Lipidomics for Geochemistry
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Manhattan, KS
Acknowledgements General Chair Daniel A. Higgins Program Chair J. Vincent Ortiz Symposia Chairs Crystal Engineering – Supramolecular Chemistry Christer Aakeröy Drug Discovery and Bioorganic Chemistry Duy H. Hua Environmental Chemistry Larry E. Erickson Methods of Electronic Structure Theory J. Vincent Ortiz Nanostructured Materials and Air Quality Kenneth J. Klabunde Sol-Gel Chemistry Maryanne M. Collinson Undergraduate Research Stefan Kraft Treasurer Yasmin Patell Exposition Chair Earline Dikeman Undergraduate Program Janie Salmon Audio/Video Resources James R. Hodgson Program Book Ruth Hathaway Printing/Publicity Ellen Stauffer KSU Div. of Continuing Education Website KSU Div. of Continuing Education Program Book Art Jessa Talamentez KSU Div. of Continuing Education Midwest Award Leah O’Brien ACS Regional Meeting Planner John Michael Sophos Welcome to the 39th Midwest Regional Meeting of the American Chemical Society October 20-22, 2004 Manhattan Holiday Inn Holidome Manhattan, KS Hosted by the Kansas State University Section Local Sections of the Midwest Region Of the American Chemical Society Ames Iowa Kansas City Kansas State University Mark Twain Mo-Kan-Ok Nebraska Omaha Ozark Sioux Valley South Central Missouri Southern Illinois St. Louis University of Kansas University of Missouri University of Arkansas Wichita MWRM 2004 39th Midwest Regional Meeting October 20-22, 2004 Table of Contents Acknowledgements inside front cover Welcome 1 Local Sections of the Midwest Region 2 Table of Contents 3 Special Greeting Brad Everett, Mayor, -
Open 1-Dissertation NEK V12 4
The Pennsylvania State University The Graduate School Department of Chemical Engineering DEVELOPMENT OF BIOLOGICAL PLATFORM FOR THE AUTOTROPHIC PRODUCTION OF BIOFUELS A Dissertation in Chemical Engineering by Nymul Khan 2015 Nymul Khan Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The dissertation of Nymul Khan was reviewed and approved* by the following: Wayne Curtis Professor, Chemical Engineering Dissertation Advisor Chair of Committee Esther Gomez Assistant Professor, Chemical Engineering Manish Kumar Assistant Professor, Chemical Engineering John Regan Professor, Environmental Engineering Phillip E. Savage Walter L. Robb Family Endowed Chair Head of the Department of Chemical Engineering *Signatures are on file in the Graduate School iii ABSTRACT The research described herein is aimed at developing an advanced biofuel platform that has the potential to surpass the natural rate of solar energy capture and CO2 fixation. The underlying concept is to use the electricity from a renewable source, such as wind or solar, to capture CO2 via a biological agent, such as a microbe, into liquid fuels that can be used for the transportation sector. In addition to being renewable, the higher rate of energy capture by photovoltaic cells than natural photosynthesis is expected to facilitate higher rate of liquid fuel production than traditional biofuel processes. The envisioned platform is part of ARPA-E’s (Advanced Research Projects Agency - Energy) Electrofuels initiative which aims at supplementing the country’s petroleum based fuel production with renewable liquid fuels that can integrate easily with the existing refining and distribution infrastructure (http://arpa- e.energy.gov/ProgramsProjects/Electrofuels.aspx). -
51Th International Mendeleev Olympiad, 2017 Astana 1St Theoretical Tour Problems
51th International Mendeleev Olympiad, 2017 Astana 1st theoretical tour Problems Problem 1 “I’ll be back” Terminator T-800 Paying tribute to my constant co-author Plastic pollution is defined as accumulation of plastic products in the environment producing a negative impact on animal and human habitats. This problem is among the most vital challenges facing humanity nowadays. Surprisingly, sometimes nature itself offers assistance, such as bioremediation. Thus, Japanese researchers have recently discovered that the bacterium Ideonella sakaiensis can use polyethylene terephthalate (PET), a polymer with an extremely high resistance towards biodegradation, as the major source of carbon and energy. O O O O n PET biodegradation involves two enzymatic steps catalyzed by hydrolases and leading to three low molecular weight (М<600 g/mole) aromatic products A, B, and C with the number of types of hydrogens of 2, 4, and 6, respectively. After penetration inside Ideonella sakaiensis cells, C is metabolized into А, which turns out to be the only source of carbon for the bacterium. 1. Show the chemical bonds (use arrows) in the PET formula that are cleaved in the process of its hydrolase-catalyzed biodegradation. 2. Draw all possible structures of A, B, and C, which are in agreement with the given data. A undergoes a three-step enzyme catalyzed metabolic transformation (all chemical equations): O 2 CO2 O2 O A A1 A2 X OH X + + + + A3 NADPH + H NADP NADP NADPH + H X is a functional group in A3, NADP+ and NADPH are oxidized and reduced co-enzyme forms, respectively. 3. Deduce the structural formula of A3 if its molar fractions of oxygen and hydrogen are equal and lower than that of carbon. -
Polyacetylene: Myth and Reality
materials Review Polyacetylene: Myth and Reality Bruce S. Hudson Department of Chemistry, Syracuse University, Syracuse, NY 13244-4100, USA; [email protected]; Tel.: +1-315-443-5805 Received: 31 December 2017; Accepted: 31 January 2018; Published: 6 February 2018 Abstract: Polyacetylene, the simplest and oldest of potentially conducting polymers, has never been made in a form that permits rigorous determination of its structure. Trans polyacetylene in its fully extended form will have a potential energy surface with two equivalent minima. It has been assumed that this results in bond length alternation. It is, rather, very likely that the zero-point energy is above the Peierls barrier. The experimental studies that purport to show bond alternation are reviewed and shown to be compromised by serious experimental inconsistencies or by the presence, for which there is considerable evidence, of finite chain polyenes. In this view, addition of dopants results in conductivity by facilitation of charge transport between finite polyenes. The double minimum potential that necessarily occurs for polyacetylene, if viewed as the result of elongation of finite 1 1 chains, originates from admixture of the 1 Ag ground electronic state with the 2 Ag excited electronic singlet state. This excitation is diradical (two electron) in character. The polyacetylene limit is an 1 equal admixture of these two Ag states making theory intractable for long chains. A method is outlined for preparation of high molecular weight polyacetylene with fully extended chains that are prevented from reacting with neighboring chains. Keywords: polyacetylene; double-minimum potential; Peierls barrier; zero-point level; cross-linking 1. Introduction/Background History Polyacetylene is selected for review because of its relative simplicity; the small periodic repeat permits polyacetylene to be treated by sophisticated computational methods. -
Expanding the Molecular Landscape of Exercise Biology
H OH metabolites OH Review Metabolomics and Lipidomics: Expanding the Molecular Landscape of Exercise Biology Mehdi R. Belhaj 1, Nathan G. Lawler 2,3 and Nolan J. Hoffman 1,* 1 Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne 3000, Australia; [email protected] 2 Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Murdoch, Perth 6150, Australia; [email protected] 3 School of Health and Medical Sciences, Edith Cowan University, Joondalup 6027, Australia * Correspondence: [email protected]; Tel.: +61-3-9230-8277 Abstract: Dynamic changes in circulating and tissue metabolites and lipids occur in response to exercise-induced cellular and whole-body energy demands to maintain metabolic homeostasis. The metabolome and lipidome in a given biological system provides a molecular snapshot of these rapid and complex metabolic perturbations. The application of metabolomics and lipidomics to map the metabolic responses to an acute bout of aerobic/endurance or resistance exercise has dramatically expanded over the past decade thanks to major analytical advancements, with most exercise-related studies to date focused on analyzing human biofluids and tissues. Experimental and analytical considerations, as well as complementary studies using animal model systems, are warranted to help overcome challenges associated with large human interindividual variability and decipher the breadth of molecular mechanisms underlying the metabolic health-promoting effects of exercise. In this review, we provide a guide for exercise researchers regarding analytical techniques and experimental workflows commonly used in metabolomics and lipidomics. Furthermore, we discuss Citation: Belhaj, M.R.; Lawler, N.G.; advancements in human and mammalian exercise research utilizing metabolomic and lipidomic Hoffman, N.J. -
Noah Burns CV 2019
Noah Z. Burns, Ph.D. Curriculum Vitae Stanford University office: 335 Lokey Department of Chemistry phone: (650) 723-2961 333 Campus Drive [email protected] Stanford, CA 94305 burnschemistry.com APPOINTMENT Associate Professor 2019 Stanford University, Stanford CA Assistant Professor 2012–2019 Stanford University, Stanford CA EDUCATION AND TRAINING Postdoctoral Fellow (NIH) 2009–2012 Harvard University, Cambridge MA Advisor: Eric N. Jacobsen Doctor of Philosophy 2004–2009 The Scripps Research Institute, La Jolla CA Advisor: Phil S. Baran Thesis: Total Syntheses of Haouamine A Bachelor of Arts, Chemistry 2000–2004 Columbia University, New York NY Advisor: James L. Leighton AWARDS AND HONORS 2019 Eli Lilly Young Investigator Award 2019: NSF CAREER Award 2018: Kavli Fellow 2017: Dean's Award for First Years of Teaching at Stanford 2017: Amgen Young Investigator Award 2013–present: Stanford Terman Fellow 2012: Thieme Chemistry Journal Award 2009–2012: NIH NRSA Postdoctoral Fellow 2006–2008: ARCS Foundation Scholarship 2006: Roche Excellence in Chemistry Award 2005–2006: TSRI Dean’s Fellow 2004: Graduated Summa Cum Laude, Columbia University 2004: Phi Beta Kappa 2003: Barry M. Goldwater Scholarship 2002: NSF Summer Undergraduate Research Fellowship PEER-REVIEWED PUBLICATIONS INDEPENDENT CAREER Smith, M. W.; Falk, I. D.; Ikemoto, H.; Burns, N. Z. “A Convenient C–H Functionalization Platform for Pyrroloiminoquinone Alkaloid Synthesis,” Tetrahedron 2019, 75, 3366–3370. [Invited contribution in honor of Professor Ryan Shenvi, recipient of the 2019 Tetrahedron Young Investigator Award.] Landry, M. L.; McKenna, G. M.; Burns, N. Z. “Enantioselective Synthesis of Azamerone,” J. Am. Chem. Soc. 2019, 141, 2867–2871. Kearney, S. E. et al. “Canvass: A Crowd-Sourced, Natural-Product Screening Library for Exploring Biological Space,” ACS Central Science 2018, 4, 1727–1741. -
Lipidomics and Metabolomics Service Gain Deeper Insights Into Exosomes
EXOSOMES LIPIDOMICS AND METABOLOMICS SERVICE GAIN DEEPER INSIGHTS INTO EXOSOMES SYSTEMBIO.COM/LIPIDOMICS HIGHLIGHTS What can lipidomics of exosomes tell you? n Discover novel circulating biomarkers Lipids are an important part of cellular physiology, and are increasingly being recognized for their importance in exosome biology as well. Exosomes were recently shown to have the highest lipid- n Learn more about exosome biology to-protein ratio of all classes of extracellular vesicles (1), with lipid content that both differs from n Send us your sample and receive data the parent cell the vesicles are shed from (2) and also changes as exosomes undergo a variety of in 4 - 6 weeks physiological processes (3). These unique lipid profiles can serve as novel circulating biomarkers, and recent evidence suggests that specific lipid species carried by exosomes can also modulate Service Overview the function of recipient cells (4). Whether you’re interested in With so much information revealed by lipid content, lipidomics studies of exosomes are a great way to identify lipid-based biomarkers and for understanding vesicle biogenesis and function (5). circulating biomarker discovery, basic exosome research, or other TUMOR MICROENVIRONMENT exosome-related studies, SBI’s CANCER CELLS CAFs EXOSOMES Exosome Lipidomics & Metabolomics Service helps you quickly and efficiently get the most information from your exosomes. Simply send Exosomes affect metabolism of cancer us your sample or purified exosomes cells A recent study by Zhao, et al, (6) and we’ll send back a report with demonstrated that exosomes from putative identifications, mass/charge patient-derived cancer-associated fibroblasts (CAFs) can reprogram EXOSOME ratios, and differential analysis (if UPTAKE the cellular machinery in cancer requested). -
Structural Identification of Ladderane and Other Membrane Lipids Of
Structural identification of ladderane and other membrane lipids of planctomycetes capable of anaerobic ammonium oxidation (anammox) Jaap S. Sinninghe Damste´ 1, W. Irene C. Rijpstra1, Jan A. J. Geenevasen2, Marc Strous3 and Mike S. M. Jetten3 1 Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Biogeochemistry and Toxicology, Texel, the Netherlands 2 van ‘t Hoff Institute for Molecular Science (HIMS), University of Amsterdam, the Netherlands 3 Department of Microbiology, Institute of Water and Wetland Research, Radboud University Nijmegen, the Netherlands Keywords The membrane lipid composition of planctomycetes capable of the an- ether lipids; fatty acids; mass spectrometry; aerobic oxidation of ammonium (anammox), i.e. Candidatus ‘Brocadia mixed glycerol ester/ether lipids; NMR anammoxidans’ and Candidatus ‘Kuenenia stuttgartiensis’, was shown to be composed mainly of so-called ladderane lipids. These lipids are com- Correspondence J. S. Sinninghe Damste´ , Royal Netherlands prised of three to five linearly concatenated cyclobutane moieties with cis Institute for Sea Research (NIOZ), ring junctions, which occurred as fatty acids, fatty alcohols, alkyl glycerol Department of Marine Biogeochemistry and monoethers, dialkyl glycerol diethers and mixed glycerol ether ⁄ esters. The Toxicology, PO Box 59, 1790 AB Den Burg, highly strained ladderane moieties were thermally unstable, which resulted the Netherlands in breakdown during their analysis with GC. This was shown by isolation Fax: +31 222 319 674 of a thermal product of these ladderanes and subsequent analysis with Tel: +31 222 369 550 two-dimensional NMR techniques. Comprehensive MS and relative retent- E-mail: [email protected] ion time data for all the encountered ladderane membrane lipids is repor- (Received 26 May 2005, revised 23 June ted, allowing the identification of ladderanes in other bacterial cultures and 2005, accepted 1 July 2005) in the environment. -
Lipidomics at the Interface of Structure and Function in Systems Biology
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Chemistry & Biology Crosstalk Lipidomics at the Interface of Structure and Function in Systems Biology Richard W. Gross1,2,3,4,* and Xianlin Han1,2 1Division of Bioorganic Chemistry and Molecular Pharmacology 2Departments of Medicine 3Developmental Biology Washington University School of Medicine, St. Louis, MO 63110, USA 4Department of Chemistry, Washington University, St. Louis, MO 63105, USA *Correspondence: [email protected] DOI 10.1016/j.chembiol.2011.01.014 Cells, tissues, and biological fluids contain a diverse repertoire of many tens of thousands of structurally distinct lipids that play multiple roles in cellular signaling, bioenergetics, and membrane structure and func- tion. In an era where lipid-related disease states predominate, lipidomics has assumed a prominent role in systems biology through its unique ability to directly identify functional alterations in multiple lipid metabolic and signaling networks. The development of shotgun lipidomics has led to the facile accrual of high density information on alterations in the lipidome mediating physiologic cellular adaptation during health and path- ologic alterations during disease. Through both targeted and nontargeted investigations, lipidomics has already revealed the chemical mechanisms underlying many lipid-related disease states. The Multiple Roles of Lipids (Zhang et al., 2002; Breen et al., 2005). Cantley, 2006; Chiang et al., 2006; Simon in Cellular -
Multi-Omics Approaches and Radiation on Lipid Metabolism in Toothed Whales
life Review Multi-Omics Approaches and Radiation on Lipid Metabolism in Toothed Whales Jayan D. M. Senevirathna 1,2,* and Shuichi Asakawa 1 1 Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; [email protected] 2 Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka * Correspondence: [email protected] Abstract: Lipid synthesis pathways of toothed whales have evolved since their movement from the terrestrial to marine environment. The synthesis and function of these endogenous lipids and affecting factors are still little understood. In this review, we focused on different omics approaches and techniques to investigate lipid metabolism and radiation impacts on lipids in toothed whales. The selected literature was screened, and capacities, possibilities, and future approaches for identify- ing unusual lipid synthesis pathways by omics were evaluated. Omics approaches were categorized into the four major disciplines: lipidomics, transcriptomics, genomics, and proteomics. Genomics and transcriptomics can together identify genes related to unique lipid synthesis. As lipids interact with proteins in the animal body, lipidomics, and proteomics can correlate by creating lipid-binding proteome maps to elucidate metabolism pathways. In lipidomics studies, recent mass spectroscopic methods can address lipid profiles; however, the determination of structures of lipids are challeng- ing. As an environmental stress, the acoustic radiation has a significant effect on the alteration of Citation: Senevirathna, J.D.M.; Asakawa, S. Multi-Omics Approaches lipid profiles. Radiation studies in different omics approaches revealed the necessity of multi-omics and Radiation on Lipid Metabolism applications. -
Short Chain Ladderanes: Oxic Biodegradation Products of Anammox Lipids
UvA-DARE (Digital Academic Repository) Short chain ladderanes: oxic biodegradation products of anammox lipids Rush, D.; Jaeschke, A.; Hopmans, E.C.; Geenevasen, J.A.J.; Schouten, S.; Sinninghe Damsté, J.S. DOI 10.1016/j.gca.2011.01.013 Publication date 2011 Document Version Final published version Published in Geochimica et Cosmochimica Acta Link to publication Citation for published version (APA): Rush, D., Jaeschke, A., Hopmans, E. C., Geenevasen, J. A. J., Schouten, S., & Sinninghe Damsté, J. S. (2011). Short chain ladderanes: oxic biodegradation products of anammox lipids. Geochimica et Cosmochimica Acta, 75(6), 1662-1671. https://doi.org/10.1016/j.gca.2011.01.013 General rights 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), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:29 Sep 2021 Available online at www.sciencedirect.com Geochimica et Cosmochimica Acta 75 (2011) 1662–1671 www.elsevier.com/locate/gca Short chain ladderanes: Oxic biodegradation products of anammox lipids Darci Rush a,⇑, Andrea Jaeschke a,1, Ellen C. -
(12) United States Patent (10) Patent No.: US 8,535,916 B2 Del Cardayre Et Al
US008535916B2 (12) United States Patent (10) Patent No.: US 8,535,916 B2 Del Cardayre et al. (45) Date of Patent: Sep. 17, 2013 (54) MODIFIEDMICROORGANISMS AND USES (51) Int. Cl. THEREFOR CI2P 7/64 (2006.01) (52) U.S. Cl. (75) Inventors: Stephen B. Del Cardayre, Belmont, CA USPC .......................................................... 435/134 (US); Shane Brubaker, Oakland, CA (58) Field of Classification Search (US); Jay D. Keasling, Berkeley, CA USPC .......................................................... 435/134 (US) See application file for complete search history. (73) Assignee: LS9, Inc., South San Francisco, CA (US) (56) References Cited (*) Notice: Subject to any disclaimer, the term of this PUBLICATIONS patent is extended or adjusted under 35 IPER PCT/US2007/003736 (2007).* U.S.C. 154(b) by 497 days. Ohmiya et al. Journal of Bioscience and Bioengineering,95(6): 549 561 (2003).* (21) Appl. No.: 12/526,209 * cited by examiner (22) PCT Filed: Feb. 13, 2007 Primary Examiner — Tekchand Saidha (86). PCT No.: PCT/US2007/003736 (74) Attorney, Agent, or Firm — Brigitte A. Hajos S371 (c)(1), (57) ABSTRACT (2), (4) Date: Dec. 6, 2010 The invention provides a genetically modified microorgan ism that acquires the ability to consume a renewable feed (87) PCT Pub. No.: WO2008/100251 stock (such as cellulose) and produce products. This organ PCT Pub. Date: Aug. 21, 2008 ism can be used to ferment cellulose, one of the most abundant renewable resources available, and produce prod (65) Prior Publication Data uctS. US 2011 FOO97769 A1 Apr. 28, 2011 8 Claims, 1 Drawing Sheet U.S. Patent Sep. 17, 2013 US 8,535,916 B2 Anchor Peptide - Scaffoldin US 8,535,916 B2 1.