Review of the Center for Computational Sciences, University of Tsukuba 2020
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Harmful Algae 91 (2020) 101587
Harmful Algae 91 (2020) 101587 Contents lists available at ScienceDirect Harmful Algae journal homepage: www.elsevier.com/locate/hal Review Progress and promise of omics for predicting the impacts of climate change T on harmful algal blooms Gwenn M.M. Hennona,c,*, Sonya T. Dyhrmana,b,* a Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States b Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States c College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks, AK, United States ARTICLE INFO ABSTRACT Keywords: Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past Genomics twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have trans- Transcriptomics formed that data landscape of many fields including the study of HABs. Advances in technology have facilitated Proteomics the creation of many publicly available omics datasets that are complementary and shed new light on the Metabolomics mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity Climate change and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species Phytoplankton Harmful algae responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In Cyanobacteria this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. -
A Persistent Giant Algal Virus, with a Unique Morphology, Encodes An
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 persistent giant algal virus, with a unique morphology, encodes an 2 unprecedented number of genes involved in energy metabolism 3 4 Romain Blanc-Mathieu1,2, Håkon Dahle3, Antje Hofgaard4, David Brandt5, Hiroki 5 Ban1, Jörn Kalinowski5, Hiroyuki Ogata1 and Ruth-Anne Sandaa6* 6 7 1: Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan 8 2: Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, 9 CNRS, INRA, IRIG, Grenoble, France 10 3: Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, 11 University of Bergen, Bergen, Norway 12 4: Department of Biosciences, University of Oslo, Norway 13 5: Center for Biotechnology, Universität Bielefeld, Bielefeld, 33615, Germany 14 6: Department of Biological Sciences, University of Bergen, Bergen, Norway 15 *Corresponding author: Ruth-Anne Sandaa, +47 55584646, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 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. 16 Abstract 17 Viruses have long been viewed as entities possessing extremely limited metabolic 18 capacities. -
Diversity and Evolution of Protist Mitochondria: Introns, Gene Content and Genome Architecture
Diversity and Evolution of Protist Mitochondria: Introns, Gene Content and Genome Architecture 著者 西村 祐貴 内容記述 この博士論文は内容の要約のみの公開(または一部 非公開)になっています year 2016 その他のタイトル プロティストミトコンドリアの多様性と進化:イン トロン、遺伝子組成、ゲノム構造 学位授与大学 筑波大学 (University of Tsukuba) 学位授与年度 2015 報告番号 12102甲第7737号 URL http://hdl.handle.net/2241/00144261 Diversity and Evolution of Protist Mitochondria: Introns, Gene Content and Genome Architecture A Dissertation Submitted to the Graduate School of Life and Environmental Sciences, the University of Tsukuba in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Science (Doctral Program in Biologial Sciences) Yuki NISHIMURA Table of Contents Abstract ........................................................................................................................... 1 Genes encoded in mitochondrial genomes of eukaryotes ..................................................... 3 Terminology .......................................................................................................................... 4 Chapter 1. General introduction ................................................................................ 5 The origin and evolution of mitochondria ............................................................................ 5 Mobile introns in mitochondrial genome .............................................................................. 6 The organisms which are lacking in mitochondrial genome data ........................................ 8 Chapter 2. Lateral transfers of mobile introns -
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. -
Introns, Gene Content and Genome Architecture
Diversity and Evolution of Protist Mitochondria: Introns, Gene Content and Genome Architecture A Dissertation Submitted to the Graduate School of Life and Environmental Sciences, the University of Tsukuba in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Science (Doctral Program in Biologial Sciences) Yuki NISHIMURA Table of Contents Abstract ........................................................................................................................... 1 Genes encoded in mitochondrial genomes of eukaryotes ..................................................... 3 Terminology .......................................................................................................................... 4 Chapter 1. General introduction ................................................................................ 5 The origin and evolution of mitochondria ............................................................................ 5 Mobile introns in mitochondrial genome .............................................................................. 6 The organisms which are lacking in mitochondrial genome data ........................................ 8 Chapter 2. Lateral transfers of mobile introns among distantly related mitochondrial genomes ................................................................................................ 11 Summary ................................................................................................................................ 11 2-1. Leucocryptos -
Public Incentives Harmful to Biodiversity
REPORTS & DOCUMENTS Public Incentives Harmful to Biodiversity Sustainable Development Report of the commission chaired by Guillaume Sainteny Public Incentives Harmful to Biodiversity Guillaume Sainteny Chairman Jean-Michel Salles Vice-Chairman Peggy Duboucher, Géraldine Ducos, Vincent Marcus, Erwan Paul Rapporteurs Dominique Auverlot, Jean-Luc Pujol Coordinators October 2011 March 2015 for the English version Foreword Public debate has sometimes tended to equate preservation of biodiversity with the emblematic fate of certain endangered species. We now know the importance of protecting fauna and flora as a whole, not only in certain “hotspots” upon the earth, but even in our local meadows and lawns. Of course, this involves not only the variety of species – and thereby the planet’s genetic heritage –, but also the many interactions between the latter (through pollination, predation and symbiosis) and the full scope of “services rendered” to mankind. For even though we are not always aware of it, mankind benefits from the immense services freely provided by ecosystems. This is the source from which we draw our food, as well as fuel and building materials. Apart from these “appropriable” goods, biodiversity enables the purification of water, climate stabilisation and mitigation, and the regulation of floods, droughts and epidemics. In short, biodiversity is vital for us. Yet, throughout the world, an increasingly rapid rate of decline in biodiversity has been observed for several decades, giving rise to fears of serious upheavals in our -
Integrative Taxonomy of the Pavlovophyceae (Haptophyta): a Reassessment
Protist, Vol. 162, 738–761, November 2011 http://www.elsevier.de/protis Published online date 28 June 2011 ORIGINAL PAPER Integrative Taxonomy of the Pavlovophyceae (Haptophyta): A Reassessment El Mahdi Bendifa,b,1, Ian Proberta,2, Annie Hervéc, Chantal Billardb, Didier Gouxd, Christophe Lelongb, Jean-Paul Cadoretc, and Benoît Vérona,b,3 aUniversité de Caen Basse-Normandie, Algobank-Caen, IFR 146, 14032 Caen, France bUniversité de Caen Basse-Normandie, UMR 100 PE2 M - IFREMER, 14032 Caen, France cIFREMER, Laboratoire de Physiologie et Biotechnologie des Algues, rue de l’Ile d’Yeu, BP21105, 44311 Nantes, France dUniversité de Caen Basse-Normandie, Centre de Microscopie Appliquée à la Biologie, IFR 146, 14032 Caen, France Submitted October 18, 2010; Accepted March 15, 2011 Monitoring Editor: Barry S. C. Leadbeater. The Pavlovophyceae (Haptophyta) contains four genera (Pavlova, Diacronema, Exanthemachrysis and Rebecca) and only thirteen characterised species, several of which are important in ecological and eco- nomic contexts. We have constructed molecular phylogenies inferred from sequencing of ribosomal gene markers with comprehensive coverage of the described diversity, using type strains when avail- able, together with additional cultured strains. The morphology and ultrastructure of 12 of the described species was also re-examined and the pigment signatures of many culture strains were determined. The molecular analysis revealed that sequences of all described species differed, although those of Pavlova gyrans and P. pinguis were nearly identical, these potentially forming a single cryptic species complex. Four well-delineated genetic clades were identified, one of which included species of both Pavlova and Diacronema. Unique combinations of morphological/ultrastructural characters were iden- tified for each of these clades. -
The Morphology of Chrysochromulina Rotalis Sp. Nov. (Prymnesiophyceae, Haptophyta), Isolated from the Skagerrak
The morphology of Chrysochromulina rotalis sp. nov. (Prymnesiophyceae, Haptophyta), isolated from the Skagerrak Wenche Eikrem & Jahn Throndsen Eikrem W, Throndsen J. 1999. The morphology of Chrysochromulina rotalis sp. nov. (Prymnesiophyceae, SARSIA Haptophyta), isolated from the Skagerrak. Sarsia 84:445-449. Chrysochromulina rotalis sp. nov. was isolated from surface water in the Skagerrak (58°11'N, 09°06'E) using the serial dilution culture method. The cells are saddle shaped with the appendages inserted subapically on the ventral side of the cell. The coiling haptonema measures 2-4 times the length of the flagella when extended. The cells contain two golden brown chloroplasts. The periplast is cov- ered by two types of scale with dimorphic scale faces. The scales constituting the outer layer bear a short spine supported by four struts, the inner layer scales lack protrusions. Wenche Eikrem & Jahn Throndsen, University of Oslo, Department of Biology, Section for Marine Botany, PO Box 1069 Blindern, N-0316 Oslo, Norway. E-mail: [email protected] – [email protected] Keywords: Morphology; Chrysochromulina; Prymnesiophyceae; Haptophyta. INTRODUCTION mally described Chrysochromulina species (e.g. Green & Leadbeater 1972; Hällfors & Niemi 1974; Estep & The haptophyte genus Chrysochromulina Lackey has a al. 1984; Hällfors & Thomsen 1985; Moestrup & worldwide distribution and more than 50 species have Thomsen 1986; Kawachi & Inouye 1993). been described, 38 of them have been reported from The cells of the Chrysochromulina species have two Scandinavian waters (e.g. Throndsen 1969; Leadbeater golden brown chloroplasts, two flagella, a haptonema 1972a, 1972b; Espeland & Throndsen 1986; and a scale covered periplast. The cells may vary in Kuylenstierna & Karlson 1997; Eikrem & al. -
"Phycology". In: Encyclopedia of Life Science
Phycology Introductory article Ralph A Lewin, University of California, La Jolla, California, USA Article Contents Michael A Borowitzka, Murdoch University, Perth, Australia . General Features . Uses The study of algae is generally called ‘phycology’, from the Greek word phykos meaning . Noxious Algae ‘seaweed’. Just what algae are is difficult to define, because they belong to many different . Classification and unrelated classes including both prokaryotic and eukaryotic representatives. Broadly . Evolution speaking, the algae comprise all, mainly aquatic, plants that can use light energy to fix carbon from atmospheric CO2 and evolve oxygen, but which are not specialized land doi: 10.1038/npg.els.0004234 plants like mosses, ferns, coniferous trees and flowering plants. This is a negative definition, but it serves its purpose. General Features Algae range in size from microscopic unicells less than 1 mm several species are also of economic importance. Some in diameter to kelps as long as 60 m. They can be found in kinds are consumed as food by humans. These include almost all aqueous or moist habitats; in marine and fresh- the red alga Porphyra (also known as nori or laver), an water environments they are the main photosynthetic or- important ingredient of Japanese foods such as sushi. ganisms. They are also common in soils, salt lakes and hot Other algae commonly eaten in the Orient are the brown springs, and some can grow in snow and on rocks and the algae Laminaria and Undaria and the green algae Caulerpa bark of trees. Most algae normally require light, but some and Monostroma. The new science of molecular biology species can also grow in the dark if a suitable organic carbon has depended largely on the use of algal polysaccharides, source is available for nutrition. -
Phylogenomics Invokes the Clade Housing Cryptista, Archaeplastida, and Microheliella Maris
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.29.458128; this version posted August 31, 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 Phylogenomics invokes the clade housing Cryptista, 2 Archaeplastida, and Microheliella maris. 3 4 Euki Yazaki1, †, *, Akinori Yabuki2, †, *, Ayaka Imaizumi3, Keitaro Kume4, Tetsuo Hashimoto5,6, 5 and Yuji Inagaki6,7 6 7 1: RIKEN iTHEMS, Wako, Saitama 351-0198, Japan 8 2: Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 236-0001, 9 Japan 10 3: College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan. 11 4: Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan 12 5: Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305- 13 8572, Japan 14 6: Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 15 Ibaraki, 305-8572, Japan 16 7: Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, 17 Japan 18 19 †EY and AY equally contributed to this work. 20 *Correspondence addressed to Euki Yazaki: [email protected] and Akinori Yabuki: 21 [email protected] 22 23 Running title: The clade housing Cryptista, Archaeplastida, and Microheliella maris. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.08.29.458128; this version posted August 31, 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. -
Initiating an Arctic Marine Biodiversity Observing Network (AMBON) Award Number: NA14NOS0120158 Reporting Term: October 1, 2015
Initiating an Arctic Marine Biodiversity Observing Network (AMBON) PI: Katrin Iken University of Alaska Fairbanks, College of Fisheries and Ocean Sciences, Fairbanks AK 99775 Phone: (907) 474-5192 Fax: (907)-474-7204 Email: [email protected] Co-PIs: Seth Danielson Phone: (907) 474-7834 Fax: (907)-474-7204 Email: [email protected] Franz Mueter Phone: (907) 796-5448 Fax: (907)-796-5447 Email: [email protected] Eric Collins Phone: (907) 474-6482 Fax: (907)-474-7204 Email: [email protected] Russ Hopcroft Phone: (907) 474-7842 Fax: (907)-474-7204 Email: [email protected] All: University of Alaska Fairbanks, College of Fisheries and Ocean Sciences, Fairbanks AK 99775 Jacqueline Grebmeier Phone: (410) 326-7334 Fax: (410)-326-7341 Email: [email protected] Lee Cooper Phone: (410) 326-7359 Fax: (410)-326-7359 Email: [email protected] Both: University of Maryland Center for Environmental Science, Chesapeake Biological Laboratory, Solomons MD 20688 Kate Stafford Phone: (206) 685-8617 Fax: (206)-543-6785 Email: [email protected] University of Washington, Applied Physics Laboratory, Seattle, WA 98105 Kathy Kuletz Phone: (907)-786-3453 Fax: (+1147)-786-3641 Email: [email protected] US Fish and Wildlife Service, Anchorage, AK 99503 Sue Moore Phone: (206) 526-6889 Email: [email protected] NOAA, Pacific Marine Environmental Laboratory, Seattle, WA 98115 Rob Bochenek Axiom Data Science, 1016 W 6th Ave Ste 105, Anchorage AK 99501 Phone: (907) 230-0304 Email: [email protected] Bodil Bluhm Phone: (+1147)-776-44382 Email: [email protected] University of Tromso, Norway Award Number: NA14NOS0120158 Reporting Term: October 1, 2015 to September 30, 2016 http://ambon-us.org LONG-TERM GOALS The goal of the Arctic Marine Biodiversity Observing Network (AMBON) project is to demonstrate and build an operational marine biodiversity observation network (MBON) for the US Chukchi Sea continental shelf as a prototype network for the nation. -
Viruses Infecting the Marine Prymnesiophyte Chrysochromulina Spp.: Isolation, Preliminary Characterization and Natural Abundance
MARINE ECOLOGY PROGRESS SERIES Vol. 118: 275-282,1995 Published March 9 Mar. Ecol. Prog. Ser. I Viruses infecting the marine Prymnesiophyte Chrysochromulina spp.: isolation, preliminary characterization and natural abundance Curtis A. Suttle, Amy M. Chan Marine Science Institute, The University of Texas at Austin, PO Box 1267, Port Aransas, Texas 78373-1267, USA ABSTRACT: Sixty-four natural virus communities were concentrated from seawater collected from 3 locations in Texas (USA) coastal waters (Gulf of Mexico, 27" 31' N, 96" 18' W; Aransas Pass, 27" 50' N, 97" 02' W; Laguna Madre, 27' 30' N, 97' 18' W) and screened for the presence of lytic pathogens which infect the marine Prymnesiophyte (Haptophyte) Chrysochromuljna brevifilum. Viruses were detected in 16 of the samples and ranged in abundance from 2 to 688 infectious units 1-' The pathogens were detected at the 3 locations, but not on all dates, from December through June when water temperatures were less than 28°C. A clonal isolate of the virus (CbV-PW1) was obtained by determining the concen- tration of the infectious agent by a most-probable-number assay and adding 0.2 of an infective unit into each of 20 exponentially growing cultures, removing an aliquot from a culture which lysed and repeat- ing the procedure. The isolate also caused lysis of C. strobllus, but did not lyse 8 other isolates of Chrysochromulina or 5 other genera of Prymnesiophytes that were screened. The double-stranded DNA virus is a polyhedron of about 145 to 170 nm in diameter with a heavily staining central region that is distinct from the capsid.