Differentiating Two Closely Related Alexandrium Species Using Comparative Quantitative Proteomics
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Molecular Data and the Evolutionary History of Dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Un
Molecular data and the evolutionary history of dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Universitat Heidelberg, 1993 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES Department of Botany We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA November 2003 © Juan Fernando Saldarriaga Echavarria, 2003 ABSTRACT New sequences of ribosomal and protein genes were combined with available morphological and paleontological data to produce a phylogenetic framework for dinoflagellates. The evolutionary history of some of the major morphological features of the group was then investigated in the light of that framework. Phylogenetic trees of dinoflagellates based on the small subunit ribosomal RNA gene (SSU) are generally poorly resolved but include many well- supported clades, and while combined analyses of SSU and LSU (large subunit ribosomal RNA) improve the support for several nodes, they are still generally unsatisfactory. Protein-gene based trees lack the degree of species representation necessary for meaningful in-group phylogenetic analyses, but do provide important insights to the phylogenetic position of dinoflagellates as a whole and on the identity of their close relatives. Molecular data agree with paleontology in suggesting an early evolutionary radiation of the group, but whereas paleontological data include only taxa with fossilizable cysts, the new data examined here establish that this radiation event included all dinokaryotic lineages, including athecate forms. Plastids were lost and replaced many times in dinoflagellates, a situation entirely unique for this group. Histones could well have been lost earlier in the lineage than previously assumed. -
Ancient Metaproteomics: a Novel Approach for Understanding Disease And
Ancient metaproteomics: a novel approach for understanding disease and diet in the archaeological record Jessica Hendy PhD University of York Archaeology August, 2015 ii Abstract Proteomics is increasingly being applied to archaeological samples following technological developments in mass spectrometry. This thesis explores how these developments may contribute to the characterisation of disease and diet in the archaeological record. This thesis has a three-fold aim; a) to evaluate the potential of shotgun proteomics as a method for characterising ancient disease, b) to develop the metaproteomic analysis of dental calculus as a tool for understanding both ancient oral health and patterns of individual food consumption and c) to apply these methodological developments to understanding individual lifeways of people enslaved during the 19th century transatlantic slave trade. This thesis demonstrates that ancient metaproteomics can be a powerful tool for identifying microorganisms in the archaeological record, characterising the functional profile of ancient proteomes and accessing individual patterns of food consumption with high taxonomic specificity. In particular, analysis of dental calculus may be an extremely valuable tool for understanding the aetiology of past oral diseases. Results of this study highlight the value of revisiting previous studies with more recent methodological approaches and demonstrate that biomolecular preservation can have a significant impact on the effectiveness of ancient proteins as an archaeological tool for this characterisation. Using the approaches developed in this study we have the opportunity to increase the visibility of past diseases and their aetiology, as well as develop a richer understanding of individual lifeways through the production of molecular life histories. iii iv List of Contents Abstract ............................................................................................................................... -
The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?
bioRxiv preprint doi: https://doi.org/10.1101/587352; this version posted May 2, 2019. 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. Bjorbækmo et al., 23.03.2019 – preprint copy - BioRxiv The planktonic protist interactome: where do we stand after a century of research? Marit F. Markussen Bjorbækmo1*, Andreas Evenstad1* and Line Lieblein Røsæg1*, Anders K. Krabberød1**, and Ramiro Logares2,1** 1 University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N- 0316 Oslo, Norway 2 Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain * The three authors contributed equally ** Corresponding authors: Ramiro Logares: Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. Phone: 34-93-2309500; Fax: 34-93-2309555. [email protected] Anders K. Krabberød: University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N-0316 Oslo, Norway. Phone +47 22845986, Fax: +47 22854726. [email protected] Abstract Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years. -
Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile (Supplement Data)
Protocols for monitoring Harmful Algal Blooms for sustainable aquaculture and coastal fisheries in Chile (Supplement data) Provided by Kyoko Yarimizu, et al. Table S1. Phytoplankton Naming Dictionary: This dictionary was constructed from the species observed in Chilean coast water in the past combined with the IOC list. Each name was verified with the list provided by IFOP and online dictionaries, AlgaeBase (https://www.algaebase.org/) and WoRMS (http://www.marinespecies.org/). The list is subjected to be updated. Phylum Class Order Family Genus Species Ochrophyta Bacillariophyceae Achnanthales Achnanthaceae Achnanthes Achnanthes longipes Bacillariophyta Coscinodiscophyceae Coscinodiscales Heliopeltaceae Actinoptychus Actinoptychus spp. Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Akashiwo Akashiwo sanguinea Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Amphidinium Amphidinium spp. Ochrophyta Bacillariophyceae Naviculales Amphipleuraceae Amphiprora Amphiprora spp. Bacillariophyta Bacillariophyceae Thalassiophysales Catenulaceae Amphora Amphora spp. Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Anabaenopsis Anabaenopsis milleri Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema Anagnostidinema amphibium Anagnostidinema Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema lemmermannii Cyanobacteria Cyanophyceae Oscillatoriales Microcoleaceae Annamia Annamia toxica Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Aphanizomenon Aphanizomenon flos-aquae -
Microzooplankton Composition and Dynamics in Lake Erie
MICROZOOPLANKTON COMPOSITION AND DYNAMICS IN LAKE ERIE A Thesis Presented to The Graduate Faculty of the University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Kenneth M. Moats May 2006 MICROZOOPLANKTON COMPOSITION AND DYNAMICS IN LAKE ERIE Kenneth M. Moats Thesis Approved: Accepted: ______________________________ ______________________________ Advisor Department Chair Peter J. Lavrentyev Richard L. Londraville ______________________________ ______________________________ Committee Member Dean of the College R. Joel Duff Ronald F. Levant ______________________________ ______________________________ Committee Member Dean of the Graduate School David M. Klarer George R. Newkome ______________________________ Date ii ACKNOWLEDGEMENTS I would like to thank my graduate advisor Dr. Peter Lavrentyev for introducing me to the study of aquatic microbial ecology and for the opportunity to conduct this study. The importance of his guidance and expertise in every aspect of this research cannot be understated. I would also like to thank him for the patience, support, and encouragement he provided throughout my tenure. I would also like to thank the other members of my advisory committee, Dr. Joel Duff and Dr. David Klarer, for the helpful advice and comments offered during the preparation of this manuscript. I would like to extend my thanks to Dr. Klarer and the staff of Old Woman Creek NERR for logistical support and the sharing of unpublished data on Old Woman Creek. I thank Dr. Frank Jochem of Florida International University, Dr. Henry Vanderploeg and Dr. Stuart Ludsin of Great Lakes Environmental Research Laboratory, and the Captain and crew of the US EPA R/V Lake Guardian for logistical support during the Lake Erie experiments. -
N-Carbamoylation of 2,4-Diaminobutyrate Reroutes the Outcome in Padanamide Biosynthesis
Chemistry & Biology Article N-Carbamoylation of 2,4-Diaminobutyrate Reroutes the Outcome in Padanamide Biosynthesis Yi-Ling Du,1 Doralyn S. Dalisay,1 Raymond J. Andersen,1,2 and Katherine S. Ryan1,* 1Department of Chemistry 2Department of Earth, Ocean and Atmospheric Sciences University of British Columbia, Vancouver, BC V6T 1Z1, Canada *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chembiol.2013.06.013 SUMMARY literature. It is interesting that a compound identical to padana- mide A, named actinoramide A (Nam et al., 2011), was indepen- Padanamides are linear tetrapeptides notable for the dently reported from Streptomyces sp. CNQ-027. This actinomy- absence of proteinogenic amino acids in their struc- cete strain was isolated from sediment on the opposite side of the tures. In particular, two unusual heterocycles, (S)- Pacific Ocean, near San Diego, CA, suggesting a potentially wide 3-amino-2-oxopyrrolidine-1-carboxamide (S-Aopc) distribution of the padanamides/actinoramides. It is intriguing and (S)-3-aminopiperidine-2,6-dione (S-Apd), are that, whereas padanamide A and actinoramide A are identical, found at the C-termini of padanamides A and B, the minor compounds (actinoramides B and C) co-isolated from Streptomyces sp. CNQ-027 are unique (Figure 1A). Total respectively. Here we identify the padanamide synthesis of padanamides A and B was recently reported (Long biosynthetic gene cluster and carry out systematic et al., 2013), confirming the previous structural elucidations. gene inactivation studies. Our results show that The padanamides attracted our attention for their many padanamides are synthesized by highly dissociated unusual chemical features. -
Polyketide Biosynthesis Beyond the Type I, II and III Polyketide Synthase Paradigms Ben Shen
285 Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms Ben Shen Recent literature on polyketide biosynthesis suggests that Three types of bacterial PKSs are known to date. First, polyketide synthases have much greater diversity in both type I PKSs are multifunctional enzymes that are orga- mechanism and structure than the current type I, II and III nized into modules, each of which harbors a set of distinct, paradigms. These examples serve as an inspiration for searching non-iteratively acting activities responsible for the cata- novel polyketide synthases to give new insights into polyketide lysis of one cycle of polyketide chain elongation, as biosynthesis and to provide new opportunities for combinatorial exemplified by the 6-deoxyerythromycin B synthase biosynthesis. (DEBS) for the biosynthesis of reduced polyketides (i.e. macrolides, polyethers and polyene) such as erythro- Addresses mycin A (1)(Figure 1a) [1]. Second, type II PKSs are Division of Pharmaceutical Sciences and Department of Chemistry, multienzyme complexes that carry a single set of iteratively University of Wisconsin, Madison, WI 53705, USA acting activities, as exemplified by the tetracenomycin e-mail: [email protected] PKS for the biosynthesis of aromatic polyketides (often polycyclic) such as tetracenomycin C (2)(Figure 1b) [2]. Current Opinion in Chemical Biology 2003, 7:285–295 Third, type III PKSs, also known as chalcone synthase- like PKSs, are homodimeric enzymes that essentially are This review comes from a themed section on iteratively acting condensing enzymes, as exemplified by Biocatalysis and biotransformation Edited by Tadhg Begley and Ming-Daw Tsai the RppA synthase for the biosynthesis of aromatic poly- ketides (often monocyclic or bicyclic), such as flavolin (3) 1367-5931/03/$ – see front matter (Figure 1c) [3]. -
Plant Life MagillS Encyclopedia of Science
MAGILLS ENCYCLOPEDIA OF SCIENCE PLANT LIFE MAGILLS ENCYCLOPEDIA OF SCIENCE PLANT LIFE Volume 4 Sustainable Forestry–Zygomycetes Indexes Editor Bryan D. Ness, Ph.D. Pacific Union College, Department of Biology Project Editor Christina J. Moose Salem Press, Inc. Pasadena, California Hackensack, New Jersey Editor in Chief: Dawn P. Dawson Managing Editor: Christina J. Moose Photograph Editor: Philip Bader Manuscript Editor: Elizabeth Ferry Slocum Production Editor: Joyce I. Buchea Assistant Editor: Andrea E. Miller Page Design and Graphics: James Hutson Research Supervisor: Jeffry Jensen Layout: William Zimmerman Acquisitions Editor: Mark Rehn Illustrator: Kimberly L. Dawson Kurnizki Copyright © 2003, by Salem Press, Inc. All rights in this book are reserved. No part of this work may be used or reproduced in any manner what- soever or transmitted in any form or by any means, electronic or mechanical, including photocopy,recording, or any information storage and retrieval system, without written permission from the copyright owner except in the case of brief quotations embodied in critical articles and reviews. For information address the publisher, Salem Press, Inc., P.O. Box 50062, Pasadena, California 91115. Some of the updated and revised essays in this work originally appeared in Magill’s Survey of Science: Life Science (1991), Magill’s Survey of Science: Life Science, Supplement (1998), Natural Resources (1998), Encyclopedia of Genetics (1999), Encyclopedia of Environmental Issues (2000), World Geography (2001), and Earth Science (2001). ∞ The paper used in these volumes conforms to the American National Standard for Permanence of Paper for Printed Library Materials, Z39.48-1992 (R1997). Library of Congress Cataloging-in-Publication Data Magill’s encyclopedia of science : plant life / edited by Bryan D. -
Removal of the Toxic Dinoflagellate Alexandrium Tamarense (Dinophyta
Revista de Biología Marina y Oceanografía Vol. 50, Nº2: 347-352, agosto 2015 DOI 10.4067/S0718-19572015000300012 RESEARCH NOTE Removal of the toxic dinoflagellate Alexandrium tamarense (Dinophyta, Gonyaulacales) by Mnemiopsis leidyi (Ctenophora, Lobata) in controlled experimental conditions Remoción del dinoflagelado tóxico Alexandrium tamarense (Dinophyta, Gonyaulacales) por Mnemiopsis leidyi (Ctenophora, Lobata) en condiciones experimentales controladas Sergio Bolasina1,2, Hugo Benavides1,4, Nora Montoya1, José Carreto1,4, Marcelo Acha1,3,4 and Hermes Mianzan1,3,4 1Instituto Nacional de Investigación y Desarrollo Pesquero - INIDEP, Paseo Victoria Ocampo N°1, Escollera Norte, (7602), Mar del Plata, Buenos Aires, Argentina. [email protected] 2Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé -NUPEM/UFRJ, Rua São José do Barreto 764, Macaé, Rio de Janeiro, Brasil. (Present address) 3Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina 4Universidad Nacional de Mar del Plata, Funes 3350 (7600) Mar del Plata, Buenos Aires, Argentina Abstract.- The objective of the present study is to estimate the removal capability of the ctenophore Mnemiopsis leidyi (Ctenophora, Lobata) on cultures of the toxic dinoflagellate Alexandrium tamarense (Dinophyta, Gonyaulacales). For this purpose, observations on its clearance and survival rates were made in controlled experiments, using different A. tamarense cell concentrations. Mnemiopsis leidyi is able to remove dinoflagellates actively from the water column only at the lowest density tested (150 cells mL-1). Animals exposed to 300 cells mL-1 presented negative clearance and removal rates (survival= 67%). All ctenophores exposed at the highest concentrations of toxic dinoflagellates (600 cells mL-1) died after 4 h. Removal may occur mainly by incorporating and entangling cells in the mucus strands formed by the ctenophore, and in a lesser way by ingestion. -
Letters to Nature
letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997). -
Insights Into Alexandrium Minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis Through Comprehensive Transcriptome Survey
biology Article Insights into Alexandrium minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis through Comprehensive Transcriptome Survey Muhamad Afiq Akbar 1, Nurul Yuziana Mohd Yusof 2 , Fathul Karim Sahrani 2, Gires Usup 2, Asmat Ahmad 1, Syarul Nataqain Baharum 3 , Nor Azlan Nor Muhammad 3 and Hamidun Bunawan 3,* 1 Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; muhdafi[email protected] (M.A.A.); [email protected] (A.A.) 2 Department of Earth Science and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; [email protected] (N.Y.M.Y.); [email protected] (F.K.S.); [email protected] (G.U.) 3 Institute of System Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; [email protected] (S.N.B.); [email protected] (N.A.N.M.) * Correspondence: [email protected]; Tel.: +60-389-214-570 Simple Summary: Alexandrium minutum is one of the causing organisms for the occurrence of harmful algae bloom (HABs) in marine ecosystems. This species produces saxitoxin, one of the deadliest neurotoxins which can cause human mortality. However, molecular information such as genes and proteins catalog on this species is still lacking. Therefore, this study has successfully Citation: Akbar, M.A.; Yusof, N.Y.M.; characterized several new molecular mechanisms regarding A. minutum environmental adaptation Sahrani, F.K.; Usup, G.; Ahmad, A.; and saxitoxin biosynthesis. Ultimately, this study provides a valuable resource for facilitating future Baharum, S.N.; Muhammad, N.A.N.; dinoflagellates’ molecular response to environmental changes. -
Article (Refereed) - Postprint
Article (refereed) - postprint Rogers, Geraint B.; Cuthbertson, Leah; Hoffman, Lucas R.; Wing, Peter A.C.; Pope, Christopher; Hooftman, Danny A.P.; Lilley, Andrew K.; Oliver, Anna; Carroll, Mary P.; Bruce , Kenneth D.; van der Gast, Christopher J.. 2013 Reducing bias in bacterial community analysis of lower respiratory infections. ISME Journal, 7 (4). 10.1038/ismej.2012.145 Copyright © 2013 International Society for Microbial Ecology This version available http://nora.nerc.ac.uk/20879/ NERC has developed NORA to enable users to access research outputs wholly or partially funded by NERC. Copyright and other rights for material on this site are retained by the rights owners. Users should read the terms and conditions of use of this material at http://nora.nerc.ac.uk/policies.html#access This document is the author’s final manuscript version of the journal article following the peer review process. Some differences between this and the publisher’s version may remain. You are advised to consult the publisher’s version if you wish to cite from this article. www.nature.com/ Contact CEH NORA team at [email protected] The NERC and CEH trademarks and logos (‘the Trademarks’) are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner. 1 Towards unbiased bacterial community analysis in lower respiratory infections 2 3 Geraint B. Rogers1, Leah Cuthbertson2, Lucas R. Hoffman3, Peter A. C. Wing4, Christopher Pope3, Danny A. 4 P. Hooftman2, Andrew K. Lilley1, Anna Oliver2, Mary P. Carroll4, Kenneth D. Bruce1, Christopher J.