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Expression and Characterisation ofa Gene Enc oding RbpD, an RNA- Bind ing Protein in Anabaena sp. strain PeC 7120 by Rob in lee Tremblay A lhesis submitted to the Scltool of Graduale Studies in partial fulfilment of the requirements fOl" the degree of Master of Science Department of BiochemistrylFacultyof Science Memorial University of Newfoundland January 2000 SI.JOM'S Newfoun dland Abs t ra ct The RNA-binding protein RbpD, from the cyano bacterium Anaba ena sp, strain Pe C 7120 was expressed in £Sch~ ric h ia coli and successfully purified using me IMPACT I system (New England Biolabs). The rbp D gene was cloned into the pCYBt expre ssion vector by using polymerase chain reaction to introduce Ndel and SapI restriction sites at the 5' end 3' ends of the gene respect ively. The 3'.-end mutagenesis also chan ged the stop codon into a cysteine codon. The resulting gene encoded a fusion protein consisting of RbpD, the Saccharomyces cerev isiae VMA intein and a chitin binding domain.. Expressi on of the fusion protein was observed in £ coli strain MCI061 but Western blot analysis using an intein-directed ant ibody indicated that significant in vivo fmeln-direcred splicing of the fusion protein occurred. We were unable to eliminate this problem; no fusion protein expression was observed in 8 other E coli strains tested. Wild -type RbpD was purified following binding of the fusion protein 10 a chitin column and overnight cleavage in the presence of a reducing agent, dlthicthrehc l. A number of modifications to the manufacturer' s purification protocol were found to be necessary for success ful purification. -
Purification and Characterisation of a Protease (Tamarillin) from Tamarillo Fruit
Purification and characterisation of a protease (tamarillin) from tamarillo fruit Item Type Article Authors Li, Zhao; Scott, Ken; Hemar, Yacine; Zhang, Huoming; Otter, Don Citation Li Z, Scott K, Hemar Y, Zhang H, Otter D (2018) Purification and characterisation of a protease (tamarillin) from tamarillo fruit. Food Chemistry. Available: http://dx.doi.org/10.1016/ j.foodchem.2018.02.091. Eprint version Post-print DOI 10.1016/j.foodchem.2018.02.091 Publisher Elsevier BV Journal Food Chemistry Rights NOTICE: this is the author’s version of a work that was accepted for publication in Food Chemistry. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Food Chemistry, [, , (2018-02-16)] DOI: 10.1016/j.foodchem.2018.02.091 . © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ Download date 29/09/2021 23:19:14 Link to Item http://hdl.handle.net/10754/627180 Accepted Manuscript Purification and characterisation of a protease (tamarillin) from tamarillo fruit Zhao Li, Ken Scott, Yacine Hemar, Huoming Zhang, Don Otter PII: S0308-8146(18)30327-3 DOI: https://doi.org/10.1016/j.foodchem.2018.02.091 Reference: FOCH 22475 To appear in: Food Chemistry Received Date: 25 October 2017 Revised Date: 13 February 2018 Accepted Date: 16 February 2018 Please cite this article as: Li, Z., Scott, K., Hemar, Y., Zhang, H., Otter, D., Purification and characterisation of a protease (tamarillin) from tamarillo fruit, Food Chemistry (2018), doi: https://doi.org/10.1016/j.foodchem. -
ANABOLISM III: Biosynthesis Amino Acids & Nucleotides
BI/CH 422/622 ANABOLISM OUTLINE: Photosynthesis Carbohydrate Biosynthesis in Animals Biosynthesis of Fatty Acids and Lipids Biosynthesis of Amino Acids and Nucleotides Nitrogen fixation nitrogenase Nitrogen assimilation Glutamine synthetase Glutamate synthase Amino-acid Biosynthesis non-essential essential Nucleotide Biosynthesis RNA precursors purines pyrimidines DNA precursors deoxy-nucleotides Biosynthesis of secondary products of amino acids ANABOLISM III: Biosynthesis Amino Acids & Nucleotides Dr. Kornberg: Lecture 04.26.17 (0:00-5:06) 5 min 1 Biosynthesis Amino Acids & Nucleotides How are Ribonucleic Acid Precursors So far: converted to Deoxyribonucleic Acid GMPàGDPàGTP Precursors? ….....and how is dTTP made? AMPàADPàATP 2’C-OH bond is directly reduced to 2’-H UMPàUDPàUTPà bond …without activating the carbon for CDPßCTP dehydration, etc.! catalyzed by ribonucleotide reductase Specific kinases, Non-specific kinase, e.g., UMP kinase, nucleoside GMP kinase, diphosphate kinase Very unique enzyme in all of biochemistry – use of free Adenylate kinase (works on both oxy- and radicals etc. deoxy-ribose GDPàdGDP nucleosides) Mechanism: Two H atoms are donated ADPàdADP by NADPH and carried by thioredoxin or glutaredoxin to the active site. UDPàdUDP –Substrates are the NDPs and the products CDPàdCDP are dNDP. Biosynthesis Amino Acids & Nucleotides Source of Reducing Structure of Ribonucleotide Reductase a2 are regulatory Electrons for and half the Ribonucleotide catalytic site; need to be reduced. Reductase b 2 are the other half (a b ) of the active site, 2 2 and the free- radical generators • NADPH serves as the electron donor. • Funneled through glutathione or JoAnne Stubbe thioredoxin pathways (1946– ) 2 •Most forms of enzyme have two catalytic/ regulatory subunits and two radical- generating subunits. -
Discovery of Industrially Relevant Oxidoreductases
DISCOVERY OF INDUSTRIALLY RELEVANT OXIDOREDUCTASES Thesis Submitted for the Degree of Master of Science by Kezia Rajan, B.Sc. Supervised by Dr. Ciaran Fagan School of Biotechnology Dublin City University Ireland Dr. Andrew Dowd MBio Monaghan Ireland January 2020 Declaration I hereby certify that this material, which I now submit for assessment on the programme of study leading to the award of Master of Science, is entirely my own work, and that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge breach any law of copyright, and has not been taken from the work of others save and to the extent that such work has been cited and acknowledged within the text of my work. Signed: ID No.: 17212904 Kezia Rajan Date: 03rd January 2020 Acknowledgements I would like to thank the following: God, for sending me angels in the form of wonderful human beings over the last two years to help me with any- and everything related to my project. Dr. Ciaran Fagan and Dr. Andrew Dowd, for guiding me and always going out of their way to help me. Thank you for your patience, your advice, and thank you for constantly believing in me. I feel extremely privileged to have gotten an opportunity to work alongside both of you. Everything I’ve learnt and the passion for research that this project has sparked in me, I owe it all to you both. Although I know that words will never be enough to express my gratitude, I still want to say a huge thank you from the bottom of my heart. -
Electron Transfer and Substrate Reduction in Nitrogenase
Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 5-2014 Electron Transfer and Substrate Reduction in Nitrogenase Karamatullah Danyal Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Biochemistry Commons Recommended Citation Danyal, Karamatullah, "Electron Transfer and Substrate Reduction in Nitrogenase" (2014). All Graduate Theses and Dissertations. 2181. https://digitalcommons.usu.edu/etd/2181 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. ELECTRON TRANSFER AND SUBSTRATE REDUCTON IN NITROGENASE by Karamatullah Danyal A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biochemistry Approved: ________________________ _______________________ Lance C. Seefeldt Scott A. Ensign Major Professor Committee Member ________________________ _______________________ Alvan C. Hengge Sean J. Johnson Committee Member Committee Member ________________________ _______________________ Korry Hintze Mark R. McLellan Committee Member Vice President for Research and Dean of the School of Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2014 ii Copyright © Karamatullah Danyal 2014 All Rights Reserved iii ABSTRACT Electron Transfer and Substrate Reduction in Nitrogenase by Karamatullah Danyal, Doctor of Philosophy Utah State University, 2014 Major Professor: Dr. Lance C. Seefeldt Department: Chemistry and Biochemistry Population growth over the past ~50 years accompanied by the changes in dietary habits due to economic growth have markedly increased the demand for fixed nitrogen. Aided by biological nitrogen fixation, the Haber-Bosch process has been able to fulfill these demands. -
Molybdenum Hazards to Fish, Wildlife, and Invertebrates: a Synoptic Review
Biological Report 85(1.19) Contaminant Hazard Reviews August 1989 Report No. 19 MOLYBDENUM HAZARDS TO FISH, WILDLIFE, AND INVERTEBRATES: A SYNOPTIC REVIEW by Ronald Eisler U.S. Fish and Wildlife Service Patuxent Wildlife Research Center Laurel, MD 20708 SUMMARY The element molybdenum (Mo) is found in all living organisms and is considered to be an essential or beneficial micronutrient. However, the molybdenum poisoning of ruminants has been reported in at least 15 States and 8 foreign countries. Molybdenum is used primarily in the manufacture of steel alloys. Its residues tend to be elevated in plants and soils near Mo mining and reclamation sites, fossil-fuel power plants, and Mo disposal areas. Concentrations of Mo are usually lower in fish and wildlife than in terrestrial macrophytes. Aquatic organisms are comparatively resistant to Mo salts: adverse effects on growth and survival usually appeared only at water concentrations >50 mg Mo/l. But in one study, 50% of newly fertilized eggs of rainbow trout (Oncorhynchus mykiss) died in 28 days at only 0.79 mg Mo/l. High bioconcentration of Mo by certain species of aquatic algae and invertebrates--up to 20 grams of Mo/kg dry weight--has been recorded without apparent harm to the accumulator; however, hazard potential to upper trophic organisms (such as waterfowl) that may feed on bioconcentrators is not clear. Data on Mo effects are missing for avian wildlife and are inadequate for mammalian wildlife. In domestic birds, adverse effects on growth have been reported at dietary Mo concentrations of 200 mg Mo/kg, on reproduction at 500 mg/kg, and on survival at 6,000 mg/kg. -
Metals in Cyanobacteria: Analysis of the Copper, Nickel, Cobalt and Arsenic Homeostasis Mechanisms
Life 2014, 4, 865-886; doi:10.3390/life4040865 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Review Metals in Cyanobacteria: Analysis of the Copper, Nickel, Cobalt and Arsenic Homeostasis Mechanisms María José Huertas 1,†, Luis López-Maury 1,†, Joaquín Giner-Lamia 2, Ana María Sánchez-Riego 1 and Francisco Javier Florencio 1,* 1 Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092 Sevilla, Spain; E-Mails: [email protected] (M.J.H.); [email protected] (L.L.-M.); [email protected] (A.M.S.-R.) 2 Systems Biology and Bioinformatics Laboratory, IBB-CBME, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; E-Mail: [email protected] † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +34-954-48-95-09; Fax: +34-954-46-00-65. External Editors: John C. Meeks and Robert Haselkorn Received: 30 October 2014; in revised form: 27 November 2014 / Accepted: 4 December 2014 / Published: 9 December 2014 Abstract: Traces of metal are required for fundamental biochemical processes, such as photosynthesis and respiration. Cyanobacteria metal homeostasis acquires an important role because the photosynthetic machinery imposes a high demand for metals, making them a limiting factor for cyanobacteria, especially in the open oceans. On the other hand, in the last two centuries, the metal concentrations in marine environments and lake sediments have increased as a result of several industrial activities. In all cases, cells have to tightly regulate uptake to maintain their intracellular concentrations below toxic levels. -
Redox-Based Transcriptional Regulation in Prokaryotes: Revisiting Model Mechanisms
Antioxidants and Redox Signaling Page 1 of 134 © Mary Ann Liebert, Inc. DOI: 10.1089/ars.2017.7442 1 Comprehensive Invited Review Redox-based transcriptional regulation in prokaryotes: revisiting model mechanisms Emma Sevilla1,2, M. Teresa Bes1,2, Andrés González2,3, M. Luisa Peleato1,2 and María F. 1, 2 Fillat differ fromthis proof. 1 Departamento de Bioquímica y Biología Molecular y Celular. Universidad de Zaragoza, 50009. Zaragoza, Spain 2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018. Zaragoza, Spain. Grupo de Bioquímica, Biofísica y Biología Computacional inal published version may (BIFI, UNIZAR), Unidad Asociada al CSIC. 3 Instituto de Investigación Sanitaria Aragón (IIS Aragón). Avenida San Juan Bosco 13, 50009 Zaragoza, Spain ting and proof correction. The f ting and proof ng model mechanisms (DOI: 10.1089/ars.2017.7442) 10.1089/ars.2017.7442) (DOI: mechanisms model ng Running title: Redox-based transcriptional regulation in bacteria Corresponding author: María F. Fillat. Departamento de Bioquímica y Biología Molecular y Antioxidants and Redox Signaling and Redox Signaling Antioxidants Celular. Universidad de Zaragoza, 50009. Zaragoza, Spain. Phone number: +34 976761282. but has yet tocopyedi undergo FAX: +34 976762123. E-mail: [email protected]. 18896 words 415 references Downloaded by Queen Mary & Westfield Coll from www.liebertpub.com at 08/29/18. For personal use only. 19 greyscale illustrations Redox-based transcriptional regulation in prokaryotes: revisitiregulation transcriptionalRedox-based Manuscript keywords: redox-sensing, transcriptional regulation, two-component systems, photosensors Reviewing Editors: Haike Antelmann, Francesca Cutruzzolà, Jaekwon Lee, Brandan Pedre This paper has been peer-reviewed and accepted for publication, and Dana Reichmann Page 2 of 134 2 Abstract The successful adaptation of microorganisms to ever-changing environments depends to a great extent on their ability to maintain redox homeostasis. -
The Author Has Granted A
National Library Bibliothèque nationale of Canada du Canada Acquisitions and Acquisitions et Bibliographic Services senrices bibliographiques 395 Wellington Street 395, rue Wellington Ottawa ON KIA ON4 OttawaON KIAON4 Canada Canada Your hie Votre mHrence Our tî& Notre relérence The author has granted a non- L'auteur a accordé une licence non exclusive licence allowing the exclusive permettant a la National Library of Canada to Bibliothèque nationale du Canada de reproduce, loan, distribute or sel1 reproduire, prêter, distribuer ou copies of this thesis in microform, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfiche/filrn, de reproduction sur papier ou sur format électronique. The author retains ownership of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantial extracts fiom it Ni la thèse ni des extraits substantiels may be printed or otherwise de celle-ci ne doivent être imprimés reproduced without the author's ou autrement reproduits sans son permission. autorisation. CHARACTERIZATION OF A GENE ENCODING AN RNA-BINDING PROTEIN (rbpA)IN THE CYANOBACTERIUM SMVECHOCOCCUS SP. PCC 7942 Thomas James Belbin A thesis submitted to the School of Graduate Studies in partial fulfilment of the requirements for the degree of Doctor of Philosophy Department of Biochemistry Mernorial University of New foundland May 1999 St. John's Newfoundland ABSTRACT Many species of cyanobacteria possess genes whose products are highly similar to the RNP family of RNA-binding proteins found in eukaryotes. This work describes the characterization of rbpA, one of two RNA-binding protein (rbp) genes now known to exist in the unicellular cvanobacterium S~~iecliococciissp. -
Roles of Glutaredoxin and Thioredoxin-Like Nfu Proteins in Iron
ROLES OF GLUTAREDOXIN AND THIOREDOXIN-LIKE NFU PROTEINS IN IRON- SULFUR CLUSTER BIOGENESIS by SIBALI BANDYOPADHYAY (Under the Direction of Michael K. Johnson) ABSTRACT Iron-sulfur (Fe-S) clusters are one of the most ancient, ubiquitous and functionally versatile prosthetic groups in nature. Based on the organization of genes in bacterial operons, three highly conserved types of machinery for the biogenesis of Fe-S clusters have emerged, namely the NIF (Ni trogen Fixation), the ISC (Iron-Sulfur Cluster) and the SUF (Su lfur Mobilization) systems. However, recent studies have implicated roles in Fe-S cluster biogenesis for accessory proteins such as glutaredoxins and thioredoxin-like Nfu proteins that are not encoded by genes in nif , isc , or suf operons. This research project was designed to elucidate the role of dithiol and monothiol glutaredoxins and thioredoxin-like Nfu proteins in Fe-S cluster biogenesis. The approach involved structural and/or spectroscopic characterization of clusters assembled on plant dithiol and monothiol glutaredoxins and Azotobacter vinelandii NfuA protein coupled with in vitro studies of cluster transfer to physiologically relevant acceptor proteins and in vivo assessment of function via gene knock out or complementation studies. The A. vinelandii NfuA protein was shown to assemble a subunit-bridging [4Fe-4S] 2+ cluster which is capable of activating apo aconitase at physiologically relevant rates. Taken together with in vivo studies, which indicate impaired maturation of Fe-S proteins in strains inactivated for nfuA , the results indicate a role of NfuA as a class of intermediate [Fe-S] cluster carrier proteins in bacteria. Spectroscopic, mutagenesis and crystallographic studies of the cytosolic poplar dithiol glutaredoxin C1 (CGYC active site) have demonstrated that dithiol glutaredoxins can assemble a novel glutathione-ligated [2Fe-2S] 2+ cluster at the subunit interface of the homodimer and have established the active-site sequence requirement for Fe-S cluster incorporation. -
Molecular and Environmental Studies of Bacterial Arsenate Respiration
Molecular and Environmental Studies of Bacterial Arsenate Respiration Thesis by Davin Malasarn In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy CALIFORNIA INSTITUTE OF TECHNOLOGY Pasadena, California 2007 (Defended February 8, 2007) ii © 2007 Davin Malasarn All Rights Reserved iii Acknowledgements I moved into my home on Wilson Avenue on December 24, 2000, just days before I started my rotation in Dianne Newman's lab. Now, in February of 2007, I'm attempting to thank everyone who has helped me throughout my studies at Caltech. It's impossible, of course, and I'm sure over the years, names and faces of additional people who I don't mention here will creep up in happy memories. Dianne, I'm so grateful to you for taking me into your lab. It has been an honor to work under someone as intellectually elegant and as scientifically daring as you. I really appreciate your support and your nurturing attitude. Being systematic and organized is not my strongest suit, but you helped me get better at that, and you always encouraged my creative side. Graduate school is the hardest and most rewarding thing I have ever done so far, and I feel very fortunate to have you as my guide in science and in life. To my committee, past and present, I'm grateful to be able to rely on a group of professors that inspire me. Paul Sternberg, you were the reason I came to Caltech, and I always appreciate your openness and your passion. Harry Gray, I deeply admire the fact that you make all of your hard work and brilliance look so easy. -
Unicellular Cyanobacteria Exhibit Light-Driven, Oxygen-Tolerant
bioRxiv preprint doi: https://doi.org/10.1101/619353; this version posted May 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Unicellular Cyanobacteria Exhibit Light-Driven, Oxygen-Tolerant, 2 Constitutive Nitrogenase Activity Under Continuous Illumination 3 James Young, Liping Gu, Michael Hildreth, Ruanbao Zhou 4 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 5 6 7 8 9 10 11 12 13 14 15 16 17 18 bioRxiv preprint doi: https://doi.org/10.1101/619353; this version posted May 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 Abstract 20 Cyanobacteria have played a profound role in shaping the biosphere, most notably 21 through the Great Oxygenation Event (GOE) with the advent of photosynthesis1. Cyanobacteria 22 also contribute to global primary production through biological nitrogen fixation (BNF) using 23 nitrogenase2,3, an oxygen-labile enzyme complex that evolutionarily predates the GOE4. Current 24 literature reports nitrogenase activity in unicellular cyanobacteria is protected from oxygen 25 through diurnal separation of photosynthesis and BNF5. However, historic conditions of 26 continuous-light and warm temperature at polar latitudes during the Triassic and Cretaceous may 27 have created a selective advantage amongst unicellular cyanobacteria for non-temporal 28 mechanisms of maintaining nitrogenase activity in the presence of oxygen. Here we report 29 constitutive nitrogenase activity concurrent with a net-gain of oxygen through photosynthesis in 30 a continuous-light adapted culture of the unicellular cyanobacteria, Cyanothece sp.