial diversity ......................................................................................... 17 1.2.2 Microbial function.......................................................................................... 18 1.3 Aplysina aerophoba ............................................................................................... 19 1.3.1 Geographic distribution and physical properties ............................................ 19 1.3.2 The A. aerophoba microbiome ...................................................................... 20 1.4 Sequence-based analyses of microbiomes .......................................................... 21 1.4.1 Recent developments in sequencing technologies ......................................... 22 1.4.2 Why short-reads fall short .............................................................................. 24 1.4.3 Long-read sequencing in metagenomics ........................................................ 24 2 MATERIAL AND METHODS................................................................................... 26 2.1 Research questions and aims .............................................................................. 26 2.2 Sponge collection and enrichment of prokaryotic cells .................................... 27 2.3 Sequencing and analysis of cyanobacterial sponge symbionts ......................... 28 2.3.1 Laboratory methods: From sample to sequence ............................................. 28 2.3.2 Bioinformatic methods: From sequencing reads to genome comparison ...... 30 2.4 Development of a hybrid assembly pipeline for PacBio long-reads and Illumina short-reads ........................................................................................................ 32 2.4.1 Simulating sequencing reads for a test dataset ............................................... 32 2.4.2 Testing assemblers and settings ..................................................................... 33 2.4.3 Comparing and evaluating of assemblies and bins ........................................ 34 2.5 Apylsina aerophoba metagenomics ..................................................................... 36 2.5.1 Laboratory methods: DNA extraction and sequencing .................................. 36 2.5.2 Bioinformatic methods: From assembly to annotation .................................. 36 2.5.3 Statistical analysis: Comparison to references and within symbionts ............ 37 v 3 RESULTS ..................................................................................................................... 40 3.1 Assessing the genome of the “Ca. Synechococcus spongiarum” group ........... 40 3.1.1 Assessment of clade F genomes from A. aerophoba ..................................... 40 3.1.2 Comparison within the “Ca. Synechococcus spongiarum” group and to free- living references ............................................................................................................. 44 3.2 PacBio-Illumina hybrid assembly pipeline development ................................. 63 3.2.1 Statistics of the tested assembly strategies ..................................................... 63 3.2.2 Comparison back to original reference genomes ........................................... 64 3.2.3 Reference-independent binning ..................................................................... 65 3.3 Binning 37 symbiont genomes from the metagenome of A. aerophoba ........... 68 3.3.1 Assessment of metagenomic DNA extraction and sequencing ...................... 68 3.3.2 Comparison of Illumina-only and PacBio-Illumina hybrid assemblies ......... 69 3.3.3 Bacterial genomes binned from hybrid assembly .......................................... 72 3.3.4 Symbiont-reference comparison .................................................................... 78 3.3.5 Within-symbiont comparison ......................................................................... 84 4 DISCUSSION ............................................................................................................... 88 4.1 “Ca. Synechococcus spongiarum” group – closely related but different in gene content ............................................................................................................................... 88 4.1.1 An optimal candidate for ‘mini-metagenomics’ ............................................ 88 4.1.2 Lifestyle evolution in cyanobacterial symbionts of sponges ......................... 89 4.2 PacBio-Illumina hybrid assembly pipeline development ................................. 97 4.3 Metagenomic bins from the microbiome of A. aerophoba reveal unity in defense but metabolic specialization .............................................................................. 98 4.3.1 Breaking new ground in assembly strategy and choice of references ............ 98 4.3.2 Unity in defense ............................................................................................
Load more

Recommended publications
  • A New Michaelis Complex Leads to Efficient Transition State Charge Offset
    Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset Charlotte M. Mitona,1, Stefanie Jonasa,2, Gerhard Fischera,3, Fernanda Duarteb,3,4, Mark F. Mohameda, Bert van Looa,5, Bálint Kintsesa,6, Shina C. L. Kamerlinb, Nobuhiko Tokurikia,c, Marko Hyvönena, and Florian Hollfeldera,7 aDepartment of Biochemistry, University of Cambridge, CB2 1GA Cambridge, United Kingdom; bDepartment of Chemistry, Biomedicinskt Centrum (BMC), Uppsala University, 751 23 Uppsala, Sweden; and cMichael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada Edited by Daniel Herschlag, Stanford University, Stanford, CA, and accepted by Editorial Board Member Michael A. Marletta May 31, 2018 (received for review January 31, 2018) The recruitment and evolutionary optimization of promiscuous catalytic residues but also occurs at the periphery of the catalytic enzymes is key to the rapid adaptation of organisms to changing machinery, even in positions as remote as the second and third environments. Our understanding of the precise mechanisms shells of the active site (23). In studies examining detailed evo- underlying enzyme repurposing is, however, limited: What are lutionary transitions, function-altering mutations led to the dis- the active-site features that enable the molecular recognition of placement of a catalytic metal ion or the repositioning of a multiple substrates with contrasting catalytic requirements? To nucleophile (24–26). In further cases, the position of the catalytic gain insights into the molecular determinants of adaptation in residues remained unaltered, but other structural features, for promiscuous enzymes, we performed the laboratory evolution of an arylsulfatase to improve its initially weak phenylphosphonate Significance hydrolase activity.
    [Show full text]
  • Appendix: Some Important Early Collections of West Indian Type Specimens, with Historical Notes
    Appendix: Some important early collections of West Indian type specimens, with historical notes Duchassaing & Michelotti, 1864 between 1841 and 1864, we gain additional information concerning the sponge memoir, starting with the letter dated 8 May 1855. Jacob Gysbert Samuel van Breda A biography of Placide Duchassaing de Fonbressin was (1788-1867) was professor of botany in Franeker (Hol­ published by his friend Sagot (1873). Although an aristo­ land), of botany and zoology in Gent (Belgium), and crat by birth, as we learn from Michelotti's last extant then of zoology and geology in Leyden. Later he went to letter to van Breda, Duchassaing did not add de Fon­ Haarlem, where he was secretary of the Hollandsche bressin to his name until 1864. Duchassaing was born Maatschappij der Wetenschappen, curator of its cabinet around 1819 on Guadeloupe, in a French-Creole family of natural history, and director of Teyler's Museum of of planters. He was sent to school in Paris, first to the minerals, fossils and physical instruments. Van Breda Lycee Louis-le-Grand, then to University. He finished traveled extensively in Europe collecting fossils, especial­ his studies in 1844 with a doctorate in medicine and two ly in Italy. Michelotti exchanged collections of fossils additional theses in geology and zoology. He then settled with him over a long period of time, and was received as on Guadeloupe as physician. Because of social unrest foreign member of the Hollandsche Maatschappij der after the freeing of native labor, he left Guadeloupe W etenschappen in 1842. The two chief papers of Miche­ around 1848, and visited several islands of the Antilles lotti on fossils were published by the Hollandsche Maat­ (notably Nevis, Sint Eustatius, St.
    [Show full text]
  • Individualistic Patterns in the Budding Morphology of the Mediterranean Demosponge Aplysina Aerophoba
    Short Communication Mediterranean Marine Science Indexed in WoS (Web of Science, ISI Thomson) and SCOPUS The journal is available on line at http://www.medit-mar-sc.net DOI: http://dx.doi.org/10.12681/mms.19332 Individualistic patterns in the budding morphology of the Mediterranean demosponge Aplysina aerophoba Julio A. DÍAZ1, 2, Juancho MOVILLA3 and Pere FERRIOL1 1 Interdisciplinary Ecology Group, Biology Department, Universidad de las Islas Baleares, Palma, Spain 2 Instituto Español de Oceanografía, Centre Oceanogràfic de Balears, Palma de Mallorca, Spain 3 Instituto Español de Oceanografía, Centre Oceanogràfic de Balears, Estació d’Investigació Jaume Ferrer, Menorca, Spain Corresponding author: [email protected] Handling Editor: Eleni VOULTSIADOU Received: 10 December 2018; Accepted: 18 April 2019; Published on line: 28 May 2019 Abstract The external morphology of sponges is characterized by high plasticity, generally considered to be shaped by environmental factors, and modulated through complex morphogenetic pathways. This work shows for the first time that explants of the At- lanto-Mediterranean demosponge Aplysina aerophoba reared in aquaria under different pH and temperature conditions produce reproductive buds with a phenotype determined by the donor individual. These results suggest, therefore, that genotype may be an important factor controlling different phenotypes in this species. Keywords: Mediterranean Sea; Aplysina aerophoba; Asexual reproduction; Morphogenesis; Sponge budding. Introduction 1986). This was tested on field experiments involving tropical sponges, in which the relationship between the Sponges are invertebrates with a relatively simple phenotype and genetic identity of individuals was ver- body design, formed by an external layer, the pinaco- ified with graft histocompatibility bioassays (Hildeman derm; an inner layer, the mesohyl; and an aquiferous sys- et al., 1979; Jokiel et al., 1982; Neigel & Avisse, 1983; tem composed of canals and choanocyte chambers.
    [Show full text]
  • 1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
    Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN.
    [Show full text]
  • A Soft Spot for Chemistry–Current Taxonomic and Evolutionary Implications of Sponge Secondary Metabolite Distribution
    marine drugs Review A Soft Spot for Chemistry–Current Taxonomic and Evolutionary Implications of Sponge Secondary Metabolite Distribution Adrian Galitz 1 , Yoichi Nakao 2 , Peter J. Schupp 3,4 , Gert Wörheide 1,5,6 and Dirk Erpenbeck 1,5,* 1 Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany; [email protected] (A.G.); [email protected] (G.W.) 2 Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan; [email protected] 3 Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University Oldenburg, 26111 Wilhelmshaven, Germany; [email protected] 4 Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg (HIFMB), 26129 Oldenburg, Germany 5 GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany 6 SNSB-Bavarian State Collection of Palaeontology and Geology, 80333 Munich, Germany * Correspondence: [email protected] Abstract: Marine sponges are the most prolific marine sources for discovery of novel bioactive compounds. Sponge secondary metabolites are sought-after for their potential in pharmaceutical applications, and in the past, they were also used as taxonomic markers alongside the difficult and homoplasy-prone sponge morphology for species delineation (chemotaxonomy). The understanding Citation: Galitz, A.; Nakao, Y.; of phylogenetic distribution and distinctiveness of metabolites to sponge lineages is pivotal to reveal Schupp, P.J.; Wörheide, G.; pathways and evolution of compound production in sponges. This benefits the discovery rate and Erpenbeck, D. A Soft Spot for yield of bioprospecting for novel marine natural products by identifying lineages with high potential Chemistry–Current Taxonomic and Evolutionary Implications of Sponge of being new sources of valuable sponge compounds.
    [Show full text]
  • Naturally Prefabricated Marine Biomaterials: Isolation and Applications of Flat Chitinous 3D Scaffolds from Ianthella Labyrinthus (Demospongiae: Verongiida)
    International Journal of Molecular Sciences Article Naturally Prefabricated Marine Biomaterials: Isolation and Applications of Flat Chitinous 3D Scaffolds from Ianthella labyrinthus (Demospongiae: Verongiida) Mario Schubert 1, Björn Binnewerg 1, Alona Voronkina 2 , Lyubov Muzychka 3, Marcin Wysokowski 4,5 , Iaroslav Petrenko 5, Valentine Kovalchuk 6, Mikhail Tsurkan 7 , Rajko Martinovic 8 , Nicole Bechmann 9 , Viatcheslav N. Ivanenko 10 , Andriy Fursov 5, Oleg B. Smolii 3, Jane Fromont 11 , Yvonne Joseph 5 , Stefan R. Bornstein 12,13, Marco Giovine 14, Dirk Erpenbeck 15 , Kaomei Guan 1,* and Hermann Ehrlich 5,* 1 Institute of Pharmacology and Toxicology, Technische Universität Dresden, 01307 Dresden, Germany; [email protected] (M.S.); [email protected] (B.B.) 2 Department of Pharmacy, National Pirogov Memorial Medical University, Vinnytsya, 21018 Vinnytsia, Ukraine; [email protected] 3 V.P Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, Murmanska Str. 1, 02094 Kyiv, Ukraine; [email protected] (L.M.); [email protected] (O.B.S.) 4 Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland; [email protected] 5 Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, Gustav-Zeuner str. 3, 09599 Freiberg, Germany; [email protected] (I.P.); [email protected] (A.F.); [email protected] (Y.J.) 6 Department of Microbiology,
    [Show full text]
  • Proposal for a Revised Classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3*
    Morrow and Cárdenas Frontiers in Zoology (2015) 12:7 DOI 10.1186/s12983-015-0099-8 DEBATE Open Access Proposal for a revised classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3* Abstract Background: Demospongiae is the largest sponge class including 81% of all living sponges with nearly 7,000 species worldwide. Systema Porifera (2002) was the result of a large international collaboration to update the Demospongiae higher taxa classification, essentially based on morphological data. Since then, an increasing number of molecular phylogenetic studies have considerably shaken this taxonomic framework, with numerous polyphyletic groups revealed or confirmed and new clades discovered. And yet, despite a few taxonomical changes, the overall framework of the Systema Porifera classification still stands and is used as it is by the scientific community. This has led to a widening phylogeny/classification gap which creates biases and inconsistencies for the many end-users of this classification and ultimately impedes our understanding of today’s marine ecosystems and evolutionary processes. In an attempt to bridge this phylogeny/classification gap, we propose to officially revise the higher taxa Demospongiae classification. Discussion: We propose a revision of the Demospongiae higher taxa classification, essentially based on molecular data of the last ten years. We recommend the use of three subclasses: Verongimorpha, Keratosa and Heteroscleromorpha. We retain seven (Agelasida, Chondrosiida, Dendroceratida, Dictyoceratida, Haplosclerida, Poecilosclerida, Verongiida) of the 13 orders from Systema Porifera. We recommend the abandonment of five order names (Hadromerida, Halichondrida, Halisarcida, lithistids, Verticillitida) and resurrect or upgrade six order names (Axinellida, Merliida, Spongillida, Sphaerocladina, Suberitida, Tetractinellida). Finally, we create seven new orders (Bubarida, Desmacellida, Polymastiida, Scopalinida, Clionaida, Tethyida, Trachycladida).
    [Show full text]
  • University of Groningen Cultivation of Bacteria from Aplysina Aerophoba
    University of Groningen Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients Gutleben, J.; Loureiro, C.; Ramírez Romero, L.A.; Shetty, S.; Wijffels, R.H.; Smidt, H.; Sipkema, D. Published in: Frontiers in Microbiology DOI: 10.3389/fmicb.2020.00175 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2020 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Gutleben, J., Loureiro, C., Ramírez Romero, L. A., Shetty, S., Wijffels, R. H., Smidt, H., & Sipkema, D. (2020). Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients. Frontiers in Microbiology, 11, [175]. https://doi.org/10.3389/fmicb.2020.00175 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
    [Show full text]
  • 2020 Annual Report
    EMBRC: 2020 annual report Marine biodiversity is becoming an increasing concern with climate change and marine pollution, and, as a result, is of high relevance in the forthcoming UN Decade of the Ocean and Europe’s Green Deal. One of EMBRC’s principal activities is the provision of access to marine biodiversity, in all its forms. EMBRC Operators include some of the oldest marine institutes in the world and operate long-term observations, host biodiversity monitoring activities, and conduct research. In order to provide holistic information on biodiversity composition at these sites, EMBRC will establish EMO BON, a coordinated European Marine Omics Biodiversity Observation Network across its partners. This will constitute a new approach for EMBRC, and a step in a new direction, toward data generation and long-term observation. EMO BON presents an important need for the EMBRC user community and the opportunity to start filling the void in biological observation that we currently face in regard to physical and chemical observation. This is also an exciting opportunity to generate data for the marine microbiome studies currently in progress, and support Atlantic strategies, such as the Atlantic Ocean Research Alliance (AORA). Knowledge-based management of our blue planet is only possible by unified global monitoring using comparable data, which, in the case of biodiversity, cannot currently be assessed by remote sensing. In this context, EMBRC wishes to contribute to the global coordination of marine biodiversity by –omics approaches, integrating forthcoming technologies as appropriate. We aim to reach and interact with other relevant initiatives, offering the advantages of a sustainable RI that can support active research and underpin the development and optimisation of new methods.
    [Show full text]
  • Bioactive Bromotyrosine Derivatives from the Pacific Marine
    marine drugs Article Bioactive Bromotyrosine Derivatives from the Pacific Marine Sponge Suberea clavata (Pulitzer-Finali, 1982) Céline Moriou 1, Damien Lacroix 1, Sylvain Petek 2,* , Amr El-Demerdash 1 , Rozenn Trepos 2 , Tinihauarii Mareva Leu 3, Cristina Florean 4, Marc Diederich 5 , Claire Hellio 2 ,Cécile Debitus 2 and Ali Al-Mourabit 1,* 1 CNRS, Institut de Chimie des Substances Naturelles, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France; [email protected] (C.M.); [email protected] (D.L.); [email protected] (A.E.-D.) 2 IRD, CNRS, Ifremer, LEMAR, Univ Brest, F-29280 Plouzane, France; [email protected] (R.T.); [email protected] (C.H.); [email protected] (C.D.) 3 IRD, Ifremer, ILM, EIO, Univ de la Polynésie française, F-98713 Papeete, French Polynesia; [email protected] 4 Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg; cristina.fl[email protected] 5 Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; [email protected] * Correspondence: [email protected] (S.P.); [email protected] (A.A.-M.); Tel.: +33-298-498-651 (S.P.); +33-169-824-585 (A.A.-M.) Abstract: Chemical investigation of the South-Pacific marine sponge Suberea clavata led to the isola- tion of eight new bromotyrosine metabolites named subereins 1–8 (2–9) along with twelve known co-isolated congeners. The detailed configuration determination of the first representative major compound of this family 11-epi-fistularin-3 (11R,17S)(1) is described.
    [Show full text]
  • S. Nagel Et Al., Microarray Analysis of the Global Gene Expression Profile Following Hypothermia and Transient Focal Cerebral Ischemia Neuroscience 2012
    S. Nagel et al., Microarray analysis of the global gene expression profile following hypothermia and transient focal cerebral ischemia Neuroscience 2012 Supplementary Table 1 Gene Symbol Entrez Gene Name Affymetrix SNP ID Fold Change PEBP1 phosphatidylethanolamine binding protein 1 E05646cds_s_at 36,571 KIFC1 kinesin family member C1 AF035951_at 29,307 SERP1 stress-associated endoplasmic reticulum protein 1 AF100470_at 23,16 FDXR ferredoxin reductase D63761_g_at 22,504 SYNPO synaptopodin AB013130_at 21,174 ID1 inhibitor of DNA binding 1, dominant negative helix-loop-helix protein L23148_g_at 16,233 GTF2F2 general transcription factor IIF, polypeptide 2, 30kDa L01267_at 15,592 PPP2R2C protein phosphatase 2, regulatory subunit B, gamma D38261_at 15,356 RASGRP1 RAS guanyl releasing protein 1 (calcium and DAG-regulated) AF081196_at 15,142 UBB -- D16554_at 14,996 SLC37A4 solute carrier family 37 (glucose-6-phosphate transporter), member 4 AF080468_g_at 14,757 LIMK2 LIM domain kinase 2 D31874_at 14,254 PPP1R15A protein phosphatase 1, regulatory (inhibitor) subunit 15A AF020618_g_at 13,988 HPCAL4 hippocalcin like 4 D13125_at 13,128 FAIM2 Fas apoptotic inhibitory molecule 2 AF044201_at 12,77 GJA5 gap junction protein, alpha 5, 40kDa AF022136_at 12,751 SLC2A3 solute carrier family 2 (facilitated glucose transporter), member 3 D13962_g_at 12,245 TRIM23 tripartite motif containing 23 L04760_at 12,122 PIP4K2C phosphatidylinositol-5-phosphate 4-kinase, type II, gamma AF030558_at 11,698 SBK1 SH3-binding domain kinase 1 AB010154_at 11,523 PLEKHA1 pleckstrin
    [Show full text]
  • N-Acetylgalactosamine-6-Sulfate Sulfatase in Man. Absence of the Enzyme in Morquio Disease
    N-acetylgalactosamine-6-sulfate sulfatase in man. Absence of the enzyme in Morquio disease. J Singh, … , P Niebes, D Tavella J Clin Invest. 1976;57(4):1036-1040. https://doi.org/10.1172/JCI108345. Research Article Human N-acetylgalactosamine-6-sulfate sulfatase (6-sulfatase) activity is measured by using as a substrate a sulfated tetrasaccharide obtained by digesting purified chondroitin-6-sulfate (C-6-S) with testicular hyaluronidase. The amount of inorganic sulfate released is measured turbidimetrically. The enzyme from human kidney has a pH optimum of 4.8; its activity is augmented by low levels of NaCl and inhibited by phosphate and high levels of NaCl. Free glucuronate, acetylgalactosamine, inorganic sulfate, polymeric C-6-S, or tetrasaccharide obtained from chondroitin-4-sulfate do not affect the enzyme activity. The method may be used for the diagnosis of Morquio disease since extracts of Morquio fibroblasts are devoid of 6-sulfatase activity. Find the latest version: https://jci.me/108345/pdf N-Acetylgalactosamine-6-Sulfate Sulfatase in Man ABSENCE OF THE ENZYME IN MORQUIO DISEASE JAGAT SINGH, NICOLA Di FERRANTE, PAUL NIEBES, and DANIELA TAVELLA From the Departments of Biochemistry and Medicine, and the Division of Orthopedic Surgery of the Department of Surgery, Baylor College of Medicine, Houston, Texas 77025 and Zyma, S.A., Nyon, Switzerland A B S T R A C T Human N-acetylgalactosamine-6-sulfate measurement, and the need to ascertain whether the sulfatase (6-sulfatase) activity is measured by using as sulfate released was in position 4 or 6 of the galactos- a substrate a sulfated tetrasaccharide obtained by di- amine moieties make the method (1) rather laborious gesting purified chondroitin-6-sulfate (C-6-S) with tes- and not ideal for the routine assay of the enzyme ac- ticular hyaluronidase.
    [Show full text]