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The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion Anna Karnkowska,*,1,2 Sebastian C
The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion Anna Karnkowska,*,1,2 Sebastian C. Treitli,1 Ondrej Brzon, 1 Lukas Novak,1 Vojtech Vacek,1 Petr Soukal,1 Lael D. Barlow,3 Emily K. Herman,3 Shweta V. Pipaliya,3 TomasPanek,4 David Zihala, 4 Romana Petrzelkova,4 Anzhelika Butenko,4 Laura Eme,5,6 Courtney W. Stairs,5,6 Andrew J. Roger,5 Marek Elias,4,7 Joel B. Dacks,3 and Vladimır Hampl*,1 1Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic 2Department of Molecular Phylogenetics and Evolution, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland 3Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada 4Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Downloaded from https://academic.oup.com/mbe/article-abstract/36/10/2292/5525708 by guest on 13 January 2020 5Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada 6Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden 7Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic *Corresponding authors: E-mails: [email protected]; [email protected]. Associate editor: Fabia Ursula Battistuzzi Abstract The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organ- elles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. -
Biochemistrystanford00kornrich.Pdf
University of California Berkeley Regional Oral History Office University of California The Bancroft Library Berkeley, California Program in the History of the Biosciences and Biotechnology Arthur Kornberg, M.D. BIOCHEMISTRY AT STANFORD, BIOTECHNOLOGY AT DNAX With an Introduction by Joshua Lederberg Interviews Conducted by Sally Smith Hughes, Ph.D. in 1997 Copyright 1998 by The Regents of the University of California Since 1954 the Regional Oral History Office has been interviewing leading participants in or well-placed witnesses to major events in the development of Northern California, the West, and the Nation. Oral history is a method of collecting historical information through tape-recorded interviews between a narrator with firsthand knowledge of historically significant events and a well- informed interviewer, with the goal of preserving substantive additions to the historical record. The tape recording is transcribed, lightly edited for continuity and clarity, and reviewed by the interviewee. The corrected manuscript is indexed, bound with photographs and illustrative materials, and placed in The Bancroft Library at the University of California, Berkeley, and in other research collections for scholarly use. Because it is primary material, oral history is not intended to present the final, verified, or complete narrative of events. It is a spoken account, offered by the interviewee in response to questioning, and as such it is reflective, partisan, deeply involved, and irreplaceable. ************************************ All uses of this manuscript are covered by a legal agreement between The Regents of the University of California and Arthur Kornberg, M.D., dated June 18, 1997. The manuscript is thereby made available for research purposes. All literary rights in the manuscript, including the right to publish, are reserved to The Bancroft Library of the University of California, Berkeley. -
Prokaryotic and Eukaryotic Organisms Pdf
Prokaryotic and eukaryotic organisms pdf Continue There are two types of cells: prokaryotic and eukaryotic. In this section, we will examine the similarities and differences between the two types. The objectives of the training to identify features common to all cells contrast the composition and size of prokaryotic and eukaryotic cells fall into one of two broad categories: prokaryotic and eukaryotic. Single-celled organisms of the domains Of Bacteria and Archaea are classified as prokaryotes (pro - before; carion - core). Animal cells, plant cells, fungi and proteanists are eukaryotes (eu - truth). Components of prokaryotic cells All cells have four common components: (1) plasma membrane, external coating separating the inner part of the cell from the environment; (2) cytoplasm, consisting of a jelly-like area inside the cell in which other cellular components are located; (3) DNA, the genetic material of the cell; and (4) ribosomes, particles that synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways. Figure 1. This image shows the generalized structure of the prokaryotic cell. A prokaryotic cell is a simple single-celled organism that lacks a nucleus or any other membrane organella. Soon we will see that this is significantly different in eukaryotes. Prokaryotic DNA is found in the central part of the cell: a darkened area called a nucleoid (Figure 1). Unlike archaea and eukaryote, bacteria have a cell wall of peptidoglycan consisting of sugars and amino acids, and many of them have a polysaccharide capsule (Figure 1). The cell wall acts as an additional layer of protection, helps the cell maintain its shape and prevents dehydration. -
Crucible of Science: the Story of the Cori Laboratory
Crucible of Science This page intentionally left blank Crucible of Science THE STORY OF THE CORI LABORATORY JOHN H. EXTON 3 3 Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide. Oxford New York Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With offi ces in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan Poland Portugal Singapore South Korea Switzerland Th ailand Turkey Ukraine Vietnam Oxford is a registered trademark of Oxford University Press in the UK and certain other countries. Published in the United States of America by Oxford University Press 198 Madison Avenue, New York, NY 10016 © Oxford University Press 2013 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitt ed, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitt ed by law, by license, or under terms agreed with the appropriate reproduction rights organization. Inquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above. You must not circulate this work in any other form and you must impose this same condition on any acquirer. CIP data is on fi le at the Library of Congress ISBN 978–0–19–986107–1 9 8 7 6 5 4 3 2 1 Printed in the United States of America on acid-free paper Dedicated to Charles Rawlinson (Rollo) Park This page intentionally left blank Contents Acknowledgments ix I n t r o d u c t i o n xi 1. -
Novel Lineages of Oxymonad Flagellates from the Termite Porotermes Adamsoni (Stolotermitidae): the Genera Oxynympha and Termitim
Protist, Vol. 170, 125683, December 2019 http://www.elsevier.de/protis Published online date 21 October 2019 ORIGINAL PAPER Novel Lineages of Oxymonad Flagellates from the Termite Porotermes adamsoni (Stolotermitidae): the Genera Oxynympha and Termitimonas a,1 b a c b,1 Renate Radek , Katja Meuser , Samet Altinay , Nathan Lo , and Andreas Brune a Evolutionary Biology, Institute for Biology/Zoology, Freie Universität Berlin, 14195 Berlin, Germany b Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany c School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia Submitted January 21, 2019; Accepted October 9, 2019 Monitoring Editor: Alastair Simpson The symbiotic gut flagellates of lower termites form host-specific consortia composed of Parabasalia and Oxymonadida. The analysis of their coevolution with termites is hampered by a lack of informa- tion, particularly on the flagellates colonizing the basal host lineages. To date, there are no reports on the presence of oxymonads in termites of the family Stolotermitidae. We discovered three novel, deep-branching lineages of oxymonads in a member of this family, the damp-wood termite Porotermes adamsoni. One tiny species (6–10 m), Termitimonas travisi, morphologically resembles members of the genus Monocercomonoides, but its SSU rRNA genes are highly dissimilar to recently published sequences of Polymastigidae from cockroaches and vertebrates. A second small species (9–13 m), Oxynympha loricata, has a slight phylogenetic affinity to members of the Saccinobaculidae, which are found exclusively in wood-feeding cockroaches of the genus Cryptocercus, the closest relatives of termites, but shows a combination of morphological features that is unprecedented in any oxymonad family. -
Patterns of Conservation of Spliceosomal Intron Structures and Spliceosome Divergence in Representatives of the Diplomonad and Parabasalid Lineages Andrew J
Hudson et al. BMC Evolutionary Biology (2019) 19:162 https://doi.org/10.1186/s12862-019-1488-y RESEARCH ARTICLE Open Access Patterns of conservation of spliceosomal intron structures and spliceosome divergence in representatives of the diplomonad and parabasalid lineages Andrew J. Hudson1,2†, David C. McWatters1,2†, Bradley A. Bowser3, Ashley N. Moore1,2, Graham E. Larue3, Scott W. Roy3,4 and Anthony G. Russell1,2* Abstract Background: Two spliceosomal intron types co-exist in eukaryotic precursor mRNAs and are excised by distinct U2- dependent and U12-dependent spliceosomes. In the diplomonad Giardia lamblia, small nuclear (sn) RNAs show hybrid characteristics of U2- and U12-dependent spliceosomal snRNAs and 5 of 11 identified remaining spliceosomal introns are trans-spliced. It is unknown whether unusual intron and spliceosome features are conserved in other diplomonads. Results: We have identified spliceosomal introns, snRNAs and proteins from two additional diplomonads for which genome information is currently available, Spironucleus vortens and Spironucleus salmonicida, as well as relatives, including 6 verified cis-spliceosomal introns in S. vortens. Intron splicing signals are mostly conserved between the Spironucleus species and G. lamblia. Similar to ‘long’ G. lamblia introns, RNA secondary structural potential is evident for ‘long’ (> 50 nt) Spironucleus introns as well as introns identified in the parabasalid Trichomonas vaginalis. Base pairing within these introns is predicted to constrain spatial distances between splice junctions to similar distances seen in the shorter and uniformly-sized introns in these organisms. We find that several remaining Spironucleus spliceosomal introns are ancient. We identified a candidate U2 snRNA from S. vortens, and U2 and U5 snRNAs in S. -
A Free-Living Protist That Lacks Canonical Eukaryotic DNA Replication and Segregation Systems
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.14.435266; 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. 1 A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems 2 Dayana E. Salas-Leiva1, Eelco C. Tromer2,3, Bruce A. Curtis1, Jon Jerlström-Hultqvist1, Martin 3 Kolisko4, Zhenzhen Yi5, Joan S. Salas-Leiva6, Lucie Gallot-Lavallée1, Geert J. P. L. Kops3, John M. 4 Archibald1, Alastair G. B. Simpson7 and Andrew J. Roger1* 5 1Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB), Department of 6 Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada, B3H 4R2 2 7 Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom 8 3Oncode Institute, Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences) 9 and University Medical Centre Utrecht, Utrecht, The Netherlands 10 4Institute of Parasitology Biology Centre, Czech Acad. Sci, České Budějovice, Czech Republic 11 5Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, 12 South China Normal University, Guangzhou 510631, China 13 6CONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y 14 energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136 Chihuahua, Chih., México 15 7Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB), Department of 16 Biology, Dalhousie University, Halifax, NS, Canada, B3H 4R2 17 *corresponding author: [email protected] 18 D.E.S-L ORCID iD: 0000-0003-2356-3351 19 E.C.T. -
Phylogenomic Analyses Support the Monophyly of Excavata and Resolve Relationships Among Eukaryotic ‘‘Supergroups’’
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic ‘‘supergroups’’ Vladimir Hampla,b,c, Laura Huga, Jessica W. Leigha, Joel B. Dacksd,e, B. Franz Langf, Alastair G. B. Simpsonb, and Andrew J. Rogera,1 aDepartment of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5; bDepartment of Biology, Dalhousie University, Halifax, NS, Canada B3H 4J1; cDepartment of Parasitology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; dDepartment of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; eDepartment of Cell Biology, University of Alberta, Edmonton, AB, Canada T6G 2H7; and fDepartement de Biochimie, Universite´de Montre´al, Montre´al, QC, Canada H3T 1J4 Edited by Jeffrey D. Palmer, Indiana University, Bloomington, IN, and approved January 22, 2009 (received for review August 12, 2008) Nearly all of eukaryotic diversity has been classified into 6 strong support for an incorrect phylogeny (16, 19, 24). Some recent suprakingdom-level groups (supergroups) based on molecular and analyses employ objective data filtering approaches that isolate and morphological/cell-biological evidence; these are Opisthokonta, remove the sites or taxa that contribute most to these systematic Amoebozoa, Archaeplastida, Rhizaria, Chromalveolata, and Exca- errors (19, 24). vata. However, molecular phylogeny has not provided clear evi- The prevailing model of eukaryotic phylogeny posits 6 major dence that either Chromalveolata or Excavata is monophyletic, nor supergroups (25–28): Opisthokonta, Amoebozoa, Archaeplastida, has it resolved the relationships among the supergroups. To Rhizaria, Chromalveolata, and Excavata. With some caveats, solid establish the affinities of Excavata, which contains parasites of molecular phylogenetic evidence supports the monophyly of each of global importance and organisms regarded previously as primitive Rhizaria, Archaeplastida, Opisthokonta, and Amoebozoa (16, 18, eukaryotes, we conducted a phylogenomic analysis of a dataset of 29–34). -
Mitochondrial Respiratory States and Rates
MitoFit Preprint Arch (2019) doi:10.26124/mitofit:190001 Posted online 2019-02-12 Open Access Freely available online Mitochondrial respiratory states and rates Gnaiger E, Aasander Frostner E, Abdul Karim N, Abumrad NA, Acuna-Castroviejo D, Adiele RC, Ahn B, Ali SS, Alton L, Alves MG, Amati F, Amoedo ND, Andreadou I, Aragó M, Aragones J, Aral C, Arandarčikaitė O, Armand AS, Arnould T, Avram VF, Bailey DM, Bajpeyi S, Bajzikova M, Bakker BM, Barlow J, Bastos Sant'Anna Silva AC, Batterson P, Battino M, Bazil J, Beard DA, Bednarczyk P, Bello F, Ben-Shachar D, Bergdahl A, Berge RK, Bergmeister L, Bernardi P, Berridge MV, Bettinazzi S, Bishop D, Blier PU, Blindheim DF, Boardman NT, Boetker HE, Borchard S, Boros M, Børsheim E, Borutaite V, Botella J, Bouillaud F, Bouitbir J, Boushel RC, Bovard J, Breton S, Brown DA, Brown GC, Brown RA, Brozinick JT, Buettner GR, Burtscher J, Calabria E, Calbet JA, Calzia E, Cannon DT, Cano Sanchez M, Canto AC, Cardoso LHD, Carvalho E, Casado Pinna M, Cassar S, Cassina AM, Castelo MP, Castro L, Cavalcanti-de-Albuquerque JP, Cervinkova Z, Chabi B, Chakrabarti L, Chakrabarti S, Chaurasia B, Chen Q, Chicco AJ, Chinopoulos C, Chowdhury SK, Cizmarova B, Clementi E, Coen PM, Cohen BH, Coker RH, Collin A, Crisóstomo L, Dahdah N, Dalgaard LT, Dambrova M, Danhelovska T, Darveau CA, Das AM, Dash RK, Davidova E, Davis MS, De Goede P, De Palma C, Dembinska-Kiec A, Detraux D, Devaux Y, Di Marcello M, Dias TR, Distefano G, Doermann N, Doerrier C, Dong L, Donnelly C, Drahota Z, Duarte FV, Dubouchaud H, Duchen MR, Dumas JF, -
Marine Biological Laboratory) Data Are All from EST Analyses
TABLE S1. Data characterized for this study. rDNA 3 - - Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2 Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878. -
5. Bioenergetics
Life Sciences - LS (Molecules and their interaction relevant to Biology) 5. BIOENERGETICS Oxidative Phosphorylation Oxidative phosphorylation (or OXPHOS in short) is the metabolic pathway in which the mitochondria in cells use their structure, enzymes, and energy released by the oxidation of nutrients to reform ATP. Although the many forms of life on earth use a range of different nutrients, ATP is the molecule that supplies energy to metabolism. Almost all aerobic organisms carry out oxidative phosphorylation. Oxidative phosphorylation began with the report in 1906 by Arthur Harden of a vital role for phosphate in cellular fermentation, but initially only sugar phosphates were known to be involved. 1940s, Herman Kalckar work on this between the oxidation of sugars and the generation of ATP was firmly established, confirming the central role of ATP in energy transfer that had been proposed by Fritz Albert Lipmann in 1941. Later, in 1949, Morris Friedkin and Albert L. Lehninger proved that the coenzyme NADH linked metabolic pathways such as the citric acid cycle and the synthesis of ATP. This pathway is probably so pervasive because it is a highly efficient way of releasing energy, compared to alternative fermentation processes such as anaerobic glycolysis. 5.1 Electron Transport Chain The electron transport chain (aka ETC) is a process in which the NADH and [FADH ] produced 2 during glycolysis, -oxidation, and other catabolic processes are oxidized thus releasing energy in the form of ATP. The mechanism by which ATP is formed in the ETC is called chemiosmotic phosphorylation. Fig. : Electron Transport Chain Overview The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and the plasma membrane of prokaryotes. -
KALCKAR, HERMAN MORITZ (B
ndsbv4_K 9/25/07 1:11 PM Page 71 K KALCKAR, HERMAN MORITZ (b. ily members were “mainly free-thinkers” and his father Copenhagen, Denmark, 26 March 1908; d. Cambridge, was primarily secular, his mother was more observant and Massachusetts, 17 May 1991), biochemistry, enzymology, encouraged some religious education. Thus, Kalckar molecular biology. learned “a minimum of Hebrew” at the Copenhagen main synagogue (Kalckar, 1991, p. 2). Kalckar’s biochemical contributions were multifac- eted. His initial work opened an investigative pathway to Kalckar attended the Østre Borgerdyd Skole, located what has come to be called oxidative phosphorylation. As a short distance from home, which he described as “inter- a mature investigator, his utilized his laboratory to play a esting and rewarding” and having an “Athenian flavor,” a characteristic that arose from the headmaster, a world- significant role in the rapidly evolving field of enzymol- renowned Greek scholar. His early scientific education ogy, and Kalckar introduced innovative ways of measuring also benefited from “a formidable and passionately enzymatic activity. A significant part of his enzymological devoted teacher in mathematical physics,” who signifi- work focused on galactose metabolism, and he was one of cantly influenced Kalckar’s decision to pursue a career in the first investigators to clarify the nature of the genetic research and teaching. The Danish Nobel Prize–winning disorder galactosemia. Like many twentieth-century bio- (Physiology or Medicine, 1920) physiologist August chemists, Kalckar did not restrict his work to any single Krogh shaped Kalckar’s biological interests by some organism or tissue, and he contributed equally to the human physiology demonstrations.