Cytokinins in Dictyostelia – a Unique Model for Studying the Functions of Signaling Agents from Species to Kingdoms Megan Aoki, R
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Protozoologica Special Issue: Protists in Soil Processes
Acta Protozool. (2012) 51: 201–208 http://www.eko.uj.edu.pl/ap ActA doi:10.4467/16890027AP.12.016.0762 Protozoologica Special issue: Protists in Soil Processes Review paper Ecology of Soil Eumycetozoans Steven L. STEPHENSON1 and Alan FEEST2 1Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA; 2Institute of Advanced Studies, University of Bristol and Ecosulis ltd., Newton St Loe, Bath, United Kingdom Abstract. Eumycetozoans, commonly referred to as slime moulds, are common to abundant organisms in soils. Three groups of slime moulds (myxogastrids, dictyostelids and protostelids) are recognized, and the first two of these are among the most important bacterivores in the soil microhabitat. The purpose of this paper is first to provide a brief description of all three groups and then to review what is known about their distribution and ecology in soils. Key words: Amoebae, bacterivores, dictyostelids, myxogastrids, protostelids. INTRODUCTION that they are amoebozoans and not fungi (Bapteste et al. 2002, Yoon et al. 2008, Baudalf 2008). Three groups of slime moulds (myxogastrids, dic- One of the idiosyncratic branches of the eukary- tyostelids and protostelids) are recognized (Olive 1970, otic tree of life consists of an assemblage of amoe- 1975). Members of the three groups exhibit consider- boid protists referred to as the supergroup Amoebozoa able diversity in the type of aerial spore-bearing struc- (Fiore-Donno et al. 2010). The most diverse members tures produced, which can range from exceedingly of the Amoebozoa are the eumycetozoans, common- small examples (most protostelids) with only a single ly referred to as slime moulds. Since their discovery, spore to the very largest examples (certain myxogas- slime moulds have been variously classified as plants, trids) that contain many millions of spores. -
Comparative Genomics of the Social Amoebae Dictyostelium Discoideum
Sucgang et al. Genome Biology 2011, 12:R20 http://genomebiology.com/2011/12/2/R20 RESEARCH Open Access Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Richard Sucgang1†, Alan Kuo2†, Xiangjun Tian3†, William Salerno1†, Anup Parikh4, Christa L Feasley5, Eileen Dalin2, Hank Tu2, Eryong Huang4, Kerrie Barry2, Erika Lindquist2, Harris Shapiro2, David Bruce2, Jeremy Schmutz2, Asaf Salamov2, Petra Fey6, Pascale Gaudet6, Christophe Anjard7, M Madan Babu8, Siddhartha Basu6, Yulia Bushmanova6, Hanke van der Wel5, Mariko Katoh-Kurasawa4, Christopher Dinh1, Pedro M Coutinho9, Tamao Saito10, Marek Elias11, Pauline Schaap12, Robert R Kay8, Bernard Henrissat9, Ludwig Eichinger13, Francisco Rivero14, Nicholas H Putnam3, Christopher M West5, William F Loomis7, Rex L Chisholm6, Gad Shaulsky3,4, Joan E Strassmann3, David C Queller3, Adam Kuspa1,3,4* and Igor V Grigoriev2 Abstract Background: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. Results: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. -
Dictyostelid Cellular Slime Molds from Caves
John C. Landolt, Steven L. Stephenson, and Michael E. Slay – Dictyostelid cellular slime molds from caves. Journal of Cave and Karst Studies, v. 68, no. 1, p. 22–26. DICTYOSTELID CELLULAR SLIME MOLDS FROM CAVES JOHN C. LANDOLT Department of Biology, Shepherd University, Shepherdstown, WV 2544 USA [email protected] STEVEN L. STEPHENSON Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701 USA [email protected] MICHAEL E. SLAY The Nature Conservancy, 601 North University Avenue, Little Rock, AR 72205 USA [email protected] Dictyostelid cellular slime molds associated with caves in Alabama, Arkansas, Indiana, Missouri, New York, Oklahoma, South Carolina, Tennessee, West Virginia, Puerto Rico, and San Salvador in the Bahamas were investigated during the period of 1990–2005. Samples of soil material collected from more than 100 caves were examined using standard methods for isolating dictyostelids. At least 17 species were recovered, along with a number of isolates that could not be identified completely. Four cos- mopolitan species (Dictyostelium sphaerocephalum, D. mucoroides, D. giganteum and Polysphondylium violaceum) and one species (D. rosarium) with a more restricted distribution were each recorded from more than 25 different caves, but three other species were present in more than 20 caves. The data gen- erated in the present study were supplemented with all known published and unpublished records of dic- tyostelids from caves in an effort to summarize what is known about their occurrence in this habitat. INTRODUCTION also occur on dung and were once thought to be primarily coprophilous (Raper, 1984). However, perhaps the most Dictyostelid cellular slime molds (dictyostelids) are single- unusual microhabitat for dictyostelids is the soil material celled, eukaryotic, phagotrophic bacterivores usually present found in caves. -
What Substrate Cultures Can Reveal: Myxomycetes and Myxomycete-Like Organisms from the Sultanate of Oman
Mycosphere 6 (3): 356–384(2015) ISSN 2077 7019 www.mycosphere.org Article Mycosphere Copyright © 2015 Online Edition Doi 10.5943/mycosphere/6/3/11 What substrate cultures can reveal: Myxomycetes and myxomycete-like organisms from the Sultanate of Oman Schnittler M1, Novozhilov YK2, Shadwick JDL3, Spiegel FW3, García-Carvajal E4, König P1 1Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Soldmannstr. 15, D-17487 Greifswald, Germany 2V.L. Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov St. 2, 197376 St. Petersburg, Russia 3University of Arkansas, Department of Biological Sciences, SCEN 601, 1 University of Arkansas, Fayetteville, AR 72701, USA 4Royal Botanic Garden (CSIC), Plaza de Murillo, 2, Madrid, E-28014, Spain Schnittler M, Novozhilov YK, Shadwick JDL, Spiegel FW, García-Carvajal E, König P 2015 – What substrate cultures can reveal: Myxomycetes and myxomycete-like organisms from the Sultanate of Oman. Mycosphere 6(3), 356–384, doi 10.5943/mycosphere/6/3/11 Abstract A total of 299 substrate samples collected throughout the Sultanate of Oman were analyzed for myxomycetes and myxomycete-like organisms (MMLO) with a combined approach, preparing one moist chamber culture and one agar culture for each sample. We recovered 8 forms of Myxobacteria, 2 sorocarpic amoebae (Acrasids), 19 known and 6 unknown taxa of protostelioid amoebae (Protostelids), and 50 species of Myxomycetes. Moist chambers and agar cultures completed each other. No method alone can detect the whole diversity of myxomycetes as the most species-rich group of MMLO. A significant overlap between the two methods was observed only for Myxobacteria and some myxomycetes with small sporocarps. -
(12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall Et Al
USOO9689046B2 (12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall et al. (45) Date of Patent: Jun. 27, 2017 (54) SYSTEM AND METHODS FOR THE FOREIGN PATENT DOCUMENTS DETECTION OF MULTIPLE CHEMICAL WO O125472 A1 4/2001 COMPOUNDS WO O169245 A2 9, 2001 (71) Applicants: Robert Matthew Mayall, Calgary (CA); Emily Candice Hicks, Calgary OTHER PUBLICATIONS (CA); Margaret Mary-Flora Bebeselea, A. et al., “Electrochemical Degradation and Determina Renaud-Young, Calgary (CA); David tion of 4-Nitrophenol Using Multiple Pulsed Amperometry at Christopher Lloyd, Calgary (CA); Lisa Graphite Based Electrodes', Chem. Bull. “Politehnica” Univ. Kara Oberding, Calgary (CA); Iain (Timisoara), vol. 53(67), 1-2, 2008. Fraser Scotney George, Calgary (CA) Ben-Yoav. H. et al., “A whole cell electrochemical biosensor for water genotoxicity bio-detection”. Electrochimica Acta, 2009, 54(25), 6113-6118. (72) Inventors: Robert Matthew Mayall, Calgary Biran, I. et al., “On-line monitoring of gene expression'. Microbi (CA); Emily Candice Hicks, Calgary ology (Reading, England), 1999, 145 (Pt 8), 2129-2133. (CA); Margaret Mary-Flora Da Silva, P.S. et al., “Electrochemical Behavior of Hydroquinone Renaud-Young, Calgary (CA); David and Catechol at a Silsesquioxane-Modified Carbon Paste Elec trode'. J. Braz. Chem. Soc., vol. 24, No. 4, 695-699, 2013. Christopher Lloyd, Calgary (CA); Lisa Enache, T. A. & Oliveira-Brett, A. M., "Phenol and Para-Substituted Kara Oberding, Calgary (CA); Iain Phenols Electrochemical Oxidation Pathways”, Journal of Fraser Scotney George, Calgary (CA) Electroanalytical Chemistry, 2011, 1-35. Etesami, M. et al., “Electrooxidation of hydroquinone on simply prepared Au-Pt bimetallic nanoparticles'. Science China, Chem (73) Assignee: FREDSENSE TECHNOLOGIES istry, vol. -
This Thesis Has Been Submitted in Fulfilment of the Requirements for a Postgraduate Degree (E.G
This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Protein secretion and encystation in Acanthamoeba Alvaro de Obeso Fernández del Valle Doctor of Philosophy The University of Edinburgh 2018 Abstract Free-living amoebae (FLA) are protists of ubiquitous distribution characterised by their changing morphology and their crawling movements. They have no common phylogenetic origin but can be found in most protist evolutionary branches. Acanthamoeba is a common FLA that can be found worldwide and is capable of infecting humans. The main disease is a life altering infection of the cornea named Acanthamoeba keratitis. Additionally, Acanthamoeba has a close relationship to bacteria. Acanthamoeba feeds on bacteria. At the same time, some bacteria have adapted to survive inside Acanthamoeba and use it as transport or protection to increase survival. When conditions are adverse, Acanthamoeba is capable of differentiating into a protective cyst. -
Evolution of Developmental Signalling in Dictyostelid Social Amoebas
Available online at www.sciencedirect.com ScienceDirect Evolution of developmental signalling in Dictyostelid social amoebas Pauline Schaap Dictyostelia represent a tractable system to resolve the The developmental programme has been most thoroughly evolution of cell-type specialization, with some taxa studied in Dictyostelium discoideum, a robust laboratory differentiating into spores only, and other taxa with additionally model that uses cAMP as a chemoattractant for aggrega- one or up to four somatic cell types. One of the latter forms, tion. The development of genetic transformation, gene Dictyostelium discoideum, is a popular model system for cell knock-out, targeted mutagenesis and high resolution im- biology and developmental biology with key signalling aging techniques in the ’80 and ’90s, make it the organism pathways controlling cell-specialization being resolved of choice for research into fundamental problems in cell recently. For the most dominant pathways, evolutionary origins biology and developmental biology [3]. More recently, it were retraced to a stress response in the unicellular ancestor, has also gained popularity for studies into social conflict while modifications in the ancestral pathway were associated [4], prey–predator interactions [5] and evolution of multi- with acquisition of multicellular complexity. This review cellular complexity [6]. In this review, I will first describe summarizes our current understanding of developmental the developmental signalling mechanisms that control the signalling in D. discoideum and its evolution. life cycle of D. discoideum and next summarize studies aimed to elucidate in which order specific aspects of Address complexity evolved, and how this was associated with School of Life Sciences, University of Dundee, DD15EH Dundee, UK innovations in intercellular communication. -
The Characterization of Map Kinase Regulation of Cyclic
THE CHARACTERIZATION OF MAP KINASE REGULATION OF CYCLIC AMP SIGNALING IN DICTYOSTELIUM By NIRAKAR ADHIKARI Bachelor of Science in Microbiology Tribhuvan University Kirtipur, Nepal 2006 Master of Science in Microbiology Tribhuvan University Kirtipur, Nepal 2008 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY December, 2018 THE CHARATERIZATION OF MAP KINASE REGULATION OF CYCLIC AMP SIGNALING IN DICTYOSTELIUM Dissertation Approved: Dr. Jeffrey A Hadwiger Dissertation Adviser Dr. Rolf Prade Dr. Robert L. Burnap Dr. Erika Lutter Dr. Ming Yang ii ACKNOWLEDGEMENTS I would like to thank my advisor Dr. Jeffrey Hadwiger for his invaluable mentorship during my stay in his laboratory as a PhD student. I would like to acknowledge my other PhD committee members for their guidance in research. I am thankful to my departmental colleagues, staffs and faculty members at Oklahoma State University. I am grateful towards my parents for their unconditional love and guidance. I would like to express gratitude to my wife, Sabita, for incredible support during my PhD studies. Finally, I would like to thank my brother, Diwakar, for his encouragement to pursue my PhD study. iii Acknowledgements reflect the views of the author and are not endorsed by committee members or Oklahoma State University. Name: NIRAKAR ADHIKARI Date of Degree: DECEMBER, 2018 Title of Study: THE CHARATERIZATION OF MAP KINASE REGULATION OF CYCLIC AMP SIGNALING IN DICTYOSTELIUM Major Field: MICROBIOLOGY AND CELL AND MOLECULAR BIOLOGY Abstract: cAMP signaling plays a critical role in cell development and chemotaxis of Dictyostelium discoideum. -
Phylogeny-Wide Analysis of Social Amoeba Genomes Highlights Ancient Origins for Complex Intercellular Communication
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Research Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication Andrew J. Heidel,1 Hajara M. Lawal,2 Marius Felder,1 Christina Schilde,2 Nicholas R. Helps,2 Budi Tunggal,3 Francisco Rivero,4 Uwe John,5 Michael Schleicher,6 Ludwig Eichinger,3 Matthias Platzer,1 Angelika A. Noegel,3 Pauline Schaap,2,8 and Gernot Glo¨ckner1,3,7,8 1Leibniz Institute for Age Research–Fritz Lipmann Institute, D-07745 Jena, Germany; 2College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; 3Institute of Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, D-50931 Cologne, Germany; 4Hull York Medical School and Department of Biological Sciences, University of Hull, Hull HU6 7RX, United Kingdom; 5Alfred Wegener Institute, D-27570 Bremerhaven, Germany; 6Institute for Anatomy and Cell Biology, and Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-University Munich, D-80336 Munich, Germany; 7Leibniz-Institute of Freshwater Ecology and Inland Fisheries, D-12587 Berlin, Germany Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced the genomes of Dictyostelium fasciculatum (DF) and Polysphondylium pallidum (PP), which represent the early diverging groups 1 and 2, respectively. -
Dictyostelium, the Social Amoeba Joan E. Strassmann1, Sandra L
Dictyostelium, the Social Amoeba Joan E. Strassmann1, Sandra L. Baldauf2 1Washington University in St. Louis MO USA 2Uppsala University, Uppsala Sweden [email protected] [email protected] Glossary entries: Altruism: A behavior that is costly to the performer’s fitness, but beneficial to others. Greenbeard gene: A gene that affects copies of itself via three effects: production of trait, recognition of the trait in others, and differential treatment based on that trait. Sometimes not considered as part of kin selection because benefits go not to relatives but to actual bearers of the gene. Mutualism: An interaction that benefits both parties. Can be used for interactions within and between species. Social amoeba: A eukaryote in the Dictyostelia, a kingdom in the Amoebozoa. Social evolution: Evolution of traits of organisms that have fitness consequences for others of the same species, in particular those traits that may benefit others at a cost to oneself. Evolution of social interactions. Sociogenomics: Study of the genetic and genomic foundations of social behaviors. Symbiosis: Living together in close association in ways that may be beneficial or harmful for either party. Keywords Altruism Dictyostelium Greenbeard gene Mutualism Protist Social amoeba Social evolution Sociogenomics Symbiosis Abstract: The Dictyostelia present a splendid opportunity for the study of mutualism, sociality and genetic conflicts of interest. These amoebae aggregate upon starvation to form cooperative multicellular structures in which some formerly independent cells die to form a stalk. This serves to lift the other cells above the substrate where their chances of dispersal are greatly enhanced, for example by sticking to passing invertebrates. -
Genomics of Sorocarpic Amoebae
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1516 Genomics of Sorocarpic Amoebae SANEA SHEIKH ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-554-9913-6 UPPSALA urn:nbn:se:uu:diva-320432 2017 Dissertation presented at Uppsala University to be publicly examined in Lindhalsalen, Norbyvägen 18D, Uppsala, Friday, 9 June 2017 at 09:00 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Assistant professor Matthew W. Brown (Department of Biological Sciences, Mississippi State University, USA). Abstract Sheikh, S. 2017. Genomics of Sorocarpic Amoebae. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1516. 45 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9913-6. Sorocarpy is the aggregation of unicellular organisms to form multicellular fruiting bodies (sorocarps). This thesis is about the two best-known groups of sorocarpic amoebae, Dictyostelids and Acrasids. Paper I describes assembly and analysis of a multigene dataset to identify the root of the dictyostelid tree. Phylogenetic analyses of 213 genes (conserved in all sequenced dictyostelid genomes and an outgroup) place the root between Groups 1+2 and 3+4 (now: Cavenderiaceae + Acytosteliaceae and Raperosteliaceae + Dictyosteliaceae). Resolution of the dictyostelid root made it possible to proceed with a major taxonomic revision of the group. Paper II focuses on the taxonomic revision of Dictyostelia based on molecular phylogeny and SSU ribosomal RNA sequence signatures. The two major divisions were treated at the rank of order as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders were given the rank of family. -
Genome-Wide Transcriptome and Proteome Analysis on Different Developmental Stages of Cordyceps Militaris
Genome-Wide Transcriptome and Proteome Analysis on Different Developmental Stages of Cordyceps militaris Yalin Yin1, Guojun Yu1, Yijie Chen1, Shuai Jiang1, Man Wang1, Yanxia Jin1, Xianqing Lan1, Yi Liang1,2, Hui Sun1,3,4* 1 State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China, 2 Department of Clinical Immunology, Guangdong Medical College, Dongguan, People’s Republic of China, 3 Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, People’s Republic of China, 4 Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan, People’s Republic of China Abstract Background: Cordyceps militaris, an ascomycete caterpillar fungus, has been used as a traditional Chinese medicine for many years owing to its anticancer and immunomodulatory activities. Currently, artificial culturing of this beneficial fungus has been widely used and can meet the market, but systematic molecular studies on the developmental stages of cultured C. militaris at transcriptional and translational levels have not been determined. Methodology/Principal Findings: We utilized high-throughput Illumina sequencing to obtain the transcriptomes of C. militaris mycelium and fruiting body. All clean reads were mapped to C. militaris genome and most of the reads showed perfect coverage. Alternative splicing and novel transcripts were predicted to enrich the database. Gene expression analysis revealed that 2,113 genes were up-regulated in mycelium and 599 in fruiting body. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to analyze the genes with expression differences. Moreover, the putative cordycepin metabolism difference between different developmental stages was studied.