DOCSLIB.ORG

Geobiology of the Stratified Central Baltic Sea Water Column

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Geobiology of the Stratified Central Baltic Sea Water Column Geobiology of the stratified central Baltic Sea water column Dissertation zur Erlangung des mathematisch-naturwissenschaftlichen Doktorgrades „Doctor rerum naturalium“ der Georg-August-Universität Göttingen im Promotionsprogramm Geowissenschaften der Georg-August University School of Science (GAUSS) vorgelegt von Christine Berndmeyer aus Cloppenburg Göttingen, 2014 Betreuungsausschuss Prof. Dr. Volker Thiel, GZG, Abteilung Geobiologie Dr. Martin Blumenberg, Bundesanstalt für Geowissenschaften und Rohstoffe Mitglieder der Prüfungskomission Referent: Prof. Dr. Volker Thiel, GZG, Abteilung Geobiologie Korreferent: Dr. Martin Blumenberg, Bundesanstalt für Geowissenschaften und Rohstoffe weitere Mitglieder der Prüfungskomission: Prof. Dr. Joachim Reitner, GZG, Abteilung Geobiologie Prof. Dr. Daniel Jackson, Courant Research Center Geobiology Dr. Steffen Kiel, GZG, Abteilung Geobiologie Dr. Oliver Schmale, Leibnizinstitut für Ostseeforschung Warnemünde Tag der mündlichen Prüfung: 20. August 2014 Acknowledgments Working in this project was a great experience and although Göttingen is not necessarily famous for its maritime flair, my work here allowed me keeping my marine background. First of all, I cordially thank Martin Blumenberg for the opportunity to work in this Baltic Sea project, for his patient and diligent mentoring and his support during all stages of this thesis. I furthermore thank Volker Thiel for his scientific support, good advice, the hours spent for proofreading, and critical questions. I thank Joachim Reitner, Daniel Jackson, Steffen Kiel, and Oliver Schmale for being members of my thesis committee. In addition, I thank Oliver Schmale for help with sampling and onboard ship, and for constructive discussions. I am very thankful to my co-doctoral candidate Gunnar Jakobs for the nice times spent onboard ships, the scientific discussions and exchange of ideas, the non- scientific discussions and the mutual support. Thomas Bode and Nadine Schäfer have always been helpful with any PC problems. For help in laboratory and analytical support, I thank Cornelia Conradt, Lukas Kammel, Birgit Röhring, Andreas Reimer, Tobias Licha, Karsten Nödler and Jens Dyckmans. Thanks to my colleagues Jan Bauermeister, Juliane Germer, Ines Herlitze, Jennifer Hohagen, Tim Leefmann, Eva-Maria Sadowski, and Leyla Seyfullah for lunch breaks, chats on the roof, and help with this work. Special thanks to Jan-Peter Duda for all his support during years of study in Bremen and the current support for our “double-finish”. I am very grateful to my family for never ending support, help, encouragement, and interest in what I am doing. I am especially indebted to Timo Köhnsen who always supported my work but steadily reminds me what is really important. This thesis was written as a part of the DFG research project “Aerobic and anaerobic methane consumption in the central Baltic Sea water column”. This thesis is dedicated to Anette and Klaus Berndmeyer. Preface The following papers and manuscripts are part of this doctoral thesis: Berndmeyer, C., Thiel, V., Blumenberg, M., 2014. Test of microwave, ultrasound and Bligh & Dyer extraction for quantitative extraction of bacteriohopanepolyols (BHPs) from marine sediments. Organic Geochemistry 68, 90-94. Berndmeyer, C., Thiel, V., Schmale, O., Blumenberg, M., 2013. Biomarkers for aerobic methanotrophy in the water column of the stratified Gotland Deep (Baltic Sea). Organic Geochemistry 55, 103-111. Berndmeyer, C., Thiel, V., Schmale, O., Wasmund, N., Blumenberg, M., 2014b. Biomarkers in the stratified water column of the Landsort Deep (Baltic Sea). Biogeosciences Discussions 11, 9853-9887. Under review. Blumenberg, M., Berndmeyer, C., Moros, M., Muschalla, M., Schmale, O., Thiel, V., 2013. Bacteriohopanepolyols record stratification, nitrogen fixation and other biogeochemical perturbations in Holocene sediments of the central Baltic Sea. Biogeosciences 10, 2725- 2735. Schmale, O., Blumenberg, M., Kießlich, K., Jakobs, G., Berndmeyer, C., Labrenz, M., Thiel, V., Rehder, G., 2012. Microbial methane oxidation at the redoxcline of the Gotland Deep (Baltic Sea). Biogeosciences 9, 4969-4977. Contents Abstract 1 Chapter 1 - Introduction 3 1.1 Molecular biomarkers 4 1.2 Stratified water columns 7 1.3 Geobiology of stratified water columns 10 1.4 Holocene development of the Baltic Sea and the present situation 11 1.5 Sampling and analytical methods 16 1.6 Introduction to the following chapters 18 References 19 Chapter 2 – “Test of microwave, ultrasound and Bligh & Dyer extraction for quantitative extraction of bacteriohopanepolyols (BHPs) from marine sediments” 27 2.1 Abstract 27 2.2 Introduction 27 2.3 Methods 28 2.4 Results 30 2.5 Discussion 31 2.6 Conclusions 34 Acknowledgments 34 References 35 Chapter 3 – “Biomarkers in the stratified water column of the Landsort Deep (Baltic Sea)” 41 3.1 Abstract 41 3.2 Introduction 42 3.3 Material and methods 43 3.4 Results 46 3.5 Discussion 53 3.6 Conclusions 59 Acknowledgments 60 References 61 Chapter 4 – “Aerobic methanotrophy within the pelagic redox-zone of the Gotland Deep” 73 4.1 Abstract 73 4.2 Introduction 74 4.3 Methods 76 4.4 Results and discussion 79 4.5 Conclusions 85 Acknowledgments 86 References 86 Chapter 5 – “Biomarkers for aerobic methanotrophy in the water column of the stratified Gotland Deep (Baltic Sea)” 95 5.1 Abstract 95 5.2 Introduction 96 5.3 Methods 98 5.4 Results 101 5.5 Discussion 105 5.6 Conclusions and outlook 110 Acknowledgments 111 References 111 Chapter 6 – “Bacteriohopanepolyols record stratification, nitrogen fixation and other biogeochemical perturbations in Holocene sediments of the central Baltic Sea” 121 5.1 Abstract 121 5.2 Introduction 122 5.3 Study site and core stratigraphy 124 5.4 Materials and methods 126 5.5 Results 127 5.6 Discussion 130 5.7 Conclusions 137 Acknowledgments 137 References 138 Chapter 7 – Summary and conclusions 145 Curriculum Vitae 149 Abstract Abstract The central Baltic Sea water column is permanently density stratified leading to stagnating bottom waters and a zonation into an oxic, suboxic and anoxic zone. The anoxic zone of the central Baltic Sea is characterized by strong methane gradients that indicate methane consumption in the suboxic zone. This thesis comprises five papers that are based on investigations of water column and sediment samples from the central Baltic Sea. The aim of these investigations was to assess the geobiology of this stratified system using biomarkers with a focus on bacteriohopanepolyols (BHPs). First, three different extraction methods were compared with respect to BHP yields. Microwave, ultrasound, and Bligh & Dyer extraction revealed similar results for total extracted BHPs and studies were continued using microwave extraction. In the Landsort Deep, biomarkers were used to assess the geobiology in the whole water column. They mirrored the water column stratification and revealed different microbial communities. An initial multidisciplinary study including biomarker analysis revealed the presence of type I aerobic methanotrophic bacteria in the suboxic zone of the Gotland Deep. A following detailed investigation of Gotland Deep biomarkers in the oxic and suboxic zone and the underlying sediment showed high BHP concentrations in the suboxic zone and suggested that this zone is an important source layer for these compounds. The BHP signal found in the suboxic zone is also mirrored in the surface sediments. Subsequently, the Holocene geological record of BHPs was analyzed in a Gotland Deep sediment core covering all stages of the Baltic Sea development. BHPs reflected the onset of the stratification during Littorina stage and are of particular abundance during periods of pronounced anoxia. The studies presented in this thesis demonstrate biomarkers to be a versatile tool to assess microbial communities in present and past stratified environments and contribute to the general knowledge on the geobiology of stratified water columns. 1 2 Chapter 1 – Introduction 1 Introduction Geobiology is the science of the interactions between the non-living geosphere and the living biosphere. Much like the geosphere has an influence on the development and distribution of life, life, inversely, is able to change and shape the geosphere. Numerous topics such as early life environments, the photosynthetic oxygenation of the atmosphere, microbial mineral precipitation, or nutrient cycles are of geobiological interest. This thesis, however, is focused on the geobiology of the central Baltic Sea stratified water column, i.e. the distribution of microbial life in physicochemically differing water layers. A permanent pycnocline divides the present central Baltic Sea water column into an oxic, suboxic and anoxic zone. The resulting chemocline supports numerous microbial metabolisms, including the aerobic oxidation of methane. This thesis was written in the context of the multidisciplinary project “Aerobic and anaerobic methane consumption in the central Baltic Sea water column” conducted by the geobiology group of the Georg-August-University of Göttingen and the working group “trace gases” of the Leibniz Institute for Baltic Sea Research Warnemünde (IOW). Methane is known to be a highly effective greenhouse gas that is amongst others produced in marine sediments. Microbial methane oxidation in the sediments and in the water column removes large amounts of the produced methane before it can reach the atmosphere and affects climate. Little was known about the microbial key players in methane oxidation, the
Load more

Recommended publications
  • Microbial Diversity Under Extreme Euxinia: Mahoney Lake, Canada V
    Geobiology (2012), 10, 223–235 DOI: 10.1111/j.1472-4669.2012.00317.x Microbial diversity under extreme euxinia: Mahoney Lake, Canada V. KLEPAC-CERAJ,1,2 C. A. HAYES,3 W. P. GILHOOLY,4 T. W. LYONS,5 R. KOLTER2 AND A. PEARSON3 1Department of Molecular Genetics, Forsyth Institute, Cambridge, MA, USA 2Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, USA 3Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA 4Department of Earth and Planetary Sciences, Washington University, Saint Louis, MO, USA 5Department of Earth Sciences, University of California, Riverside, CA, USA ABSTRACT Mahoney Lake, British Columbia, Canada, is a stratified, 15-m deep saline lake with a euxinic (anoxic, sulfidic) hypolimnion. A dense plate of phototrophic purple sulfur bacteria is found at the chemocline, but to date the rest of the Mahoney Lake microbial ecosystem has been underexamined. In particular, the microbial community that resides in the aphotic hypolimnion and ⁄ or in the lake sediments is unknown, and it is unclear whether the sulfate reducers that supply sulfide for phototrophy live only within, or also below, the plate. Here we profiled distribu- tions of 16S rRNA genes using gene clone libraries and PhyloChip microarrays. Both approaches suggest that microbial diversity is greatest in the hypolimnion (8 m) and sediments. Diversity is lowest in the photosynthetic plate (7 m). Shallower depths (5 m, 7 m) are rich in Actinobacteria, Alphaproteobacteria, and Gammaproteo- bacteria, while deeper depths (8 m, sediments) are rich in Crenarchaeota, Natronoanaerobium, and Verrucomi- crobia. The heterogeneous distribution of Deltaproteobacteria and Epsilonproteobacteria between 7 and 8 m is consistent with metabolisms involving sulfur intermediates in the chemocline, but complete sulfate reduction in the hypolimnion.
    [Show full text]
  • Hydrogen Abstraction from Titanium and Zirconium Oxides
    The Pennsylvania State University The Graduate School Eberly College of Science NEW INSIGHTS IN THE GAS-PHASE ION CHEMISTRY OF GROUP IVB TRANSITION METAL OXIDES: CLUSTER MODELS FOR CATALYSIS A Dissertation in Chemistry by Christopher L. Harmon © 2016 Christopher L. Harmon Submitted in Partial Fulfillment Of the Requirements For the Degree of Doctor of Philosophy August 2016 The dissertation of Christopher L. Harmon was reviewed and approved* by the following: A. W. Castleman, Jr. Evan Pugh Professor of Chemistry and Physics Eberly Distinguished Chair in Science Dissertation Adviser Chair of Committee Nicholas Winograd Evan Pugh Professor of Chemistry Lasse Jensen Associate Professor of Chemistry Robert M. Rioux Friedrich G. Helfferich Associate Professor of Chemical Engineering Professor of Chemistry Kenneth S. Feldman Professor of Chemistry Graduate Program Chair *Signatures are on file in the Graduate School. ii Abstract The study of gas-phase cluster models has emerged as a useful tool to model catalytic active sites on surfaces. By observing how the reactivity of TMO clusters changes with cluster size, active site, and metal composition, we draw insights about the molecular factors governing reactivity and selectivity. The aim is to provide a conceptual framework to drive the development of improved catalysts with higher activity and selectivity. As group IVB transition metal oxides (TMOs) are widely used as catalysts and supports, we have undertaken mass spectrometric reactivity studies of titanium, zirconium, and hafnium oxide clusters with small organic molecules of interest in catalysis. We particularly note the differences in reactivity observed as the identity of the + metal in the cluster changes. We report the reactivity of MxO2x (M = Ti, Zr) clusters that contain radical atomic oxygen, O•−, with methane, ethane, propane, ethylene, and propylene.
    [Show full text]
  • MASS SPECTROSCOPY APPLIED to GAS LEAK DETECTION and FUEL IONIZATION by JAYANTH POTHIREDDY a THESIS PRESENTED to the GRADUATE
    MASS SPECTROSCOPY APPLIED TO GAS LEAK DETECTION AND FUEL IONIZATION By JAYANTH POTHIREDDY A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2003 Copyright 2003 by Jayanth Pothireddy To my friends ACKNOWLEDGMENTS I would like to sincerely thank Dr. Corin Segal for giving me this wonderful opportunity and for his unlimited support, understanding and incredible patience without which I would not have successfully completed my thesis. I would also like to thank Dr. David Mikolaitis and Dr. Martin Vala for their support and Dr. Norman Fitz-Coy for his valuable suggestions. Many thanks go to Mr. Jan Szczepanski for giving me “first lessons” on mass spectrometry, invaluable suggestions, tremendous support and help in developing the mass spectrometry system. My heartfelt thanks go to my friends Venkat, Sujith, Gopi, Anand, “Iranian bros” Amir and Omid, Weizhong, Sampath, Harsha, Adil, Anant, Sasidhar, Charan, Danny, Jonas, Nelson, Zhu Wei, Ron, “Dr” Amit, Errol, Anurag, Priya, Amit “Saale” and Balaji for their support and understanding. I thank Ron Brown for constructing a nice model of the Space Shuttle aft compartment and for his help in moving the mass spectrometer cart to and fro from “chemistry” to “aero.” iv TABLE OF CONTENTS Page ACKNOWLEDGMENTS.................................................................................................. iv LIST OF FIGURES...........................................................................................................vii
    [Show full text]
  • Mass Spectrometry (Part-II) Electrostatic Acceleration System
    S.O.s. in environmental chemistry Jiwaji university, gwalior Presentation on:- Mass Spectrometry (part-II) Electrostatic Acceleration System:- 1) The positive ions formed in the ionisation chamber are withdrawn by the electric field which exists between the first accelerator plate and the second repeller plate. 2) A strong electrostatic field between accelerator and repeller plate accelerates the ions of masses m1 m2 m3... to their final velocities. 3) The ions which escape through slit having velocities and kinetic energies give. 2 2 2 eV=1/2m1v1 =1/2m2v2 =1/2m3v3 ...... Vacuum system:- 1) A high vacuum is to be maintained. 2) The inlet system is generally maintained at 0.015 torr, the ion source at 10-15 torr and analyzer tube at 10-7 torr or as low as possible. 3) Oil diffusion and mercury diffusion pumps are commonly used in different types of combination Mass analyzers:- 1) Separate ions based on their mass-to-charge ratio (m/z) 2) Operate under high vacuum (keeps ions from bumping into gas molecules) 3) Actually measure mass-to-charge ratio of ions (m/z) Types of mass analyzers:- 1) Quadrupole mass analyzer 2) Time of flight analyzer (TOF) 3) Magnetic sector mass analyzer a) Single focusing b) Double focusing 4) Quadrupole ion trap mass analyzer Quadrupole mass analyzer:- 1) It consists of 4 voltage carrying rods. 2) The ions are pass from one end to another end 3) During this apply the radiofrequency and voltage complex oscillations will takes place. 4) Here the single positive charge ions shows the stable oscillation and the remaining the shows the unstable oscillations Magnetic Sector Mass Analyzer:- In magnetic sector analyzers ions are accelerated through a flight tube, where the ions are separated by charge to mass ratios.
    [Show full text]
  • Quadrupole and Ion Trap Mass Analysers and an Introduction to Resolution a Simple Definition of a Mass Spectrometer
    Quadrupole and Ion Trap Mass Analysers and an introduction to Resolution A simple definition of a Mass Spectrometer ◗ A Mass Spectrometer is an analytical instrument that can separate charged molecules according to their mass–to–charge ratio. The mass spectrometer can answer the questions “what is in the sample” (qualitative structural information) and “how much is present” (quantitative determination) for a very wide range of samples at high sensitivity Components of a Mass Spectrometer Atmosphere Vacuum System Sample Ionisation Mass Data Detector Inlet Method Analyser System How are mass spectra produced ? ◗ Ions are produced in the source and are transferred into the mass analyser ◗ They are separated according to their mass/charge ratio in the mass analyser (e.g. Quadrupole, Ion Trap) ◗ Ions of the various m/z values exit the analyser and are ‘counted’ by the detector What is a Mass Spectrum ? ◗ A mass spectrum is the relative abundance of ions of different m/z produced in an ion source -a “chemical fingerprint” ◗ It contains – Molecular weight information (generally) – Structural Information (mostly) – Quantitative information What does a mass spectrum look like ? ◗ Electrospray mass spectrum of salbutamol + 100 MH 240 OH NH tBu HO Base peak HO % at m/z 240 241 0 60 80 100 120 140 160 180 200 220 240 260 280 300 What information do you need from the analysis ? ◗ Low or High Mass range ◗ Average or Monoisotopic mass (empirical) ◗ Accurate Mass ◗ Quantitation - precision, accuracy, selectivity ◗ Identification ◗ Structural Information
    [Show full text]
  • Mechanistic Study of Carbazole and Triphenylamine Dimerization and Pyrrolidine
    Mechanistic Study of Carbazole and Triphenylamine Dimerization and Pyrrolidine Dehydrogenation Using Mass Spectrometry A thesis presented to the faculty of the College of Arts and Sciences of Ohio University In partial fulfillment of the requirements for the degree Master of Science Brian E. Hivick May 2019 © 2019 Brian E. Hivick. All Rights Reserved. 2 This thesis titled Mechanistic Study of Carbazole and Triphenylamine Dimerization and Pyrrolidine Dehydrogenation Using Mass Spectrometry by BRIAN E. HIVICK has been approved for the Department of Chemistry and Biochemistry and the College of Arts and Sciences by Hao Chen Professor of Chemistry and Biochemistry Joseph Shields Interim Dean, College of Arts and Sciences 3 ABSTRACT HIVICK, BRIAN E., M.S., May 2019, Chemistry Mechanistic Study of Carbazole and Triphenylamine Dimerization and Pyrrolidine Dehydrogenation Using Mass Spectrometry Director of Thesis: Hao Chen Mass spectrometry is one of the most powerful techniques used in analytical chemistry today. It has been utilized in a wide variety of fields, from synthesis to pharmaceuticals to analyzing medicinal samples. One of its greatest strengths is its ability to be combined with other techniques to further improve the collected data. In this work, the ability to couple mass spectrometry with electrochemistry in the dimerization of two aromatic amines, carbazole and triphenylamine, is explored, and insight into the underlying dimerization mechanism is achieved. In addition, photochemistry is also coupled with mass spectrometry, and the potential dehydrogenation of pyrrolidine is explored. 4 DEDICATION I dedicate this work to my parents and siblings, who have done so much for me throughout my life and have unequivocally supported me in all of my decisions.
    [Show full text]
  • An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.15.435355; this version posted March 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. An ecological basis for dual genetic code expansion in marine deltaproteobacteria 1 Veronika Kivenson1, Blair G. Paul2, David L. Valentine2* 2 1Interdepartmental Graduate Program in Marine Science, University of California, Santa Barbara, CA 3 93106, USA 4 2Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, 5 CA 93106, USA 6 * Correspondence: 7 David L. Valentine 8 [email protected] 9 Present Address 10 VK: Oregon State University, Corvallis, OR 97331 11 BGP: Marine Biological Laboratory, Woods Hole, MA 02543 12 13 Keywords: microbiome, pyrrolysine, selenocysteine, metabolism, metagenomics 14 15 Abstract 16 Marine benthic environments may be shaped by anthropogenic and other localized events, leading to 17 changes in microbial community composition evident decades after a disturbance. Marine sediments 18 in particular harbor exceptional taxonomic diversity and can shed light on distinctive evolutionary 19 strategies. Genetic code expansion may increase the structural and functional diversity of proteins in 20 cells, by repurposing stop codons to encode noncanonical amino acids: pyrrolysine (Pyl) and 21 selenocysteine (Sec). Here, we show that the genomes of abundant Deltaproteobacteria from the 22 sediments of a deep-ocean chemical waste dump site, have undergone genetic code expansion. Pyl 23 and Sec in these organisms appear to augment trimethylamine (TMA) and one-carbon metabolism, 24 representing key drivers of their ecology.
    [Show full text]
  • Agilent 6545 Q-TOF Mass Spectrometer
    The Agilent 6545 Q-TOF mass spectrometer The Agilent 6545 Q-TOF mass spectrometer, which is shown in the following picture, is a state-of-the-art quadrupole time-of-flight (Q-TOF) mass spectrometer that performs both high resolution mass spectrometry (HRMS) and high-resolution tandem mass spectrometry (HRMS/MS). It consists of a quadrupole mass analyzer, a hexapole collision cell, and a high resolution TOF mass analyzer. During HRMS analysis, the quadrupole mass analyzer and the hexapole collision cell are simply used as ion guides to transport ions. During HRMS/MS analysis, the quadrupole mass analyzer selects precursor ions that are fragmented in the hexapole collision cell into product ions, which are then impelled to the TOF mass analyzer, at an angle perpendicular to the original path. 1 The following Figure shows the ion optics of the Agilent 6545 Q-TOF mass spectrometer, with major improvements over the Agilent 6540 Q-TOF mass spectrometer identified. 1. Enhanced Wide Bore Lens 2. Identical to the lens 2 design used in the 6560, a larger orifice is used in the 6545. Ions are still conditioned via DC and RF voltages prior to quad transmission or isolation, but ions will not get in close proximity to the lens surface. The possible risk of ion deposition on the surface is greatly reduced, leading to an increased robustness of the system under high ion current conditions. 2. Slicer design. The slicer design on the 6545 is identical to the 6550. It has 2 different sizes of the opening: a larger one for high sensitivity applications, and a smaller one for high resolution applications.
    [Show full text]
  • Mass Spectrophotometry: an Advanced Technique in Biomedical
    s in que Bio ni lo h g c y e T & d M e e Paital, Adv Tech Biol Med 2016, 4:3 c Advanced Techniques in d n i c a i v n DOI: 10.4172/2379-1764.1000182 d e A ISSN: 2379-1764 Biology & Medicine Review Article OpenOpen Access Access Mass Spectrophotometry: An Advanced Technique in Biomedical Sciences Biswaranjan Paital* Department of Zoology, CBSH, Orissa University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India Abstract Present century is the era of life sciences and metabolomics is the dominating field in present day over genomics and proteomics. Powerful techniques in the later cases are useful to determine the qualitative and quantitative studies of the levels of metabolites in bio-medical samples. In past time, biochemistry had very least role because the analyses of metabolites using individual conventional biochemical techniques had been used from past centuries. Owing to this limitation, mass spectrometry (MS) was introduced in bio-medical sciences. The fundamental rule in MS is that it ionizes individual chemical species and sorts the fragmented samples at charged state (ions) on the basis of their mass to charge (m/z) ratio. Therefore, each molecule in purified form or in homogenate can be identified and quantified based on their unique m/z ratio. In other words, MS measures the masses of the fragmented samples by enabling them to be charged during measurement. This particular technique has therefore, many applications starting from quantitative to qualitative analyses of metabolites under normal, experimental and diseased conditions in organisms including human being.
    [Show full text]
  • Mass Spectrometry Interfaced with Ion Mobility Or
    MASS SPECTROMETRY INTERFACED WITH ION MOBILITY OR LIQUID CHROMATOGRAPHY SEPARATION FOR THE ANALYSIS OF COMPLEX MIXTURES A Dissertation Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Danijela Smiljanic December, 2011 MASS SPECTROMETRY INTERFACED WITH ION MOBILITY OR LIQUID CHROMATOGRAPHY SEPARATION FOR THE ANALYSIS OF COMPLEX MIXTURES Dissertation Danijela Smiljanic Approved: Accepted: ________________________________ _________________________________ Advisor Department Chair Dr. Chrys Wesdemiotis Dr. Kim C. Calvo ________________________________ _________________________________ Committee Member Dean of the College Dr. Bi-min Zhang Newby Dr. Chand K. Midha ________________________________ _________________________________ Committee Member Dean of the Graduate School Dr. David Perry Dr. George R. Newkome ________________________________ _________________________________ Committee Member Date Dr. Yi Pang ________________________________ Committee Member Dr. Peter Rinaldi ii ABSTRACT This dissertation focuses on coupling separation techniques such as ion mobility (IM) and liquid chromatography (LC) to mass spectrometry and their application to characterization of complex mixtures. Non-covalent complexes between poly(ethylene imine) (PEI) and single stranded oligodeoxynucleotides (ODNs), as well as components from black raspberries, were characterized utilizing ion mobility mass spectrometry (IM- MS) and liquid chromatography mass spectrometry (LC-MS),
    [Show full text]
  • M T T F Mass Spectrometry of Proteins, Peptides and Other Proteins
    MttfMass spectrometry of proteins, peptides and other analytes: principles and priilincipal meth hdods MttRMatt Ren frow January 7, 2011 Objectives of the Lecture 1. MkMake ions 2. Separate/Analyze 3. Detect ions 4. What is mass resolution and mass accuracy? What does a mass spectrometer do? 1. It measures mass better than any other technique. 2. It can give information about chemical structures. What are mass measurements good for? To identify, verify, and quantitate: metabolites, recombinant proteins, proteins isolated from natural sources, oligonucleotides, drug candidates, peptides, synthetic organic chemicals, polymers How is mass defined? Assigning numerical value to the intrinsic property of “mass” is based on using carbon-12, 12CasaC, as a reference point. One unit of mass is defined as a Dalton (Da). One Da lton is de fine d as 1/12 t he mass o f a s ing le carbon-12 atom. Thus, one 12C atom has a mass of 12.0000 Da. Isotopes +Most elements have more than one stable isotope. For example, most carbon atoms have a mass of 12 Da, but in nature, 1.1% of C atoms have an extra neutron, making their mass 13 Da. +Why do we care? Mass spec trome ters can “ see” i so tope peak s if th ei r resol uti on is high enough. If an MS instrument has resolution higggh enough to resolve these isotopes, better mass accuracy is achieved. Stable isotopes of most abundant elements of peptides Element Mass Abundance H 1.0078 99.985% 2.0141 0.015 C 12.0000 98.89 13.0034 1.11 N 14.0031 99.64 15.
    [Show full text]
  • Bacterial H2S Generation in Oil Sands Process Wastes
    Goldschmidt 2012 Conference Abstracts Bacterial H2S Generation in Oil Unraveling the Genetic Basis of an Sands Process Wastes: Where Does it Ancient Geochemical Biomarker Begin? 1* 2 R.E. COLLINS , B. WING 1* 1 1Origins Institute, McMaster University, Hamilton, ON, Canada, TARA COLENBRANDER NELSON , STEVEN P. HOLLAND , 1 1 2 [email protected] (* presenting author) KATHRYN KENDRA , KATE STEPHENSON , TARA PENNER 1 2Earth & Planetary Sciences, McGill University, Montreal, QC, Canada, AND LESLEY A. WARREN [email protected] 1 School of Geography and Earth Sciences, McMaster University, Hamilton, Canada, [email protected] (* presenting author) Abstract 2 Syncrude Environmental Research, Edmonton, Canada, Based on phylogenetic and geochemical evidence, the cycling of [email protected] inorganic sulfur compounds was likely among the first metabolisms used by life. Sulfur isotope fractionation is a geochemical biomarker which has Reclamation of tailings, wastewater, and afflicted land been observed in marine sediments dating back more than 2.5 billion represents one of the largest challenges facing the Alberta Oil Sands years, but the cellular-level processes responsible for the fractionation industry. Syncrude Canada Ltd., one of the largest producers in the effect are not well understood. Utilizing bioinformatic approaches in Alberta Oil Sands, is assessing a novel reclamation strategy combination with measurements of sulfur isotope fractionation in pure involving the establishment of a freshwater fen overlying a sand-cap cultures we seek to make quantitative links between SRB and their topped, gypsum (CaSO4·2H2O)-amended, composite tailings (CT) geochemical biomarkers. waste material. However, a recent phenomenon resulting in the unpredicted generation of H2S gas in CT dewatering wells has The intrinsic sulfur isotope fractionation effect, ε, is essentially a indicated the importance of constraining microbial S dynamics in measure of the preferential use of 32S-substituted sulfate over 34S- the tailings system.
    [Show full text]