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Effects of Environmental Contaminants on Gene Expression, DNA Methylation and Gut Microbiota in Buff-Tailed Bumble Bee - Bombus Terrestris
UNIVERSITYOF LEICESTER DOCTORAL THESIS Effects of environmental contaminants on gene expression, DNA methylation and gut microbiota in Buff-tailed Bumble bee - Bombus terrestris Author: Supervisor: Pshtiwan BEBANE Eamonn MALLON A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy in the Department of Genetics and Genome Biology March 2019 Abstract Bee populations are increasingly at risk. In this thesis, I explore various mechanisms through which environmental contaminants, namely imidacloprid and black carbon, can affect bumble bee epigenetics, behaviour and gut microbiota. I found imidacloprid has numerous epigenetic effects on Bombus terrestris non reproductive workers. I analysed three whole methylome (BS-seq) libraries and seven RNA-seq libraries of the brains of imidacloprid exposed workers and three BS-seq libraries and nine RNA-seq li- braries from unexposed, control workers. I found 79, 86 and 16 genes differentially methylated at CpGs, CHHs and CHGs sites respectively between groups. I found CpG methylation much more focused in exon regions compared with methylation at CHH or CHG sites. I found 378 genes that were differentially expressed between imidacloprid treated and control bees. In ad- dition, I found 25 genes differentially alternatively spliced between control and imidacloprid samples. I used Drosophila melanogaster as a model for the behavioural effects of imidacloprid on in- sects. Imidacloprid did not affect flies’ periodicity. Low doses (2.5 ppb) of imidacloprid in- creased flies’ activity while high doses (20 ppb) decreased activity. Canton-S strain was more sensitive to imidacloprid during geotaxis assay than M1217. I proposed that a possible modulator of imidacloprid’s effects on insects is its effects on insects’ gut microbiota. -
Curriculum Vitae Vern Lee Schramm
September 2011 CURRICULUM VITAE VERN LEE SCHRAMM Department of Biochemistry Albert Einstein College of Medicine of Yeshiva University 1300 Morris Park Avenue Bronx, New York 10461 Phone: (718) 430-2813 Fax: (718) 430-8565 E-mail: [email protected] Personal Information: Date of Birth: November 9, 1941 Place of Birth: Howard, South Dakota Citizenship: U.S.A. Home Address: 68 Hampton Oval New Rochelle, NY 10805 Home Telephone: (914) 576-2578 Education: Sept 1959 – June 1963 B.S. in Bacteriology (chemistry emphasis), South Dakota State College Sept 1963 – June 1965 Masters Degree in Nutrition (biochemistry emphasis), Harvard University Research Advisor, Dr. R.P. Geyer Oct 1965 – April 1969 Ph.D. in Mechanism of Enzyme Action, Department of Biochemistry, Australian National University Research Advisor, Dr. John Morrison Postdoctoral Experience: Aug 1969 – Aug 1971 NRC-NSF Postdoctoral Research Associate at NASA Ames Research Center, Biological Adaptation Branch Appointments: July 1999 – Present University Professor of the Albert Einstein College of Medicine July 1995 – Present Ruth Merns Endowed Chair of Biochemistry Aug 1987 – Present Professor and Chairman, Department of Biochemistry, Albert Einstein College of Medicine July 1981 - July 1987 Professor of Biochemistry, Temple University School of Medicine July 1976 - June 1981 Associate Professor of Biochemistry, Temple University School of Medicine Aug 1971 - July 1976 Assistant Professor of Biochemistry, Temple University School of Medicine Vern L. Schramm 2 Fields of Interest: Enzymatic -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
ARCOPOL the Atlantic Regions' Coastal Pollution Response
Airborne Pollution Propagation from water incidents: State of the art of air pollution models Activity 4 Task 4.2.1 ARCOPOL The Atlantic Regions’ Coastal Pollution Response Version: Version 2 Last updated on: 05/11/2010 Author: Meteogalicia Responsible partner: IST Involved partners: CETMAR, Meteogalicia, INTECMAR, IST, CIIMAR, EGMASA, Irish Marine Institute, Bretagne Region, Aquitaine Region Table of contents 1. Executive Summary .............................................................................................................. 3 2. Context and aims of the task ............................................................................................... 3 2.1. Summary of the 2008 Air Quality Directive ..................................................... 4 2.1.1. Concepts and definitions..................................................................................... 4 2.2. Where does the Air Quality Directive apply? .................................................. 6 2.2.1. Limits and target values for the protection of human health......................... 7 2.2.2. Limits and target values for the protection of vegetation............................... 9 2.2.3. Air quality web portals in Europe .................................................................... 9 3. Methodology........................................................................................................................ 12 3.1. When can models be used for the assessment of existing air quality? ....... 12 3.2. Combined use of measurements -
Climate Change
TRANSPORTATION RESEARCH Number E-C271 May 2021 Critical Issues in Aviation and the Environment 2021 TRANSPORTATION RESEARCH BOARD 2020 EXECUTIVE COMMITTEE OFFICERS Chair: Carlos M. Braceras, Executive Director, Utah Department of Transportation, Salt Lake City Vice Chair: Susan A. Shaheen, Adjunct Professor, Co-Director, Transportation Sustainability Research Center, University of California, Berkeley Division Chair for NRC Oversight: Chris Hendrickson, Hamerschlag University Professor Emeritus, Carnegie Mellon University, Pittsburgh, Pennsylvania Executive Director: Neil J. Pedersen, Transportation Research Board TRANSPORTATION RESEARCH BOARD 2020–2021 TECHNICAL ACTIVITIES COUNCIL Chair: Hyun-A C. Park, President, Spy Pond Partners, LLC, Arlington, Massachusetts Technical Activities Director: Ann M. Brach, Transportation Research Board Richard Bornhorst, Principal, FACTOR, Inc., Silver Spring, Maryland, Freight Systems Group Chair Michael Griffith, Director, Office of Safety Technologies, Federal Highway Administration, Washington, D.C., Safety and Operations Group Chair George Avery Grimes, CEO Advisor, Patriot Rail Company, Denver, Colorado, Rail Group Chair Brendon Hemily, Principal, Hemily and Associates, Toronto, Ontario, Public Transportation Group Chair Nikola Ivanov, Deputy Director, Center for Advanced Transportation Technology Laboratory, University of Maryland, College Park, Young Members Council Chair Pamela Keidel-Adams, Regional Vice President, Kimley-Horn and Associates, Inc., Mesa, Arizona, Aviation Group Chair C. James -
(12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall Et Al
USOO9689046B2 (12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall et al. (45) Date of Patent: Jun. 27, 2017 (54) SYSTEM AND METHODS FOR THE FOREIGN PATENT DOCUMENTS DETECTION OF MULTIPLE CHEMICAL WO O125472 A1 4/2001 COMPOUNDS WO O169245 A2 9, 2001 (71) Applicants: Robert Matthew Mayall, Calgary (CA); Emily Candice Hicks, Calgary OTHER PUBLICATIONS (CA); Margaret Mary-Flora Bebeselea, A. et al., “Electrochemical Degradation and Determina Renaud-Young, Calgary (CA); David tion of 4-Nitrophenol Using Multiple Pulsed Amperometry at Christopher Lloyd, Calgary (CA); Lisa Graphite Based Electrodes', Chem. Bull. “Politehnica” Univ. Kara Oberding, Calgary (CA); Iain (Timisoara), vol. 53(67), 1-2, 2008. Fraser Scotney George, Calgary (CA) Ben-Yoav. H. et al., “A whole cell electrochemical biosensor for water genotoxicity bio-detection”. Electrochimica Acta, 2009, 54(25), 6113-6118. (72) Inventors: Robert Matthew Mayall, Calgary Biran, I. et al., “On-line monitoring of gene expression'. Microbi (CA); Emily Candice Hicks, Calgary ology (Reading, England), 1999, 145 (Pt 8), 2129-2133. (CA); Margaret Mary-Flora Da Silva, P.S. et al., “Electrochemical Behavior of Hydroquinone Renaud-Young, Calgary (CA); David and Catechol at a Silsesquioxane-Modified Carbon Paste Elec trode'. J. Braz. Chem. Soc., vol. 24, No. 4, 695-699, 2013. Christopher Lloyd, Calgary (CA); Lisa Enache, T. A. & Oliveira-Brett, A. M., "Phenol and Para-Substituted Kara Oberding, Calgary (CA); Iain Phenols Electrochemical Oxidation Pathways”, Journal of Fraser Scotney George, Calgary (CA) Electroanalytical Chemistry, 2011, 1-35. Etesami, M. et al., “Electrooxidation of hydroquinone on simply prepared Au-Pt bimetallic nanoparticles'. Science China, Chem (73) Assignee: FREDSENSE TECHNOLOGIES istry, vol. -
Supplementary Information
Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle. -
Linear Free Energy Relationships for N(7)-Substituted Guanosines As Substrates of Calf Spleen Purine Nucleoside Phosphorylase
Linear Free Energy Relationships for N(7)-Substituted Guanosines as Substrates of Calf Spleen Purine Nucleoside Phosphorylase. Possible Role of N(7)-Protonation as an Intermediary in Phosphorolysis Agnieszka Bzowskaa, Ewa Kulikowska3, and David Shugar3 *5 a Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland b Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Rakowiecka 36, 02-532 Warsaw, Poland Z. Naturforsch. 48c, 803-811 (1993); received May 11, 1993 Purine Nucleoside, Phosphorylase, N(7)-Substituted Guanosines, Glycosidic Bond Cleavage, N(7)-Protonation, QSAR Quantitative structure-activity relationships (QSAR) for a series of N(7)-substituted guano sines as substrates for calf spleen purine nucleoside phosphorylase (PNP) were developed, and compared with those for acid hydrolysis of these analogues. There is no correlation between the rates for enzymatic phosphorolysis and acid hydrolysis, indicating that for the enzymatic reaction labilization of the glycosidic bond is not the only, nor the predominant, effect of N(7)-substitution. Multiple regression analysis of the enzymatic process revealed that optimal substrate properties (minimal Michaelis constant) are associated with the Taft electronic con stant equal zero and a substituent size, parametrized by the Taft steric constant, smaller than that for a methyl group. These results support the hypothesis of protonation of the N(7)-posi- tion of the base by the enzyme as a catalytic mechanism for calf spleen PNP. Attention is drawn to the postulated similar mechanism of action of other purine N-glycosidases, including plant antiviral proteins which function as RNA N-glycosidases, and possibly some DN A N-glycosidases which function as repair enzymes. -
A Comparative UHPLC-Q/TOF–MS-Based Eco-Metabolomics
www.nature.com/scientificreports OPEN A comparative UHPLC‑Q/ TOF–MS‑based eco‑metabolomics approach reveals temperature adaptation of four Nepenthes species Changi Wong1, Yee Soon Ling2, Julia Lih Suan Wee3, Aazani Mujahid4 & Moritz Müller1* Nepenthes, as the largest family of carnivorous plants, is found with an extensive geographical distribution throughout the Malay Archipelago, specifcally in Borneo, Philippines, and Sumatra. Highland species are able to tolerate cold stress and lowland species heat stress. Our current understanding on the adaptation or survival mechanisms acquired by the diferent Nepenthes species to their climatic conditions at the phytochemical level is, however, limited. In this study, we applied an eco‑metabolomics approach to identify temperature stressed individual metabolic fngerprints of four Nepenthes species: the lowlanders N. ampullaria, N. rafesiana and N. northiana, and the highlander N. minima. We hypothesized that distinct metabolite regulation patterns exist between the Nepenthes species due to their adaptation towards diferent geographical and altitudinal distribution. Our results revealed not only distinct temperature stress induced metabolite fngerprints for each Nepenthes species, but also shared metabolic response and adaptation strategies. The interspecifc responses and adaptation of N. rafesiana and N. northiana likely refected their natural habitat niches. Moreover, our study also indicates the potential of lowlanders, especially N. ampullaria and N. rafesiana, to produce metabolites needed to deal with increased temperatures, ofering hope for the plant genus and future adaption in times of changing climate. Nepenthes (N.), the sole genus under the family Nepenthaceae, is one of the largest families of carnivorous plants, with an extensive geographical distribution across the Malay Archipelago, specifcally in Borneo, Philippines, and Sumatra. -
Coupled Nucleoside Phosphorylase Reactions in Escherichia Coli John Lewis Ott Iowa State College
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1956 Coupled nucleoside phosphorylase reactions in Escherichia coli John Lewis Ott Iowa State College Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Biochemistry Commons, and the Microbiology Commons Recommended Citation Ott, John Lewis, "Coupled nucleoside phosphorylase reactions in Escherichia coli " (1956). Retrospective Theses and Dissertations. 13758. https://lib.dr.iastate.edu/rtd/13758 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. NOTE TO USERS This reproduction is the best copy available. UMI COUPLED NUCLEOSIDE PHOSPHORYLASE REACTIONS IN ESCHERICHIA COLI / by John Lewis Ott A Dissertation Submitted to the Graduate Faculty in Partial Fulfillment of The Requirements for the Degree of DOCTOR OF PHILOSOPHY Major Subject: Physlolgglcal Bacteriology Approved: Signature was redacted for privacy. In Charge of Major Work Signature was redacted for privacy. Head of Major Department Signature was redacted for privacy. Dean of Graduate College Iowa State College 1956 UMI Number: DP12892 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. -
(12) United States Patent (10) Patent No.: US 8,962,800 B2 Mathur Et Al
USOO89628OOB2 (12) United States Patent (10) Patent No.: US 8,962,800 B2 Mathur et al. (45) Date of Patent: Feb. 24, 2015 (54) NUCLEICACIDS AND PROTEINS AND USPC .......................................................... 530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Naperville, IL (US) PUBLICATIONS (*) Notice: Subject to any disclaimer, the term of this Nolling etal (J. Bacteriol. 183: 4823 (2001).* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 0 days. Isolates of Pseudomonas aeruginosa J. Bacteriol. (2003) 185: 1316-1325. (21) Appl. No.: 13/400,365 2002.Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (22) Filed: Feb. 20, 2012 bor New York, 2001, pp. 382-393. O O Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (65) Prior Publication Data toxicology” Toxicol. Lett. (2000) 1.12: 365-370. US 2012/O266329 A1 Oct. 18, 2012 * cited by examiner Related U.S. Application Data - - - Primary Examiner — James Martinell (62) Division of application No. 1 1/817,403, filed as (74) Attorney, Agent, or Firm — DLA Piper LLP (US) application No. PCT/US2006/007642 on Mar. 3, 2006, now Pat. No. 8,119,385. (57) ABSTRACT (60) Provisional application No. 60/658,984, filed on Mar. The invention provides polypeptides, including enzymes, 4, 2005. -
[Frontiers in Bioscience 7, D1762-1781, August 1, 2002] 1762 the NECESSITY of COMBINING GENOMIC and ENZYMATIC DATA to INFER META
[Frontiers in Bioscience 7, d1762-1781, August 1, 2002] THE NECESSITY OF COMBINING GENOMIC AND ENZYMATIC DATA TO INFER METABOLIC FUNCTION AND PATHWAYS IN THE SMALLEST BACTERIA: AMINO ACID, PURINE AND PYRIMIDINE METABOLISM IN MOLLICUTES J. Dennis Pollack Department of Molecular Virology, Immunology and Medical Genetics, The College of Medicine and Public Health, The Ohio State University, 333 West 10th Avenue, Columbus, OH 43210 TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Metabolic Linkages to Amino Acids and Proteins 4. Amino Acids: Transport 5. Amino Acids: Biosynthesis and Metabolism 6. Amino Acids: Aromatic amino acid synthesis in Acholeplasma-Anaeroplasma 7. Purine Metabolism: Transport 8. Purine Metabolism: Interconversions 9. Purine Metabolism: Intervention of the pentose phosphate pathway and glycolysis 10. Purine Metabolism: Metabolic consensus 11. Pyrimidine Metabolism: Interconversions and metabolic consensus 12. Predicting Metabolism 13. Acknowledgements 14. References 1. ABSTRACT Bacteria of the class Mollicutes have no cell wall. represent these simple microbes. Mycoplasma genitalium, a One species, Mycoplasma genitalium is the personification Mollicutes with a genome of 580 kbp and 475 ORFs, has of the simplest form of independent cell-free life. Its small the smallest genome in any free-living cell and is an genome (580 kbp) is the smallest of any cell. Mollicutes obvious example of the simplest organism. It is the minimal have unique metabolic properties, perhaps because of their cell and defines-characterizes, personifies independent limited coding space and high mutability. Based on 16S cellular life. rRNA analyses the Mollicutes Mycoplasma gallisepticum is thought to be the most mutable Bacteria. Enzyme activities All Mollicutes, like M.