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Molecular Phylogenetic Position of Hexacontium Pachydermum Jørgensen (Radiolaria)
Marine Micropaleontology 73 (2009) 129–134 Contents lists available at ScienceDirect Marine Micropaleontology journal homepage: www.elsevier.com/locate/marmicro Molecular phylogenetic position of Hexacontium pachydermum Jørgensen (Radiolaria) Tomoko Yuasa a,⁎, Jane K. Dolven b, Kjell R. Bjørklund b, Shigeki Mayama c, Osamu Takahashi a a Department of Astronomy and Earth Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501, Japan b Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway c Department of Biology, Tokyo Gakugei University, Koganei, Tokyo 184-8501, Japan article info abstract Article history: The taxonomic affiliation of Hexacontium pachydermum Jørgensen, specifically whether it belongs to the Received 9 April 2009 order Spumellarida or the order Entactinarida, is a subject of ongoing debate. In this study, we sequenced the Received in revised form 3 August 2009 18S rRNA gene of H. pachydermum and of three spherical spumellarians of Cladococcus viminalis Haeckel, Accepted 7 August 2009 Arachnosphaera myriacantha Haeckel, and Astrosphaera hexagonalis Haeckel. Our molecular phylogenetic analysis revealed that the spumellarian species of C. viminalis, A. myriacantha, and A. hexagonalis form a Keywords: monophyletic group. Moreover, this clade occupies a sister position to the clade comprising the spongodiscid Radiolaria fi Entactinarida spumellarians, coccodiscid spumellarians, and H. pachydermum. This nding is contrary to the results of Spumellarida morphological studies based on internal spicular morphology, placing H. pachydermum in the order Nassellarida Entactinarida, which had been considered to have a common ancestor shared with the nassellarians. 18S rRNA gene © 2009 Elsevier B.V. All rights reserved. Molecular phylogeny. 1. Introduction the order Entactinarida has an inner spicular system homologenous with that of the order Nassellarida. -
Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
Smith ScholarWorks Biological Sciences: Faculty Publications Biological Sciences 10-1-2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life Laura Wegener Parfrey University of Massachusetts Amherst Jessica Grant Smith College Yonas I. Tekle Smith College Erica Lasek-Nesselquist Marine Biological Laboratory Hilary G. Morrison Marine Biological Laboratory See next page for additional authors Follow this and additional works at: https://scholarworks.smith.edu/bio_facpubs Part of the Biology Commons Recommended Citation Parfrey, Laura Wegener; Grant, Jessica; Tekle, Yonas I.; Lasek-Nesselquist, Erica; Morrison, Hilary G.; Sogin, Mitchell L.; Patterson, David J.; and Katz, Laura A., "Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life" (2010). Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/126 This Article has been accepted for inclusion in Biological Sciences: Faculty Publications by an authorized administrator of Smith ScholarWorks. For more information, please contact [email protected] Authors Laura Wegener Parfrey, Jessica Grant, Yonas I. Tekle, Erica Lasek-Nesselquist, Hilary G. Morrison, Mitchell L. Sogin, David J. Patterson, and Laura A. Katz This article is available at Smith ScholarWorks: https://scholarworks.smith.edu/bio_facpubs/126 Syst. Biol. 59(5):518–533, 2010 c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: [email protected] DOI:10.1093/sysbio/syq037 Advance Access publication on July 23, 2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life LAURA WEGENER PARFREY1,JESSICA GRANT2,YONAS I. TEKLE2,6,ERICA LASEK-NESSELQUIST3,4, 3 3 5 1,2, HILARY G. -
Protist Phylogeny and the High-Level Classification of Protozoa
Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane). -
Biomineralization and Global Biogeochemical Cycles Philippe Van Cappellen Faculty of Geosciences, Utrecht University P.O
1122 Biomineralization and Global Biogeochemical Cycles Philippe Van Cappellen Faculty of Geosciences, Utrecht University P.O. Box 80021 3508 TA Utrecht, The Netherlands INTRODUCTION Biological activity is a dominant force shaping the chemical structure and evolution of the earth surface environment. The presence of an oxygenated atmosphere- hydrosphere surrounding an otherwise highly reducing solid earth is the most striking consequence of the rise of life on earth. Biological evolution and the functioning of ecosystems, in turn, are to a large degree conditioned by geophysical and geological processes. Understanding the interactions between organisms and their abiotic environment, and the resulting coupled evolution of the biosphere and geosphere is a central theme of research in biogeology. Biogeochemists contribute to this understanding by studying the transformations and transport of chemical substrates and products of biological activity in the environment. Biogeochemical cycles provide a general framework in which geochemists organize their knowledge and interpret their data. The cycle of a given element or substance maps out the rates of transformation in, and transport fluxes between, adjoining environmental reservoirs. The temporal and spatial scales of interest dictate the selection of reservoirs and processes included in the cycle. Typically, the need for a detailed representation of biological process rates and ecosystem structure decreases as the spatial and temporal time scales considered increase. Much progress has been made in the development of global-scale models of biogeochemical cycles. Although these models are based on fairly simple representations of the biosphere and hydrosphere, they account for the large-scale changes in the composition, redox state and biological productivity of the earth surface environment that have occurred over geological time. -
Plasmodiophora Brassicae
Bi et al. Phytopathology Research (2019) 1:12 https://doi.org/10.1186/s42483-019-0018-6 Phytopathology Research RESEARCH Open Access Comparative genomics reveals the unique evolutionary status of Plasmodiophora brassicae and the essential role of GPCR signaling pathways Kai Bi1,2, Tao Chen2, Zhangchao He1,2, Zhixiao Gao1,2, Ying Zhao1,2, Huiquan Liu3, Yanping Fu2, Jiatao Xie1,2, Jiasen Cheng1,2 and Daohong Jiang1,2* Abstract Plasmodiophora brassicae is an important biotrophic eukaryotic plant pathogen and a member of the rhizarian protists. This biotrophic pathogen causes clubroot in cruciferous plants via novel intracellular mechanisms that are markedly different from those of other biotrophic organisms. To date, genomes from six single spore isolates of P. brassicae have been sequenced. An accurate description of the evolutionary status of this biotrophic protist, however, remains lacking. Here, we determined the draft genome of the P. brassicae ZJ-1 strain. A total of 10,951 protein-coding genes were identified from a 24.1 Mb genome sequence. We applied a comparative genomics approach to prove the Rhizaria supergroup is an independent branch in the eukaryotic evolutionary tree. We also found that the GPCR signaling pathway, the versatile signal transduction to multiple intracellular signaling cascades in response to extracellular signals in eukaryotes, is significantly enriched in P. brassicae-expanded and P. brassicae-specific gene sets. Additionally, treatment with a GPCR inhibitor relieved the symptoms of clubroot and significantly suppressed the development of plasmodia. Our findings suggest that GPCR signal transduction pathways play important roles in the growth, development, and pathogenicity of P. brassicae. -
Cytoklepty in the Plankton: a Host Strategy to Optimize the Bioenergetic Machinery of Endosymbiotic Algae
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416644; this version posted December 9, 2020. 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. Cytoklepty in the plankton: a host strategy to optimize the bioenergetic machinery of endosymbiotic algae Uwizeye Clarisse1*, Mars Brisbin Margaret2,a*, Gallet Benoit3, Chevalier Fabien1, LeKieffre Charlotte 1, Schieber L. Nicole4, Falconet Denis1, Wangpraseurt Daniel 5,6,7, Schertel Lukas 6, Stryhanyuk Hryhoriy 8, Musat Niculina 8, Mitarai Satoshi 2, Schwab Yannick 4, Finazzi Giovanni1, Decelle Johan1§ *: these authors contributed equally to the manuscript aPresent address: Biology and Marine Chemistry & Geochemistry departments, Woods Hole Oceanographic Institution, Woods Hole, USA 1- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38000 Grenoble, FRANCE 2- Marine Biophysics Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan 3-Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France 4- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany 5-Department of Nanoengineering, University of California San Diego, San Diego, CA, USA 6-Bioinspired Photonics Group, Department of Chemistry, University of Cambridge, Cambridge, UK 7-Scripps Institution of Oceanography, University of California San Diego, San Diego, USA 8-Helmholtz Centre for Environmental Research – UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany §: Johan Decelle, Cell and Plant Physiology Department, 17 rue des Martyrs, 38054 Grenoble, France Email: [email protected] Keywords: symbiosis; oceanic plankton; 3D electron microscopy, photosynthesis, single-cell transcriptomics Author Contributions: C.U., M.M.B., S.M. -
Letter to the Editor
Letter to the Editor Toward the Monophyly of Haeckel's Radiolaria: 18S rRNA Environmental Data Support the Sisterhood of Polycystinea and Acantharea Puri®cacioÂn LoÂpez-GarcõÂa,*² Francisco RodrõÂguez-Valera,² and David Moreira* *Universite Pierre et Marie Curie, Paris and ²DivisioÂn de MicrobiologõÂa, Universidad Miguel HernaÂndez, San Juan de Alicante, Spain subsequently constructed a cosmid genomic library of the 0.2- to 5-mm biomass fraction from 500-m-deep wa- In 1887, Ernst Haeckel published a monumental ters at the same location (598199S, 558459W). The con- and amazingly illustrated monograph describing several struction of the environmental genomic libraries has a thousand different radiolarian species, which had been number of advantages over a direct PCR ampli®cation collected during the 4-year journey (1872±1876) of the of a target gene. First, the diversity retrieved is not af- British oceanographic corvette H.M.S. Challenger fected by well-known PCR-related biases. Second, these (Haeckel 1887). Radiolaria consist of diverse marine kinds of libraries offer the possibility of retrieving other planktonic protists, mostly unicellular, usually endowed gene sequences, in addition to the 18S rRNA, from the with complex, conspicuous mineral skeletons. Haeckel same genomic fragment. applied the term Radiolaria to three different groups: Our environmental genomic library was construct- Acantharea, Polycystinea (Spumellaria and Nassellaria), ed using 3.5 mg of DNA. DNA was mechanically bro- and Phaeodarea. All of them are united by the posses- ken by intense shearing and fractionated in a 0.8% low sion of a central capsule de®ning an intracapsular and melting point agarose gel. The band corresponding to an extracapsular region in the cytoplasm, and some of 35±45 kb DNA fragments was cut off and digested with them, (all Acantharea and several Spumellaria), also by gelase. -
A Perspective on Underlying Crystal Growth Mechanisms in Biomineralization: Solution Mediated Growth Versus Nanosphere Particle Accretion
CrystEngComm A perspective on underlying crystal growth mechanisms in biomineralization: solution mediated growth versus nanosphere particle accretion Journal: CrystEngComm Manuscript ID: CE-HIG-07-2014-001474.R1 Article Type: Highlight Date Submitted by the Author: 01-Dec-2014 Complete List of Authors: Gal, Assaf; Weizmann Institute of Science, Structural Biology Weiner, Steve; Weizmann Institute of Science, Structural Biology Addadi, Lia; Weizmann Institute of Science, Structural Biology Page 1 of 23 CrystEngComm A perspective on underlying crystal growth mechanisms in biomineralization: solution mediated growth versus nanosphere particle accretion Assaf Gal, Steve Weiner, and Lia Addadi Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel 76100 Abstract Many organisms form crystals from transient amorphous precursor phases. In the cases where the precursor phases were imaged, they consist of nanosphere particles. Interestingly, some mature biogenic crystals also have nanosphere particle morphology, but some are characterized by crystallographic faces that are smooth at the nanometer level. There are also biogenic crystals that have both crystallographic faces and nanosphere particle morphology. This highlight presents a working hypothesis, stating that some biomineralization processes involve growth by nanosphere particle accretion, where amorphous nanoparticles are incorporated as such into growing crystals and preserve their morphology upon crystallization. This process produces biogenic crystals with a nanosphere particle morphology. Other biomineralization processes proceed by ion-by-ion growth, and some cases of biological crystal growth involve both processes. We also identify several biomineralization processes which do not seem to fit this working hypothesis. It is our hope that this highlight will inspire studies that will shed more light on the underlying crystallization mechanisms in biology. -
Author's Manuscript (764.7Kb)
1 BROADLY SAMPLED TREE OF EUKARYOTIC LIFE Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life Laura Wegener Parfrey1†, Jessica Grant2†, Yonas I. Tekle2,6, Erica Lasek-Nesselquist3,4, Hilary G. Morrison3, Mitchell L. Sogin3, David J. Patterson5, Laura A. Katz1,2,* 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, Massachusetts 01003, USA 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, Massachusetts 01063, USA 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, Rhode Island 02912, USA 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 6Current address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA †These authors contributed equally *Corresponding author: L.A.K - [email protected] Phone: 413-585-3825, Fax: 413-585-3786 Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error, Excavata 2 An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. -
Chitosan-Based Biomimetically Mineralized Composite Materials in Human Hard Tissue Repair
molecules Review Chitosan-Based Biomimetically Mineralized Composite Materials in Human Hard Tissue Repair Die Hu 1,2 , Qian Ren 1,2, Zhongcheng Li 1,2 and Linglin Zhang 1,2,* 1 State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Disease, Sichuan University, Chengdu 610000, China; [email protected] (D.H.); [email protected] (Q.R.); [email protected] (Z.L.) 2 Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610000, China * Correspondence: [email protected] or [email protected]; Tel.: +86-028-8550-3470 Academic Editors: Mohamed Samir Mohyeldin, Katarína Valachová and Tamer M Tamer Received: 16 September 2020; Accepted: 16 October 2020; Published: 19 October 2020 Abstract: Chitosan is a natural, biodegradable cationic polysaccharide, which has a similar chemical structure and similar biological behaviors to the components of the extracellular matrix in the biomineralization process of teeth or bone. Its excellent biocompatibility, biodegradability, and polyelectrolyte action make it a suitable organic template, which, combined with biomimetic mineralization technology, can be used to develop organic-inorganic composite materials for hard tissue repair. In recent years, various chitosan-based biomimetic organic-inorganic composite materials have been applied in the field of bone tissue engineering and enamel or dentin biomimetic repair in different forms (hydrogels, fibers, porous scaffolds, microspheres, etc.), and the inorganic components of the composites are usually biogenic minerals, such as hydroxyapatite, other calcium phosphate phases, or silica. These composites have good mechanical properties, biocompatibility, bioactivity, osteogenic potential, and other biological properties and are thus considered as promising novel materials for repairing the defects of hard tissue. -
Marine Bacterial, Archaeal and Protistan Association Networks Reveal Ecological Linkages
The ISME Journal (2011), 1–12 & 2011 International Society for Microbial Ecology All rights reserved 1751-7362/11 www.nature.com/ismej ORIGINAL ARTICLE Marine bacterial, archaeal and protistan association networks reveal ecological linkages Joshua A Steele, Peter D Countway, Li Xia, Patrick D Vigil, J Michael Beman, Diane Y Kim, Cheryl-Emiliane T Chow, Rohan Sachdeva, Adriane C Jones, Michael S Schwalbach, Julie M Rose, Ian Hewson, Anand Patel, Fengzhu Sun, David A Caron and Jed A Fuhrman Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, USA Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico- chemical observations. Samples and observations were collected monthly over 3 years at a well- described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. -
Role of Phosphate in Biomineralization
Henry Ford Health System Henry Ford Health System Scholarly Commons Endocrinology Articles Endocrinology and Metabolism 7-25-2020 Role of Phosphate in Biomineralization Sanjay Kumar Bhadada Sudhaker D. Rao Henry Ford Health System, [email protected] Follow this and additional works at: https://scholarlycommons.henryford.com/endocrinology_articles Recommended Citation Bhadada SK, and Rao SD. Role of Phosphate in Biomineralization. Calcif Tissue Int 2020. This Article is brought to you for free and open access by the Endocrinology and Metabolism at Henry Ford Health System Scholarly Commons. It has been accepted for inclusion in Endocrinology Articles by an authorized administrator of Henry Ford Health System Scholarly Commons. Calcifed Tissue International https://doi.org/10.1007/s00223-020-00729-9 REVIEW Role of Phosphate in Biomineralization Sanjay Kumar Bhadada1 · Sudhaker D. Rao2,3 Received: 31 March 2020 / Accepted: 14 July 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020 Abstract Inorganic phosphate is a vital constituent of cells and cell membranes, body fuids, and hard tissues. It is a major intracel- lular divalent anion, participates in many genetic, energy and intermediary metabolic pathways, and is important for bone health. Although we usually think of phosphate mostly in terms of its level in the serum, it is needed for many biological and structural functions of the body. Availability of adequate calcium and inorganic phosphate in the right proportions at the right place is essential for proper acquisition, biomineralization, and maintenance of mass and strength of the skeleton. The three specialized mineralized tissues, bones, teeth, and ossicles, difer from all other tissues in the human body because of their unique ability to mineralize, and the degree and process of mineralization in these tissues also difer to suit the specifc functions: locomotion, chewing, and hearing, respectively.