Protists and the Wild, Wild West of Gene Expression
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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. -
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]. -
University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
A Parasite of Marine Rotifers: a New Lineage of Dinokaryotic Dinoflagellates (Dinophyceae)
Hindawi Publishing Corporation Journal of Marine Biology Volume 2015, Article ID 614609, 5 pages http://dx.doi.org/10.1155/2015/614609 Research Article A Parasite of Marine Rotifers: A New Lineage of Dinokaryotic Dinoflagellates (Dinophyceae) Fernando Gómez1 and Alf Skovgaard2 1 Laboratory of Plankton Systems, Oceanographic Institute, University of Sao˜ Paulo, Prac¸a do Oceanografico´ 191, Cidade Universitaria,´ 05508-900 Butanta,˜ SP, Brazil 2Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 7, 1870 Frederiksberg C, Denmark Correspondence should be addressed to Fernando Gomez;´ [email protected] Received 11 July 2015; Accepted 27 August 2015 Academic Editor: Gerardo R. Vasta Copyright © 2015 F. Gomez´ and A. Skovgaard. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Dinoflagellate infections have been reported for different protistan and animal hosts. We report, for the first time, the association between a dinoflagellate parasite and a rotifer host, tentatively Synchaeta sp. (Rotifera), collected from the port of Valencia, NW Mediterranean Sea. The rotifer contained a sporangium with 100–200 thecate dinospores that develop synchronically through palintomic sporogenesis. This undescribed dinoflagellate forms a new and divergent fast-evolved lineage that branches amongthe dinokaryotic dinoflagellates. 1. Introduction form independent lineages with no evident relation to other dinoflagellates [12]. In this study, we describe a new lineage of The alveolates (or Alveolata) are a major lineage of protists an undescribed parasitic dinoflagellate that largely diverged divided into three main phyla: ciliates, apicomplexans, and from other known dinoflagellates. -
|||||||III US005478731A United States Patent (19) 11 Patent Number: 5,478,731
|||||||III US005478731A United States Patent (19) 11 Patent Number: 5,478,731 Short 45 Date of Patent: Dec. 26,9 1995 54). POLYCOS VECTORS 56 References Cited 75) Inventor: Jay M. Short, Encinitas, Calif. PUBLICATIONS (73 Assignee: Stratagene, La Jolla, Calif. Ahmed (1989), Gene 75:315-321. 21 Appl. No.: 133,179 Evans et al. (1989), Gene 79:9-20. 22) PCT Filed: Apr. 10, 1992 Primary Examiner-Mindy B. Fleisher Assistant Examiner-Philip W. Carter 86 PCT No.: PCT/US92/03012 Attorney, Agent, or Firm-Albert P. Halluin; Pennie & S371 Date: Oct. 12, 1993 Edmonds S 102(e) Date: Oct. 12, 1993 57 ABSTRACT 87, PCT Pub. No.: WO92/18632 A bacteriophage packaging site-based vector system is describe that involves cloning vectors and methods for their PCT Pub. Date: Oct. 29, 1992 use in preparing multiple copy number bacteriophage librar O ies of cloned DNA. The vector is based on a DNA segment Related U.S. Application Data that comprises a nucleotide sequence defining a bacterioph 63 abandoned.continuationin-part of ser, No. 685.215,y Apr 12, 1991, ligationage packaging means usedsite locatedto concatamerize between twofragments termining of DNA 6 having compatible ligation means. Methods for preparing a (51) Int. Cl. ............................... C12N 1/21; C12N 7/01; concatameric DNA for packaging cloned DNA segments, C12N 15/10; C12N 15/11 and for packaging the concatamers to produce a library are 52 U.S. Cl. ................ 435/914; 435/1723; 435/252.33; also described. 435/235.1; 435/252.3; 536/23.1 58) Field of Search .............................. 435/91.32, 172.3, 435/320.1,914, 252.33, 252.3, 235.1; 536/23.1 18 Claims, 1 Drawing Sheet U.S. -
Phylogenomic Analysis of Balantidium Ctenopharyngodoni (Ciliophora, Litostomatea) Based on Single-Cell Transcriptome Sequencing
Parasite 24, 43 (2017) © Z. Sun et al., published by EDP Sciences, 2017 https://doi.org/10.1051/parasite/2017043 Available online at: www.parasite-journal.org RESEARCH ARTICLE Phylogenomic analysis of Balantidium ctenopharyngodoni (Ciliophora, Litostomatea) based on single-cell transcriptome sequencing Zongyi Sun1, Chuanqi Jiang2, Jinmei Feng3, Wentao Yang2, Ming Li1,2,*, and Wei Miao2,* 1 Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, PR China 2 Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan 430072, Hubei Province, PR China 3 Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, PR China Received 22 April 2017, Accepted 12 October 2017, Published online 14 November 2017 Abstract- - In this paper, we present transcriptome data for Balantidium ctenopharyngodoni Chen, 1955 collected from the hindgut of grass carp (Ctenopharyngodon idella). We evaluated sequence quality and de novo assembled a preliminary transcriptome, including 43.3 megabits and 119,141 transcripts. Then we obtained a final transcriptome, including 17.7 megabits and 35,560 transcripts, by removing contaminative and redundant sequences. Phylogenomic analysis based on a supermatrix with 132 genes comprising 53,873 amino acid residues and phylogenetic analysis based on SSU rDNA of 27 species were carried out herein to reveal the evolutionary relationships among six ciliate groups: Colpodea, Oligohymenophorea, Litostomatea, Spirotrichea, Hetero- trichea and Protocruziida. The topologies of both phylogenomic and phylogenetic trees are discussed in this paper. In addition, our results suggest that single-cell sequencing is a sound method of obtaining sufficient omics data for phylogenomic analysis, which is a good choice for uncultivable ciliates. -
Lessons from Nature: Microrna-Based Shrna Libraries
PERSPECTIVE Lessons from Nature: microRNA-based shRNA libraries methods Kenneth Chang1, Stephen J Elledge2 & Gregory J Hannon1 Loss-of-function genetics has proven essential for interrogating the functions of genes .com/nature e and for probing their roles within the complex circuitry of biological pathways. In .natur many systems, technologies allowing the use of such approaches were lacking before w the discovery of RNA interference (RNAi). We have constructed first-generation short hairpin RNA (shRNA) libraries modeled after precursor microRNAs (miRNAs) and second- http://ww generation libraries modeled after primary miRNA transcripts (the Hannon-Elledge oup libraries). These libraries were arrayed, sequence-verified, and cover a substantial portion r G of all known and predicted genes in the human and mouse genomes. Comparison of first- and second-generation libraries indicates that RNAi triggers that enter the RNAi pathway lishing through a more natural route yield more effective silencing. These large-scale resources b Pu are functionally versatile, as they can be used in transient and stable studies, and for constitutive or inducible silencing. Library cassettes can be easily shuttled into vectors Nature that contain different promoters and/or that provide different modes of viral delivery. 6 200 © RNAi is an evolutionarily conserved, sequence-specific than a decade elapsed between the discovery of the first gene-silencing mechanism that is induced by dsRNA. miRNA, Caenorhabditis elegans lin-4 (refs. 11,12) and Each dsRNA silencing trigger is processed into 21–25 bp the achievement of at least a superficial understanding dsRNAs called small interfering RNAs (siRNAs)1–3 by of the biosynthesis, processing and mode of action of Dicer, a ribonuclease III family (RNase III) enzyme4. -
Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site Madhuri Jonnalagadda Western Kentucky University
Western Kentucky University TopSCHOLAR® Masters Theses & Specialist Projects Graduate School 12-2008 Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site Madhuri Jonnalagadda Western Kentucky University Follow this and additional works at: http://digitalcommons.wku.edu/theses Part of the Cell and Developmental Biology Commons, Genetics Commons, Immunopathology Commons, and the Molecular Genetics Commons Recommended Citation Jonnalagadda, Madhuri, "Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site" (2008). Masters Theses & Specialist Projects. Paper 42. http://digitalcommons.wku.edu/theses/42 This Thesis is brought to you for free and open access by TopSCHOLAR®. It has been accepted for inclusion in Masters Theses & Specialist Projects by an authorized administrator of TopSCHOLAR®. For more information, please contact [email protected]. SITE DIRECTED MUTAGENESIS OF BACTERIOPHAGE HK639 AND IDENTIFICATION OF ITS INTEGRATION SITE A Thesis presented to The faculty of the Department of Biology Western Kentucky University Bowling Green, Kentucky. In Partial Fulfillment Of the Requirement for the Degree Master of Science By Madhuri Jonnalagadda December, 2008 Site Directed Mutagenesis of Bacteriophage HK639 and Identification of its Integration Site Date Recommended 12/4/08 Dr.Rodney A. King Director of Thesis __Dr.Jeffery Marcus Dr. Sigrid Jacobshagen _____________________________________ Dean, Graduate Studies and Research Date DEDICATION I would like to dedicate my thesis to my dear father Dr. J. Padmanabha Rao, my mother, Dr.V. Lakshmi, my sister Dr. J. Sushma for their support and encouragement. i ACKNOWLEDGEMENTS I wish to express my heartfelt gratitude to my graduate committee in the Department of Biology, Western Kentucky University. Primarily, I am thankful to my advisor, Dr. -
MORC1 Represses Transposable Elements in the Mouse Male Germline
ARTICLE Received 12 Sep 2014 | Accepted 7 Nov 2014 | Published 12 Dec 2014 DOI: 10.1038/ncomms6795 OPEN MORC1 represses transposable elements in the mouse male germline William A. Pastor1,*, Hume Stroud1,*,w, Kevin Nee1, Wanlu Liu1, Dubravka Pezic2, Sergei Manakov2, Serena A. Lee1, Guillaume Moissiard1, Natasha Zamudio3,De´borah Bourc’his3, Alexei A. Aravin2, Amander T. Clark1,4 & Steven E. Jacobsen1,4,5 The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation. 1 Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, 4028 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, California 90095, USA. 2 Division of Biology and Biochemical Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, California 91125, USA. 3 Unite´ de ge´ne´tique et biologie du de´veloppement, Instititute Curie, CNRS UMR3215, INSERM U934, Paris 75005, France. -
Genetic Diversity and Habitats of Two Enigmatic Marine Alveolate Lineages
AQUATIC MICROBIAL ECOLOGY Vol. 42: 277–291, 2006 Published March 29 Aquat Microb Ecol Genetic diversity and habitats of two enigmatic marine alveolate lineages Agnès Groisillier1, Ramon Massana2, Klaus Valentin3, Daniel Vaulot1, Laure Guillou1,* 1Station Biologique, UMR 7144, CNRS, and Université Pierre & Marie Curie, BP74, 29682 Roscoff Cedex, France 2Department de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CMIMA, CSIC. Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain 3Alfred Wegener Institute for Polar Research, Am Handelshafen 12, 27570 Bremerhaven, Germany ABSTRACT: Systematic sequencing of environmental SSU rDNA genes amplified from different marine ecosystems has uncovered novel eukaryotic lineages, in particular within the alveolate and stramenopile radiations. The ecological and geographic distribution of 2 novel alveolate lineages (called Group I and II in previous papers) is inferred from the analysis of 62 different environmental clone libraries from freshwater and marine habitats. These 2 lineages have been, up to now, retrieved exclusively from marine ecosystems, including oceanic and coastal waters, sediments, hydrothermal vents, and perma- nent anoxic deep waters and usually represent the most abundant eukaryotic lineages in environmen- tal genetic libraries. While Group I is only composed of environmental sequences (118 clones), Group II contains, besides environmental sequences (158 clones), sequences from described genera (8) (Hema- todinium and Amoebophrya) that belong to the Syndiniales, an atypical order of dinoflagellates exclu- sively composed of marine parasites. This suggests that Group II could correspond to Syndiniales, al- though this should be confirmed in the future by examining the morphology of cells from Group II. Group II appears to be abundant in coastal and oceanic ecosystems, whereas permanent anoxic waters and hy- drothermal ecosystems are usually dominated by Group I. -
Scrippsiella Trochoidea (F.Stein) A.R.Loebl
MOLECULAR DIVERSITY AND PHYLOGENY OF THE CALCAREOUS DINOPHYTES (THORACOSPHAERACEAE, PERIDINIALES) Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Fakultät für Biologie der Ludwig-Maximilians-Universität München zur Begutachtung vorgelegt von Sylvia Söhner München, im Februar 2013 Erster Gutachter: PD Dr. Marc Gottschling Zweiter Gutachter: Prof. Dr. Susanne Renner Tag der mündlichen Prüfung: 06. Juni 2013 “IF THERE IS LIFE ON MARS, IT MAY BE DISAPPOINTINGLY ORDINARY COMPARED TO SOME BIZARRE EARTHLINGS.” Geoff McFadden 1999, NATURE 1 !"#$%&'(&)'*!%*!+! +"!,-"!'-.&/%)$"-"!0'* 111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 2& ")3*'4$%/5%6%*!+1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 7! 8,#$0)"!0'*+&9&6"*,+)-08!+ 111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 :! 5%*%-"$&0*!-'/,)!0'* 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 ;! "#$!%"&'(!)*+&,!-!"#$!'./+,#(0$1$!2! './+,#(0$1$!-!3+*,#+4+).014!1/'!3+4$0&41*!041%%.5.01".+/! 67! './+,#(0$1$!-!/&"*.".+/!1/'!4.5$%"(4$! 68! ./!5+0&%!-!"#$!"#+*10+%,#1$*10$1$! 69! "#+*10+%,#1$*10$1$!-!5+%%.4!1/'!$:"1/"!'.;$*%."(! 6<! 3+4$0&41*!,#(4+)$/(!-!0#144$/)$!1/'!0#1/0$! 6=! 1.3%!+5!"#$!"#$%.%! 62! /0+),++0'* 1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111<=! -
The Roles of Moron Genes in the Escherichia Coli Enterobacteria Phage Phi-80
THE ROLES OF MORON GENES IN THE ESCHERICHIA COLI ENTEROBACTERIA PHAGE PHI-80 Yury V. Ivanov A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2012 Committee: Ray A. Larsen, Advisor Craig L. Zirbel Graduate Faculty Representative Vipa Phuntumart Scott O. Rogers George S. Bullerjahn © 2012 Yury Ivanov All Rights Reserved iii ABSTRACT Ray Larsen, Advisor The TonB system couples cytoplasmic membrane-derived proton motive force energy to drive ferric siderophore transport across the outer membrane of Gram-negative bacteria. While much effort has focused on this process, how energy is harnessed to provide for transport of ligands remains unknown. Several bacterial viruses (“phage”) are known to require the TonB system to irreversibly adsorb (i.e., establish infection) in the model organism Escherichia coli. One such phage is φ80, a “cousin” of the model temperate phage λ. Determining how φ80 is using the TonB system for infection should provide novel insights to the mechanisms of TonB-dependent processes. It had long been known that recombination between λ and φ80 results in a λ-like phage for whom TonB is now required; and this recombination involved the λ J gene, which encodes the tail-spike protein required for irreversible adsorption of λ to E. coli. Thus, we suspected that a φ80 homologue of the λ J gene product was responsible for the TonB dependence of φ80. While φ80 has long served as a tool for assaying TonB activity, it has not received the scrutiny afforded λ.