DOCSLIB.ORG

New Structural Insights Into the Extracellular Matrix And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
New Structural Insights Into the Extracellular Matrix And NEW STRUCTURAL INSIGHTS INTO THE EXTRACELLULAR MATRIX AND HYDROCARBON DIVERSITY OF Botryococcus Braunii RACE B A Dissertation by MEHMET TATLI Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Timothy P. Devarenne Committee Members, Jaan Laane Vladislav M. Panin Paul A. Lindahl Head of Department, Gregory D. Reinhart May 2018 Major Subject: Biochemistry Copyright 2018 Mehmet Tatli ABSTRACT Botryococcus braunii is a colonial green microalga that can produce large amounts of liquid isoprenoid hydrocarbons known as botryococcenes, which can be easily converted into conventional combustion engine fuels. B. braunii colony cells are held together by a complex extracellular matrix (ECM). ECM serves as a storage unit for liquid hydrocarbons, and contains a retaining wall and a polysaccharide fibrillar sheath. Analysis of “shells” revealed a single protein. Here we use peptide mass fingerprinting and bioinformatics to identify this protein called polysaccharide associated protein (PSAP). PSAP does not show similarity to any protein in databases, and contains several hydroxyproline domains and a predicted sugar binding domain. Staining studies confirm PSAP as a glycoprotein, and mass spectrometry analysis identified ten N-linked glycosylation sites comprising seven different glycans containing mostly mannose and N- acetylglucosamine with fucose and arabinose. Additionally, four hydroxyproline residues have short O-linked glycans of mainly arabinose and galactose, with 6-deoxyhexose. PSAP secretion and localization to shell material is confirmed using western blot analysis and microscopy. These studies indicate PSAP contains unique glycans and suggest its involvement in ECM polysaccharide fiber biosynthesis. Moreover, B. braunii is capable of producing many botryococcene isomers ranging in carbon number from 30 to 37, as well as several methylated squalenes. Although studies have reported the isolation of isomers based on the C31, C32, C33, and C34 botryococcene ii structures, there has not been a report of cyclic C33 botryococcenes or an isomer based on the trimethylsqualene structure until this study. Three cyclic C33 botryococcenes and one new trimethylsqualene isomer were isolated from the B race, Showa (Berkeley) strain of B. braunii. In addition, a detailed examination of the molecular structure for ten botryococcenes including the newly discovered cyclic C33 botryococcenes and five methylsqualenes isolated from race B was carried out using Raman spectroscopy and density functional theory (DFT) calculations in an effort to distinguish between these structurally similar molecules by spectroscopic approaches. A comparison of the experimental Raman spectroscopy and DFT calculations indicates several spectral regions such as those for ν(C=C) stretching, CH2/CH3 bending, and ring bending can be used to distinguish between these molecules. Altogether, these studies bring more insights into understanding the hydrocarbon diversity and ECM of B. braunii race B. iii DEDICATION I would primarily dedicate this dissertation to my mother. I would also like to dedicate this dissertation to all my family for always supporting me and sending good vibes from thousands of miles away. I cannot imagine how difficult my life would have been without feeling your support with all the decisions I have made in my life. iv ACKNOWLEDGEMENTS I would like to thank my Ph.D. thesis advisor Dr. Timothy Devarenne for his guidance and support that he has provided me throughout my Ph.D. career. I am grateful for his mentorship, patience, and the chance he has given me to grow as a scientist in his lab. I would like to thank my committee, Dr. Jaan Laane, Dr. Vlad Panin, Dr. Paul Lindahl and Dr. Andreas Holzenburg for their time, guidance, and support throughout the course of this research. My sincere thanks to Dr. Shigeru Okada and Dr. Mandar Naik for their support and suggestions on my projects. Thanks to my colleagues and current and past members of Devarenne lab – in particular Daniel Browne whom I had many valuable discussions and good times over the years with, Dr. Hem Thapa, Dongyin Su, and Incheol Yeo for their valuable suggestions. I would also like to thank the NSF REU Summer students Laura Krings and Patrick Sweet, and Texas A&M Energy Institute summer student Alyssa Dubrow that worked with me and contributed to my work and allowed me improve my mentorship skills. Last, I would like to thank all my loving family and close friends for their great support. v CONTRIBUTORS AND FUNDING SOURCES Contributors This work was supervised by a dissertation committee consisting of Dr. Timothy P. Devarenne [advisor] of the Department of Biochemistry and Biophysics, Dr. Jaan Laane of the Department of Chemistry, Dr. Vladislav M. Panin of the Department of Biochemistry and Biophysics, and Dr. Paul A. Lindahl of the Departments of Chemistry and Biochemistry and Biophysics. Most of the work for this dissertation was carried out by the student, under the supervision of Dr. Timothy P. Devarenne of the Department of Biochemistry and Biophysics. The NMR analysis of the hydrocarbons in section II was done with the help of the following collaborators: Dr. Mandar Naik of the Biomolecular NMR facility in the Department of Biochemistry and Biophysics at Texas A&M University (currently at the Department of Molecular Pharmacology, Physiology, and Biotechnology at Brown University) and Dr. Shigeru Okada of the School of Agricultural and Life Sciences at the University of Tokyo. Collaborators for section III are as follows: The DFT calculations for the hydrocarbons were done by Dr. Hye-Jin Chun and Dr. Jaan Laane of the Department of Chemistry at Texas A&M University, BCARS experiments were done by Dr. Charles H. Camp Jr. and Dr. Marcus Cicerone of the Biosystems and Biomaterials Division at the National Institute of Standards and Technology in Gaithersburg, Maryland, and in vitro Raman spectroscopy experiments of the purified hydrocarbons were vi completed with the help of Dr. Wei-Chuan Shih and Jingting Li of the Department of Electrical and Computer Engineering at University of Houston. Collaborators and their contributions to section IV are as follows: Dr. Mayumi Ishihara of the Complex Carbohydrate Research Center at University of Georgia did the glycomics studies for PSAP and Dr. Christian Heiss and Dr. Parastoo Azadi of the Complex Carbohydrate Research Center at University of Georgia provided help planning experiments for the glycomics studies for PSAP. Dr. Lawrence J. Dangott of the Protein Chemistry Laboratory in the Department of Biochemistry and Biophysics and Daniel R. Browne of the Department of Biochemistry and Biophysics at Texas A&M University provided help with the bioinformatics to find full length cDNA for PSAP. Funding sources This work was made possible in part by NSF-EFRI-PSBR under grant #1240478 to Dr. Timothy P. Devarenne; by the Robert A. Welch Foundation under grant #A-0396 to Dr. Jaan Laane; by National Science Foundation under grant #CHE-0541587 to the Texas A&M Department of Chemistry Medusa computer system; by a grant from the Japan Science and Technology (JST) agency program to Dr. Shigeru Okada.; by the U.S. Department of Energy under grant #DE-SC0015662 and by NIH under grant #1S10OD018530 and grant # P41GM103490-14 to Dr. Parastoo Azadi. vii TABLE OF CONTENTS Page ABSTRACT .......................................................................................................................ii DEDICATION .................................................................................................................. iv ACKNOWLEDGEMENTS ............................................................................................... v CONTRIBUTORS AND FUNDING SOURCES ............................................................. vi TABLE OF CONTENTS ............................................................................................... viii LIST OF FIGURES ........................................................................................................... xi LIST OF TABLES ........................................................................................................... xv 1. INTRODUCTION AND LITERATURE REVIEW .................................................. 1 1.1 Alternative energy demand and biofuels .................................................................. 1 1.2 Microalgae ................................................................................................................ 2 1.2.1 Microalgae-based biofuels ................................................................................ 3 1.2.2 Limitations of microalgae-based biofuels ......................................................... 4 1.2.3 Potential and future of microalgae for biofuel production ................................ 6 1.2.4 Microalgae-based hydrocarbons ........................................................................ 9 1.3 Botryococcus braunii ............................................................................................. 10 1.3.1 Ultrastructure of B. braunii ............................................................................. 14 1.4 ECMs in various organisms ................................................................................... 15 1.4.1 ECMs in plants ................................................................................................ 15 1.4.2
Load more

Recommended publications
  • Molecular Biogeochemistry, Lecture 8
    12.158 Lecture Pigment-derived Biomarkers (1) Colour, structure, distribution and function (2) Biosynthesis (3) Nomenclature (4) Aromatic carotenoids ● Biomarkers for phototrophic sulfur bacteria ● Alternative biological sources (5) Porphyrins and maleimides Many of the figures in this lecture were kindly provided by Jochen Brocks, RSES ANU 1 Carotenoid pigments ● Carotenoids are usually yellow, orange or red coloured pigments lutein β-carotene 17 18 19 2' 2 4 6 8 3 7 9 16 1 5 lycopenelycopene 2 Structural diversity ● More than 600 different natural structures are known, ● They are derived from the C40 carotenoid lycopene by varied hydrogenation, dehydrogenation, cyclization and oxidation reaction 17 18 19 2' 2 4 6 8 3 7 9 16 1 5 lycopene neurosporene α-carotene γ -carotene spirilloxanthin siphonaxanthin canthaxanthin spheroidenone 3 Structural diversity Purple non-sulfur bacteria peridinin 7,8-didehydroastaxanthin okenone fucoxanthin Biological distribution ● Carotenoids are biosynthesized de novo by all phototrophic bacteria, eukaryotes and halophilic archaea ● They are additionally synthesized by a large variety of non-phototrophs ● Vertebrates and invertebrates have to incorporate carotenoids through the diet, but have often the capacity to structurally modifiy them 4 Carotenoid function (1) Accessory pigments in Light Harvesting Complex (LHC) (annual production by marine phytoplancton alone: 4 million tons) e.g. LH-II Red and blue: protein complex Green: chlorophyll Yellow: lycopene (2) Photoprotection (3) photoreceptors for phototropism
    [Show full text]
  • Application of CSIA of Light Oils and Utility of Carotenoid Biomarkers in Resource Plays of North America J
    Application of CSIA of Light Oils and Utility of Carotenoid Biomarkers in Resource Plays of North America J. E. Zumberge1, C. D. Barrie1, J. B. Curtis*1, R. E. Summons2; 1. GeoMark Research, Ltd., Houston, TX, USA; 2. Massachusetts Institute of Technology, Cambridge, MA, USA. Abstract Here we examine the value in crude oil correlations and source rock depositional environment predictions based on non-standard compound-specific isotope analysis and carotenoid biomarker data. Results from various unconventional plays (e.g., Late Devonian Bakken and Woodford Fms from the Williston and Anadarko Basins; Cretaceous Second White Specks, Niobrara, Mowry and Eagle Ford Fms in the Western Interior Seaway) are discussed and compared. These data provide new insights into resource plays using novel and relatively rapid analytical methods. Molecular isotopic data and carotenoid biomarker distributions of petroleum systems tend to be distinct so that, in combination with commonly used sterane and hopane biomarkers, oil-oil and oil-source correlations can be made with much greater fidelity. Statement of the background This paper addresses novel application of compound-specific isotope analysis and carotenoid hydrocarbon characterization to better understand, and perhaps predict the productivity of hydrocarbons from source-rock reservoirs. This work provides new and detailed insight into resource play petroleum systems. Aims and Objectives Stable isotope analysis is a powerful tool in understanding the generation, history and correlation of hydrocarbons. Compound-specific δ13C measurements of oils allow detailed comparison of individual compound groupings; however, most studies separate and isolate individual fractions based on the chemistries of particular compound groups, potentially losing or corrupting valuable data.
    [Show full text]
  • Deep Sea Drilling Project Initial Reports Volume 63
    33. GEOCHEMISTRY OF TETRAPYRROLE, CAROTENOID, AND PERYLENE PIGMENTS IN SEDIMENTS FROM THE SAN MIGUEL GAP (SITE 467) AND BAJA CALIFORNIA BORDERLAND (SITE 471), DEEP SEA DRILLING PROJECT LEG 631 J. William Louda and Earl W. Baker, Organic Geochemistry Group, College of Science, Florida Atlantic University, Boca Raton, Florida INTRODUCTION for perylene, and homologues, is proposed: the role of diagenetic-geothermal history indicator. That is, as Twenty-one core samples from DSDP/IPOD Leg 63 depth of burial and in situ sediment temperature in- were analyzed for products of chlorophyll diagenesis. In creased, the proportion of C-21, C-22, and C-23 alkyl- addition to the tetrapyrrole pigments, perylene and ated derivatives of perylene (C-20) increased. On the carotenoid pigments were isolated and identified. basis of sediment depth and thermal profiles, the alkyl- The 16 core samples from the San Miguel Gap site perylenes were found to be generated prior to the ap- (467) and the five from the Baja California borderland pearance of nickel porphyrin homologues above C-32 location (471) afforded the unique opportunity of exam- and the release or formation of the vanadyl pigments. ining tetrapyrrole diagenesis in clay-rich marine sedi- Alkylation of perylene within DSDP/IPOD sample ments that are very high in total organic matter. suites has previously been mentioned (Brassell et al., The chelation reaction, whereby free-base porphyrins 1980). give rise to metalloporphyrins (viz., nickel), is well ß-Carotene was found to be present in Site 467 upper documented within the downhole sequence of sediments Pliocene and Quaternary sections (viz., 467-18-5 and from the San Miguel Gap (Site 467).
    [Show full text]
  • Gas Chromatographic-Mass Spectrometric Investigation of Seep
    RICE UNIVERSITY GAS CHROHATOGRAP! 11 C-i IASS SPECTROMCTRIC iriVESTIGATION OF SEEP OIL ISOPRENOID ALKANES by' David James Curry A THESIS SUBMITTED III PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF ARTS Thesis Director's' signature ■ficCt rfc Houston, Texas August, 1072 TABLE OF COKTENTS ACSC'IOMLEDGEMEHTS ' 1 ABSTRACT... 2 INTRODUCTION TO GEOCHEMISTRY 4. ISOPRENOID ALKANES. 10 SAMPLE DESCRIPTION ....1C EXPERIMENTAL METHODS.-. ;...20 INTERPRETATION AND DISCUSSION OF RESULTS.......20 SUMMARY. .01 POSSIBILITIES FOR FUTURE STUDY ........64 TABLES.'..... ........SO CHROMATOGRAMS 71 FOOTNOTES..... 74 SELECTED BIBLIOGRAPHY. 76 MASS SPECTRA MS 1 (Phytane) 15,43 I IS 2 (Authenti c Pri s tane)..... .. .25 MS 3 (Pristane).' 26,40 I IS 4 (Au then ti c P r.i s tane) . ...27 MS 5 (C^ Isoprenoid) ...31 OO MS 6 (3-,7-,ll-trin;ethyl tetradecana) • • « sJsJ MS 7 (C1? Unknown) ... 33 MS 8 (C10 Isoorenoid) ...36 MS 9 (Pristane) ,38 MS 18 (Ci Unknown) 41 MS 11 (C22 Isoprenoicl) 44 MS 12 (C23 Isoprenoid),. 46 IIS 13- (C2* Isoprenoicl) 48 MS 14 (C2g Isoprenoicl) 50 MS 15 (C2Q Iscprenoid)...: 51 MS 15 (COQ Isoprenoid) MS 17 (Proposed C2C Isoprenoid) 64 CHROMATOGRAMS GC I (Total Branched alkane-cycloalkane Fraction) 71 GC II (Still Residue Branched Alkane-cycloalkane Fraction)72 GC III (Total, normal Alkane Fraction) 73 (GC I,II,III were taken on 3% SE-30 phase) TABLES I: Composition of Distillation and 56 Column'Chromatography Fractions II: Approximate Relative and Absoluts 67 Amounts of Isoprenoid Components III: Off Scale Intensities of Mass..... !...68 Spectrometric Peaks IV: Initial Separatory Gas Chroma- _ 69 tographic Conditions V: .
    [Show full text]
  • This Article Was Published in an Elsevier Journal. the Attached Copy
    This article was published in an Elsevier journal. The attached copy is furnished to the author for non-commercial research and education use, including for instruction at the author’s institution, sharing with colleagues and providing to institution administration. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Author's personal copy Available online at www.sciencedirect.com Geochimica et Cosmochimica Acta 72 (2008) 1396–1414 www.elsevier.com/locate/gca Okenane, a biomarker for purple sulfur bacteria (Chromatiaceae), and other new carotenoid derivatives from the 1640 Ma Barney Creek Formation Jochen J. Brocks a,*, Philippe Schaeffer b a Research School of Earth Sciences and Centre for Macroevolution and Macroecology, The Australian National University, Canberra, ACT 0200, Australia b Laboratoire de Ge´ochimie Bio-organique, CNRS UMR 7177, Ecole Europe´enne de Chimie, Polyme`res et Mate´riaux, 25 rue Becquerel, 67200 Strasbourg, France Received 20 June 2007; accepted in revised form 12 December 2007; available online 23 December 2007 Abstract Carbonates of the 1640 million years (Ma) old Barney Creek Formation (BCF), McArthur Basin, Australia, contain more than 22 different C40 carotenoid derivatives including lycopane, c-carotane, b-carotane, chlorobactane, isorenieratane, b-iso- renieratane, renieratane, b-renierapurpurane, renierapurpurane and the monoaromatic carotenoid okenane.
    [Show full text]
  • Deep Sea Drilling Project Initial Reports Volume 66
    21. PRELIMINARY LIPID ANALYSES OF TWO QUATERNARY SEDIMENTS FROM THE MIDDLE AMERICA TRENCH, SOUTHERN MEXICO TRANSECT, DEEP SEA DRILLING PROJECT LEG 661 S. C. Brassell, G. Eglinton, and J. R. Maxwell, School of Chemistry, University of Bristol, Bristol, United Kingdom ABSTRACT We investigated the solvent-extractable hydrocarbons, ketones, alcohols, and carboxylic acids of two Quaternary sediments from the Middle America Trench (Sections 487-2-3 and 491-1-5). These lipids are derived from a mixed input of autochthonous and allochthonous materials, with minor contributions from thermally mature sources. Their com- positions are typical of those of immature Quaternary marine sediments, and their lipid distributions show many similarities to those of Japan Trench sediments. INTRODUCTION RESULTS The solvent-extractable lipids of two Quaternary sed- The distributions of aliphatic hydrocarbons, ketones, iments (Sections 487-2-3 and 491-1-5) from the oceanic alcohols, and carboxylic acids and of aromatic hydro- plate and central slope of the Middle America Trench carbons are reported herein. In addition, other suites of were investigated by gas chromatography and comput- components such as a, co-dicarboxylic acids and numer- erized gas chromatography-mass spectrometry. The sec- ous minor or unrecognized compounds were detected, tions were chosen to permit the comparison of environ- but are not included. ments on either side of the trench. This preliminary re- port describes the lipid compositions of these two sam- Aliphatic Hydrocarbons ples and interprets them in terms of their input sources, conditions of deposition, and extent of diagenesis. We Acyclic Components also make a brief comparison of their lipid distributions The n-alkanes of Sections 487-2-3 and 491-1-5 both with those of Quaternary sediments from the Japan ranged from C14 to C35 with «-C29 dominant.
    [Show full text]
  • Perturbation to the Nitrogen Cycle During Rapid Early Eocene Global Warming
    ARTICLE DOI: 10.1038/s41467-018-05486-w OPEN Perturbation to the nitrogen cycle during rapid Early Eocene global warming Christopher K. Junium 1, Alexander J. Dickson2 & Benjamin T. Uveges 1 The degree to which ocean deoxygenation will alter the function of marine communities remains unclear but may be best constrained by detailed study of intervals of rapid warming in the geologic past. The Paleocene–Eocene Thermal Maximum (PETM) was an interval of 1234567890():,; rapid warming that was the result of increasing contents of greenhouse gases in the atmo- sphere that had wide ranging effects on ecosystems globally. Here, we present stable nitrogen isotope data from the Eastern Peri-Tethys Ocean that record a significant transition in the nitrogen cycle. At the initiation of the PETM, the nitrogen isotopic composition of sediments decreased by ~6‰ to as low as −3.4‰, signaling reorganization of the marine nitrogen cycle. Warming, changes in ocean circulation, and deoxygenation caused a transition to nitrogen cycle to conditions that were most similar to those experienced during Oceanic Anoxic Events of the Mesozoic. 1 Department of Earth Sciences, Syracuse University, Syracuse, NY 13244, USA. 2 Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK. Correspondence and requests for materials should be addressed to C.K.J. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:3186 | DOI: 10.1038/s41467-018-05486-w | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-05486-w roductivity in the marine environment is ultimately con- succession was located on the northern part of the wide, shallow trolled by the cycling of nitrogen, phosphorus, iron, and Peri-Tethys seaway, which was dramatically flooded starting in P 11,12 other bio-limiting trace elements.
    [Show full text]
  • The Pennsylvania State University the Graduate School The
    The Pennsylvania State University The Graduate School The Department of Chemistry NEW ANALYTICAL APPROACHES TO UNDERSTAND BIOLOGICAL SYSTEMS WITH SECONDARY ION MASS SPECTROMETRY A Dissertation in Chemistry by Lauren Marie Jackson 2014 Lauren Marie Jackson Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2014 The dissertation of Lauren Marie Jackson was reviewed and approved* by the following: Nicholas Winograd Evan Pugh Professor of Chemistry Dissertation Advisor Chair of Committee Wayne Curtis Professor of Chemical Engineering Thomas Mallouk Evan Pugh Professor of Materials Chemistry and Physics Associate Head of the Chemistry Department Barbara Garrison Shapiro Professor of Chemistry Head of the Chemistry Department *Signatures are on file in the Graduate School iii ABSTRACT The work of this thesis has focused on investigating biological systems with the most current secondary ion mass spectrometry instrumentation and novel sample preparation techniques. The microalga biofuel candidate, Botryococcus braunii, has been thoroughly investigated by three-dimensional chemical imaging to answer several questions regarding its metabolism and chemical composition. These findings provide a breadth of information beneficial and crucial to the successful advancement of B. braunii as a biofuel. The enhancement effects and cellular vitrification capabilities of trehalose have been explored and confirmed trehalose entry into cells has been found. This work is evidence of the great contributions to
    [Show full text]
  • Selective Preservation of Organic Matter in Marine Environments; Processes and Impact on the Sedimentary Record
    Biogeosciences, 7, 483–511, 2010 www.biogeosciences.net/7/483/2010/ Biogeosciences © Author(s) 2010. This work is distributed under the Creative Commons Attribution 3.0 License. Selective preservation of organic matter in marine environments; processes and impact on the sedimentary record K. A. F. Zonneveld1, G. J. M. Versteegh1, S. Kasten2, T. I. Eglinton3, K.-C. Emeis4, C. Huguet5,6, B. P. Koch2, G. J. de Lange7, J. W. de Leeuw6,7,8, J. J. Middelburg7,9, G. Mollenhauer2, F. G. Prahl10, J. Rethemeyer2, and S. G. Wakeham11 1Fachbereich 5 – Geowissenschaften, Postfach 330440, 27412 Bremen, Germany 2Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany 3Woods Hole Oceanographic Institution, Fye 111, MS#4, Woods Hole, Ma. 02543, USA 4Zentrum fur¨ Meeres- und Klimaforschung, Universitat¨ Hamburg, Bundesstraße 55, 20146 Hamburg, Germany 5University of Washington, School of Oceanography, P.O. Box 355351, Seattle, WA 98195, USA 6Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790AB, Den Burg, The Netherlands 7Geochemistry, Faculty of Geosciences, Utrecht University P.O. Box 80.021, 3508 TA Utrecht, The Netherlands 8Institute of Environmental Biology, Faculty of Science, Utrecht University, The Netherlands 9Netherlands Institute of Ecology, Centre for Estuarine and Marine Ecology, P.O. Box 140, 4400 AC Yerseke, The Netherlands 10College of Oceanic and Atmospheric Sciences, COAS Administration Building 104, Oregon State University, Corvallis, OR 97331-5503, USA 11Skidaway Institute of Oceanography, 10 Ocean Science Circle, Savannah, GA 31411, USA Received: 3 June 2009 – Published in Biogeosciences Discuss.: 1 July 2009 Revised: 7 January 2010 – Accepted: 21 January 2010 – Published: 5 February 2010 Abstract.
    [Show full text]
  • Isoprenoid Lipids, Lecture 2
    Organic Geochemistry Wk. 2 • Polyisoprenoid lipids – Structural diversity and biosynthesis – Hydrocarbons – Complex lipids in archaea – Isoprenoids of plants and algae – Polyisoprenoids as environment and process indicators • Lacustrine environments – botryococcenes etc • Methanogenesis • Anaerobic oxidation of methane – Fossil record of Archaea O O O O O P O P O- O P O P O- 20 DMAPP O- O- 21 IPP O- O- O O O P O P O- - - 22 GPP O O 24 OH 23 shc sqmo [O2] osc 25 26 O 27 1a [9 O2] HO HO 2- carbon molecule be the major building block for the complex 27- carbon, 4- ringed structure of the cholesterol molecule? BLOCH, LYNEN, AND THE CORNFORTH / POPJAK TEAM In the late 1930s, another young Jewish émigré from Germany, Konrad Bloch, joined Clarke’s department as a graduate student. Bloch had already completed most of his thesis research at the University of Basel and had published two papers on that research. Still, the Basel faculty rejected it as “insufficient” (10). Bloch many years later learned that only one examiner on his committee had objected and that was on the grounds that the thesis failed to cite some important references – papers authored by that examiner! Looking back, Bloch realized that this may have been providential. Had he passes he decided to stay on in Germany. At any rate, when Bloch came to New York in 1936, Clarke, a guardian angel to refugee scientists, admitted him to his program and the Ph.D. was awarded about 2 years later. At that point, Schoenheimer offered a Bloch position in his Courtesy of the National Library of Medicine.
    [Show full text]
  • The Fate of Carotenoids in Sediments: an Overview
    Pure & Appl. Chem., Vol. 69, No. 10, pp. 2067-2074, 1997. Printed in Great Britain. Q 1997 IUPAC The fate of carotenoids in sediments: An overview Jaap S. Sinninghe Damst6 and Martin P. Koopmans Netherlands Institute for Sea Research (NIOZ), Department of Marine Biogeo- chemistry and Toxicology, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands Abstract: Despite carotenoids being abundant natural products, there are only scattered literature reports of carotenoid derivatives (mainly in the form of their 'perhydro' derivatives) in ancient sediments and petroleum. This was thought to be due to the sensitivity of carotenoids toward oxygen and their preservation potential in sediments was judged to be low. Detailed studies in the past years have indicated, however, that the fossil 'perhydro' derivatives of carotenoids represent only the tip of the iceberg and that a number of reactions occurring with the polyene chain (i.e. expulsion of toluene and xylene, cyclisation and aromatisation, reaction with reduced inorganic sulfur species, hydrogenation, C-C bond cleavage) determine the fate of carotenoids in ancient sediments and lead to complex mixtures of carotenoid derivatives. In addition, aromatisation of cyclohexenyl moieties (as present in e.g. p- carotene) occurs. An overview of these reactions is given. INTRODUCTION Only a minute fraction of the organic matter biosynthesised by marine photosynthetic organisms reaches the sea floor and ultimately becomes buried in ancient sediments. This is a process which leads to loss of labile biosynthetic products and carotenoids were generally thought to be included in this class of components (ref. 1). Recently, however, it has become clear that the potential for preservation of carotenoids is actually larger than anticipated and remnants of carotenoids are present in ancient rocks and crude oils as old as 450 million years.
    [Show full text]
  • The Collection of Reference Standards 2008 the Biomarker Catalogue the Collection Ofreference Standards - 2008 Innovative Standards Creative Solutions
    The Biomarker Catalogue The collection of reference standards 2008 standards The collection of reference The collection of reference standards 2008 Chiron AS Stiklestadveien 1 N-7041 Trondheim, Norway Tel: +47 73 87 44 90 The collection of reference standards Fax: +47 73 87 44 99 Mail: [email protected] - 2008 - www.chiron.no Innovative Standards Creative Solutions Reference standards Petro, Pharma, Food, Environment Joint Project Focus [email protected] www.chiron.no Professor Dr. Nils Andreas Sørensen (1909-1987) I would like to dedicate this catalogue to a great and unique chemist, teacher and personality, the late Professor Nils Andreas Sørensen. General Professor Nils Andreas Sørensen was born in Oslo in 1909, moved to Trondheim and finished his master’s degree at The Norwegian Institute of Technology (NTH) in 1933. As a stu- dent of Professor C.N. Riiber he received his doctor degree in 1937, moved to Heidelberg in 1938 where he studied with the Nobel laureate Richard Kuhn until he was appointed Professor in Organic Chemistry at NTH in 1939, at just 30 years of age. Professor Sørensen contributed to several important areas of natural product chemistry. His scientific production covers the chemistry of mutarotation of sugars, and the chemistry of carotenoids. He was also the first to discover naturally occur- ring acetylenic compounds. Professor Sørensen was, in addi- tion to being a unique chemist, an expert in botany which he combined with his chemistry background in a superb manner. He followed a tradition of natural product chemistry in Trondheim which has been manifested by later groups at NTH.
    [Show full text]