Oxytricha Nova (= Sterkiella Nova Sp
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Protists and the Wild, Wild West of Gene Expression
MI70CH09-Keeling ARI 3 August 2016 18:22 ANNUAL REVIEWS Further Click here to view this article's online features: • Download figures as PPT slides • Navigate linked references • Download citations Protists and the Wild, Wild • Explore related articles • Search keywords West of Gene Expression: New Frontiers, Lawlessness, and Misfits David Roy Smith1 and Patrick J. Keeling2 1Department of Biology, University of Western Ontario, London, Ontario, Canada N6A 5B7; email: [email protected] 2Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; email: [email protected] Annu. Rev. Microbiol. 2016. 70:161–78 Keywords First published online as a Review in Advance on constructive neutral evolution, mitochondrial transcription, plastid June 17, 2016 transcription, posttranscriptional processing, RNA editing, trans-splicing The Annual Review of Microbiology is online at micro.annualreviews.org Abstract This article’s doi: The DNA double helix has been called one of life’s most elegant structures, 10.1146/annurev-micro-102215-095448 largely because of its universality, simplicity, and symmetry. The expression Annu. Rev. Microbiol. 2016.70:161-178. Downloaded from www.annualreviews.org Copyright c 2016 by Annual Reviews. Access provided by University of British Columbia on 09/24/17. For personal use only. of information encoded within DNA, however, can be far from simple or All rights reserved symmetric and is sometimes surprisingly variable, convoluted, and wantonly inefficient. Although exceptions to the rules exist in certain model systems, the true extent to which life has stretched the limits of gene expression is made clear by nonmodel systems, particularly protists (microbial eukary- otes). -
The Macronuclear Genome of Stentor Coeruleus Reveals Tiny Introns in a Giant Cell
University of Pennsylvania ScholarlyCommons Departmental Papers (Biology) Department of Biology 2-20-2017 The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell Mark M. Slabodnick University of California, San Francisco J. G. Ruby University of California, San Francisco Sarah B. Reiff University of California, San Francisco Estienne C. Swart University of Bern Sager J. Gosai University of Pennsylvania See next page for additional authors Follow this and additional works at: https://repository.upenn.edu/biology_papers Recommended Citation Slabodnick, M. M., Ruby, J. G., Reiff, S. B., Swart, E. C., Gosai, S. J., Prabakaran, S., Witkowska, E., Larue, G. E., Gregory, B. D., Nowacki, M., Derisi, J., Roy, S. W., Marshall, W. F., & Sood, P. (2017). The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Current Biology, 27 (4), 569-575. http://dx.doi.org/10.1016/j.cub.2016.12.057 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/biology_papers/49 For more information, please contact [email protected]. The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell Abstract The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities—if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]. -
Protistology an International Journal Vol
Protistology An International Journal Vol. 10, Number 2, 2016 ___________________________________________________________________________________ CONTENTS INTERNATIONAL SCIENTIFIC FORUM «PROTIST–2016» Yuri Mazei (Vice-Chairman) Welcome Address 2 Organizing Committee 3 Organizers and Sponsors 4 Abstracts 5 Author Index 94 Forum “PROTIST-2016” June 6–10, 2016 Moscow, Russia Website: http://onlinereg.ru/protist-2016 WELCOME ADDRESS Dear colleagues! Republic) entitled “Diplonemids – new kids on the block”. The third lecture will be given by Alexey The Forum “PROTIST–2016” aims at gathering Smirnov (Saint Petersburg State University, Russia): the researchers in all protistological fields, from “Phylogeny, diversity, and evolution of Amoebozoa: molecular biology to ecology, to stimulate cross- new findings and new problems”. Then Sandra disciplinary interactions and establish long-term Baldauf (Uppsala University, Sweden) will make a international scientific cooperation. The conference plenary presentation “The search for the eukaryote will cover a wide range of fundamental and applied root, now you see it now you don’t”, and the fifth topics in Protistology, with the major focus on plenary lecture “Protist-based methods for assessing evolution and phylogeny, taxonomy, systematics and marine water quality” will be made by Alan Warren DNA barcoding, genomics and molecular biology, (Natural History Museum, United Kingdom). cell biology, organismal biology, parasitology, diversity and biogeography, ecology of soil and There will be two symposia sponsored by ISoP: aquatic protists, bioindicators and palaeoecology. “Integrative co-evolution between mitochondria and their hosts” organized by Sergio A. Muñoz- The Forum is organized jointly by the International Gómez, Claudio H. Slamovits, and Andrew J. Society of Protistologists (ISoP), International Roger, and “Protists of Marine Sediments” orga- Society for Evolutionary Protistology (ISEP), nized by Jun Gong and Virginia Edgcomb. -
Uroleptus Willii Nov. Sp., a Euplanktonic Freshwater Ciliate
Uroleptus willii nov. sp., a euplanktonic freshwater ciliate (Dorsomarginalia, Spirotrichea, Ciliophora) with algal symbionts: morphological description including phylogenetic data of the small subunit rRNA gene sequence and ecological notes * Bettina S ONNTAG , Michaela C. S TRÜDER -K YPKE & Monika S UMMERER Abstract : The eUplanktonic ciliate Uroleptus willii nov. sp. (Dorsomarginalia) was discovered in the plankton of the oligo- mesotrophic PibUrgersee in AUstria. The morphology and infraciliatUre of this new species were stUdied in living cells as well as in specimens impregnated with protargol and the phylogenetic placement was inferred from the small sUbUnit ribosomal RNA (SSrRNA) gene seqUence. In vivo, U. willii is a grass-green fUsiform spirotrich of 100– 150 µm length. It bears aboUt 80–100 sym - biotic green algae and bUilds a lorica. Uroleptus willii is a freqUent species in the sUmmer ciliate assemblage in the Upper 12 m of PibUrgersee with a mean abUndance of aboUt 170 individUals l -1 from May throUgh November. The algal symbionts of this ciliate are known to synthesise Ultraviolet radiation – absorbing compoUnds. At present, the taxonomic position of Uroleptus has not yet been solved since the morphological featUres of the genUs agree well with those of the Urostyloidea, while the molecUlar analy - ses place the genUs within the Oxytrichidae. Uroleptus willii follows this pattern and groUps UnambigUoUsly with other Uroleptus species. We assign oUr new species to the Dorsomarginalia BERGER , 2006. However, this placement is preliminary since it is based on the assUmption that the genUs Uroleptus and the Oxytrichidae are both monophyletic taxa, and the monophyly of the latter groUp has still not been confirmed by molecUlar data. -
Ciliate Biodiversity and Phylogenetic Reconstruction Assessed by Multiple Molecular Markers Micah Dunthorn University of Massachusetts Amherst, [email protected]
University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 9-2009 Ciliate Biodiversity and Phylogenetic Reconstruction Assessed by Multiple Molecular Markers Micah Dunthorn University of Massachusetts Amherst, [email protected] Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Life Sciences Commons Recommended Citation Dunthorn, Micah, "Ciliate Biodiversity and Phylogenetic Reconstruction Assessed by Multiple Molecular Markers" (2009). Open Access Dissertations. 95. https://doi.org/10.7275/fyvd-rr19 https://scholarworks.umass.edu/open_access_dissertations/95 This Open Access Dissertation is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. CILIATE BIODIVERSITY AND PHYLOGENETIC RECONSTRUCTION ASSESSED BY MULTIPLE MOLECULAR MARKERS A Dissertation Presented by MICAH DUNTHORN Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of Doctor of Philosophy September 2009 Organismic and Evolutionary Biology © Copyright by Micah Dunthorn 2009 All Rights Reserved CILIATE BIODIVERSITY AND PHYLOGENETIC RECONSTRUCTION ASSESSED BY MULTIPLE MOLECULAR MARKERS A Dissertation Presented By MICAH DUNTHORN Approved as to style and content by: _______________________________________ -
Ciliophora: Sporadotrichida: Oxytrichidae) New to Korea
Journal of Species Research 1(1):78-86, 2012 Morphological redescriptions of three Cyrtohymena ciliates (Ciliophora: Sporadotrichida: Oxytrichidae) new to Korea Yeon Uk Kim, Jung Mi Lee, Choon Bong Kwon and Mann Kyoon Shin* Department of Biological Science, College of Natural Sciences, University of Ulsan, Ulsan 680-749, Korea *Correspondent: [email protected] Three ciliate species of genus Cyrtohymena, C. australis Foissner, 1995, C. citrina (Berger & Foissner, 1987) and C. muscorum (Kahl, 1932) new to Korea, were collected from semi-terrestrial habitats. The description was based on the observation of live and silver stained specimens. Diagnostic characteristics of these species are as follows. C. autralis: size about 275×100 μm in live specimens. Cortical granules yellowish. 18-31 right and 31-40 left marginal cirri in number. Dorsal kineties eight rows. C. citrina: size about 180×50 μm in live specimens. Cortical granules yellowish. 26-32 right and 23-27 left marginal cirri in number. Dorsal kineties five to six rows. C. muscorum: size about 180×60 μm in live specimens. Cortical granules reddish. 31-34 right and 33-36 left marginal cirri in number. Dorsal kineties six rows. Three species of Cyrtohymena have been added to Korean ciliate fauna from this study. Including previous one species of C. quadrinucleata, four species of this genus in total have been recorded so far in this country. Keywords: Cyrtohymena, freshwater, morphology, soil, taxonomy, terrestrial collected from semi-terrestrial and rarely from marine INTRODUCTION habitats (Kahl, 1932; Gellért, 1956; Foissner, 1997; 1999; Berger, 1999; Song et al., 2002; Çapar, 2007). The oxytrichid genus Cyrtohymena Foissner, 1989 is In this study, we described three Cyrtohymena species highly specialized group of hypotrichous ciliates which which are new to Korea, C. -
Ciliata, Hypotrichida, Oxytrichidae)
Alli Soc. Tosc. Sci. Nat. , Mem., Serie B, 92 (1985) pagg. 15-27, figg. 3. D. AMMERMANN (*) SPECIES CHARACTERIZATION AND SPECIATION IN THE STYLONYCHIA/OXYTRICHA GROUP (CILIATA, HYPOTRICHIDA, OXYTRICHIDAE) Riassunto - Caratterizzazione delle species e speciazione nel gruppo Stylony chialOxytricha (Ciliata, Hypotrichida, Oxytrichidae). Sono state esaminate alcune ca ratteristiche morfologiche e in particolare molecolari di species appartenenti al gruppo StylonychialOxytricha. Ne viene discusso il loro significato al fine della determinazio ne a livello di species e per chiarire i rapporti filetici ai vari livelli tra i taxa dei due generi in studio. Viene sottolineato che gli isoenzimi e il modello di bandeggio del DNA macronucleare sono dei buoni marcatori per la determinazione delle specie, mentre gli isoenzimi, combinati alle caratteristiche morfologiche e morfogenetiche, possono dare un ottimo quadro dei rapporti filogenetici che intercorrono fra i mem bri del gruppo. Sono riportati poi i meccanismi di isolamento riproduttivo tra le due specie crip tiche: Stylonychia mytilus e Stylonychia lemnae. Sulla base dei dati raccolti viene avanzata l'ipotesi che, nelle aree dove le due specie si sovrappongono, esse mostrano maggior divergenza morfologica e meccanismi di isolamento rinforzato. Abstract - Several morphological and especially molecular characteristics of the species of the StylonychialOxytricha group are described. lt is discussed which value they may have for species determination and for the clarification of the phylogenetic relationship of lower and higher taxa. lt is concluded that the isoen zyme and the macronuclear DNA banding pattern are good characteristics for species determination. For the investigation of phylogenetic relationship the isoenzymes, com bined with morphology and morphogenesis of the cell, are good characteristics. -
Structure, Function and Evolution of Phosphoprotein P0 and Its Unique Insert in Tetrahymena Thermophila
University of Rhode Island DigitalCommons@URI Open Access Master's Theses 2014 STRUCTURE, FUNCTION AND EVOLUTION OF PHOSPHOPROTEIN P0 AND ITS UNIQUE INSERT IN TETRAHYMENA THERMOPHILA Giovanni Pagano University of Rhode Island, [email protected] Follow this and additional works at: https://digitalcommons.uri.edu/theses Recommended Citation Pagano, Giovanni, "STRUCTURE, FUNCTION AND EVOLUTION OF PHOSPHOPROTEIN P0 AND ITS UNIQUE INSERT IN TETRAHYMENA THERMOPHILA" (2014). Open Access Master's Theses. Paper 358. https://digitalcommons.uri.edu/theses/358 This Thesis is brought to you for free and open access by DigitalCommons@URI. It has been accepted for inclusion in Open Access Master's Theses by an authorized administrator of DigitalCommons@URI. For more information, please contact [email protected]. STRUCTURE, FUNCTION AND EVOLUTION OF PHOSPHOPROTEIN P0 AND ITS UNIQUE INSERT IN TETRAHYMENA THERMOPHILA BY GIOVANNI PAGANO A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN BIOLOGICAL AND ENVIRONMENTAL SCIENCES UNIVERSITY OF RHODE ISLAND 2014 MASTER OF SCIENCE OF GIOVANNI PAGANO APPROVED: Thesis Committee: Major Professor Linda A. Hufnagel Lenore M. Martin Roberta King Nasser H. Zawia DEAN OF THE GRADUATE SCHOOL UNIVERSITY OF RHODE ISLAND 2014 ABSTRACT Phosphoprotein P0 is a highly conserved ribosomal protein that forms the central scaffold of the large ribosomal subunit’s “stalk complex”, which is necessary for recruiting protein elongation factors to the ribosome. Evidence in the literature suggests that P0 may be involved in diseases such as malaria and systemic lupus erythematosus. We are interested in the possibility that the P0 of the “ciliated protozoa” Tetrahymena thermophila may be useful as a model system for vaccine research and drug development. -
Laura Landweber
Laura Landweber Department of Biochemistry and Molecular Biophysics (212) 305-3898 Department of Biological Sciences [email protected] th Columbia University 701 W 168 St, New York, NY 10032 FIELD OF SPECIALIZATION Molecular evolution and RNA-mediated epigenetic inheritance. EDUCATION Princeton University, A.B. in Molecular Biology, summa cum laude, June, 1989. Harvard University, M.A. in Biology, November, 1991. Harvard University, Ph.D. in Biology from the Department of Cellular and Developmental Biology, June, 1993. Topic of doctoral dissertation: “RNA editing and the evolution of mitochondrial DNA in kinetoplastid protozoa.” (Graduate advisors: Walter Gilbert and Richard Lewontin) POSITIONS HELD Columbia University, Professor of Biochemistry & Molecular Biophysics and of Biological Sciences, July 2016 – present. Princeton University, Professor, July 2009 – June 2016. Princeton University, Visiting Senior Research Scholar, July 2016 – present. Columbia University, Visiting Professor, May 2015– June 2016. Princeton University, Associate Professor with Tenure, July 2001 – 2009. California Institute of Technology, Visiting Associate in Chemical Engineering, Sept. 2001 – Jan. 2002. Princeton University, Assistant Professor of Ecology and Evolutionary Biology (EEB), 1994 – 2001. Princeton University, Associate Faculty, Department of Molecular Biology (Mol), 1994 – 2016. Harvard University, Junior Fellow of the Society of Fellows, 1993 – 1994. Massachusetts General Hospital, Assistant in Molecular Biology, 1993 – 1994 (sponsor: Jack Szostak). Harvard University, Parker Graduate Fellow in Cellular and Developmental Biology, 1992 – 1993. Harvard University, Teaching Fellow (year long tutorial) and Resident Tutor, Eliot House, 1991 – 1992. HONORS & AWARDS President, Society for Molecular Biology and Evolution, 2016 (SMBE Council 2016-2018). Division R Lecturer, American Society of Microbiology, 2014. Guggenheim Fellow, 2012. The New York Academy of Sciences, 2008 Blavatnik Award for Young Scientists. -
Insights Into Genome Diversity of Ciliates Using Single-Cell 'Omics
Smith ScholarWorks Biological Sciences: Faculty Publications Biological Sciences 8-2018 Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘Omics Maurer-Alcala X. Xyrus X. Maurer-Alcala University of Massachusetts Amherst Ying Yan Smith College Olivia A. Pilling Smith College Rob Knight University of California - San Diego Laura A. Katz Smith College, [email protected] Follow this and additional works at: https://scholarworks.smith.edu/bio_facpubs Part of the Biology Commons Recommended Citation Xyrus X. Maurer-Alcala, Maurer-Alcala X.; Yan, Ying; Pilling, Olivia A.; Knight, Rob; and Katz, Laura A., "Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘Omics" (2018). Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/60 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] GBE Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘Omics Xyrus X. Maurer-Alcala1,2,6,†,YingYan2,†, Olivia A. Pilling2, Rob Knight3,4,5, and Laura A. Katz1,2,* 1Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst 2Department of Biological Sciences, Smith College, Northampton, Massachusetts 3 Department of Pediatrics, University of California San Diego, San Diego Downloaded from https://academic.oup.com/gbe/article-abstract/10/8/1927/5045407 by guest on 27 January 2020 4Department of Computer Science and Engineering, University of California San Diego, San Diego 5Center for Microbiome Innovation, University of California San Diego, San Diego 6Present address: Institute of Cell Biology, University of Bern, Bern, Switzerland †These authors contributed equally to this work. -
Comparative Transcriptome Analyses During the Vegetative Cell Cycle in the Mono-Cellular Organism Pseudokeronopsis Erythrina (Alveolata, Ciliophora)
microorganisms Article Comparative Transcriptome Analyses during the Vegetative Cell Cycle in the Mono-Cellular Organism Pseudokeronopsis erythrina (Alveolata, Ciliophora) 1,2, 3,4, 5 1,2 1,2, Yiwei Xu y, Zhuo Shen y, Eleni Gentekaki , Jiahui Xu and Zhenzhen Yi * 1 Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China; [email protected] (Y.X.); [email protected] (J.X.) 2 Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China 3 Institute of Microbial Ecology & Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China; [email protected] 4 Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China 5 School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand; [email protected] * Correspondence: [email protected]; Tel.: +86-20-8521-0644 These authors contributed equally to this work. y Received: 30 October 2019; Accepted: 9 January 2020; Published: 12 January 2020 Abstract: Studies focusing on molecular mechanisms of cell cycles have been lagging in unicellular eukaryotes compared to other groups. Ciliates, a group of unicellular eukaryotes, have complex cell division cycles characterized by multiple events. During their vegetative cell cycle, ciliates undergo macronuclear amitosis, micronuclear mitosis, stomatogenesis and somatic cortex morphogenesis, and cytokinesis. Herein, we used the hypotrich ciliate Pseudokeronopsis erythrina, whose morphogenesis has been well studied, to examine molecular mechanisms of ciliate vegetative cell cycles. Single-cell transcriptomes of the growth (G) and cell division (D) stages were compared. The results showed that (i) More than 2051 significantly differentially expressed genes (DEGs) were detected, among which 1545 were up-regulated, while 256 were down-regulated at the D stage. -
A Database of Macronuclear and Micronuclear Genes in Spirotrichous Ciliates Andre R
D396–D398 Nucleic Acids Research, 2005, Vol. 33, Database issue doi:10.1093/nar/gki130 MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates Andre R. O. Cavalcanti, Thomas H. Clarke and Laura F. Landweber* Department of Ecology and Evolutionary Biology, Princeton University, NJ 08544, USA Received August 11, 2004; Revised and Accepted October 25, 2004 ABSTRACT can also be designated as scrambled or non-scrambled based on their location within a gene (7,8). Ciliated protozoa have two kinds of nuclei: Because most genes in spirotrichous ciliates undergo Macronuclei (MAC) and Micronuclei (MIC). In some several layers of rearrangement during macronuclear develop- ciliate classes, such as spirotrichs, most genes ment, these organisms provide ideal systems for studying the undergo several layers of DNA rearrangement during mechanisms of gene recombination and rearrangement. Cur- macronuclear development. Because of such pro- rently, several sequences are available for micronuclear and cesses, these organisms provide ideal systems for macronuclear versions of spirotrich genes. However, within studying mechanisms of recombination and gene available public databases, like GenBank, these sequences are rearrangement. Here, we describe a database that difficult to access as many of them have either incomplete or contains all spirotrich genes for which both MAC inconsistent annotation. Furthermore, many of the spirotrich and MIC versions are sequenced, with consistent macronuclear sequences are annotated under different unpub- lished guidelines, and for some micronuclear sequences, the annotation and easy access to all the features. An MDS, IES and pointer annotations are not available publicly. interface to query the database is available at http:// A further difficulty arises from the fact that the fields supported oxytricha.princeton.edu/dimorphism/database.htm.