Platyhelminthes, Tricladida, Paludicola)
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Metabarcoding in the Abyss: Uncovering Deep-Sea Biodiversity Through Environmental
Metabarcoding in the abyss : uncovering deep-sea biodiversity through environmental DNA Miriam Isabelle Brandt To cite this version: Miriam Isabelle Brandt. Metabarcoding in the abyss : uncovering deep-sea biodiversity through environmental DNA. Agricultural sciences. Université Montpellier, 2020. English. NNT : 2020MONTG033. tel-03197842 HAL Id: tel-03197842 https://tel.archives-ouvertes.fr/tel-03197842 Submitted on 14 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En Sciences de l'Évolution et de la Biodiversité École doctorale GAIA Unité mixte de recherche MARBEC Pourquoi Pas les Abysses ? L’ADN environnemental pour l’étude de la biodiversité des grands fonds marins Metabarcoding in the abyss: uncovering deep - sea biodiversity through environmental DNA Présentée par Miriam Isabelle BRANDT Le 10 juillet 2020 Sous la direction de Sophie ARNAUD-HAOND et Daniela ZEPPILLI Devant le jury composé de Sofie DERYCKE, Senior researcher/Professeur rang A, ILVO, Belgique Rapporteur -
The Effect of Caffeine and Ethanol on Flatworm Regeneration
East Tennessee State University Digital Commons @ East Tennessee State University Electronic Theses and Dissertations Student Works 8-2007 The ffecE t of Caffeine nda Ethanol on Flatworm Regeneration. Erica Leighanne Collins East Tennessee State University Follow this and additional works at: https://dc.etsu.edu/etd Part of the Chemical and Pharmacologic Phenomena Commons Recommended Citation Collins, Erica Leighanne, "The Effect of Caffeine nda Ethanol on Flatworm Regeneration." (2007). Electronic Theses and Dissertations. Paper 2028. https://dc.etsu.edu/etd/2028 This Thesis - Open Access is brought to you for free and open access by the Student Works at Digital Commons @ East Tennessee State University. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Digital Commons @ East Tennessee State University. For more information, please contact [email protected]. The Effect of Caffeine and Ethanol on Flatworm Regeneration ____________________ A thesis presented to the faculty of the Department of Biological Sciences East Tennessee State University In partial fulfillment of the requirements for the degree Master of Science in Biology ____________________ by Erica Leighanne Collins August 2007 ____________________ Dr. J. Leonard Robertson, Chair Dr. Thomas F. Laughlin Dr. Kevin Breuel Keywords: Regeneration, Planarian, Dugesia tigrina, Flatworms, Caffeine, Ethanol ABSTRACT The Effect of Caffeine and Ethanol on Flatworm Regeneration by Erica Leighanne Collins Flatworms, or planarian, have a high potential for regeneration and have been used as a model to investigate regeneration and stem cell biology for over a century. Chemicals, temperature, and seasonal factors can influence planarian regeneration. Caffeine and ethanol are two widely used drugs and their effect on flatworm regeneration was evaluated in this experiment. -
Platyhelminthes) at the Queensland Museum B.M
VOLUME 53 ME M OIRS OF THE QUEENSLAND MUSEU M BRIS B ANE 30 NOVE mb ER 2007 © Queensland Museum PO Box 3300, South Brisbane 4101, Australia Phone 06 7 3840 7555 Fax 06 7 3846 1226 Email [email protected] Website www.qm.qld.gov.au National Library of Australia card number ISSN 0079-8835 Volume 53 is complete in one part. NOTE Papers published in this volume and in all previous volumes of the Memoirs of the Queensland Museum may be reproduced for scientific research, individual study or other educational purposes. Properly acknowledged quotations may be made but queries regarding the republication of any papers should be addressed to the Editor in Chief. Copies of the journal can be purchased from the Queensland Museum Shop. A Guide to Authors is displayed at the Queensland Museum web site www.qm.qld.gov.au/organisation/publications/memoirs/guidetoauthors.pdf A Queensland Government Project Typeset at the Queensland Museum THE STUDY OF TURBELLARIANS (PLATYHELMINTHES) AT THE QUEENSLAND MUSEUM B.M. ANGUS Angus, B.M. 2007 11 30: The study of turbellarians (Platyhelminthes) at the Queensland Museum. Memoirs of the Queensland Museum 53(1): 157-185. Brisbane. ISSN 0079-8835. Turbellarian research was largely ignored in Australia, apart from some early interest at the turn of the 19th century. The modern study of this mostly free-living branch of the phylum Platyhelminthes was led by Lester R.G. Cannon of the Queensland Museum. A background to the study of turbellarians is given particularly as it relates to the efforts of Cannon on symbiotic fauna, and his encouragement of visiting specialists and students. -
The Genome of Schmidtea Mediterranea and the Evolution Of
OPEN ArtICLE doi:10.1038/nature25473 The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms Markus Alexander Grohme1*, Siegfried Schloissnig2*, Andrei Rozanski1, Martin Pippel2, George Robert Young3, Sylke Winkler1, Holger Brandl1, Ian Henry1, Andreas Dahl4, Sean Powell2, Michael Hiller1,5, Eugene Myers1 & Jochen Christian Rink1 The planarian Schmidtea mediterranea is an important model for stem cell research and regeneration, but adequate genome resources for this species have been lacking. Here we report a highly contiguous genome assembly of S. mediterranea, using long-read sequencing and a de novo assembler (MARVEL) enhanced for low-complexity reads. The S. mediterranea genome is highly polymorphic and repetitive, and harbours a novel class of giant retroelements. Furthermore, the genome assembly lacks a number of highly conserved genes, including critical components of the mitotic spindle assembly checkpoint, but planarians maintain checkpoint function. Our genome assembly provides a key model system resource that will be useful for studying regeneration and the evolutionary plasticity of core cell biological mechanisms. Rapid regeneration from tiny pieces of tissue makes planarians a prime De novo long read assembly of the planarian genome model system for regeneration. Abundant adult pluripotent stem cells, In preparation for genome sequencing, we inbred the sexual strain termed neoblasts, power regeneration and the continuous turnover of S. mediterranea (Fig. 1a) for more than 17 successive sib- mating of all cell types1–3, and transplantation of a single neoblast can rescue generations in the hope of decreasing heterozygosity. We also developed a lethally irradiated animal4. Planarians therefore also constitute a a new DNA isolation protocol that meets the purity and high molecular prime model system for stem cell pluripotency and its evolutionary weight requirements of PacBio long-read sequencing12 (Extended Data underpinnings5. -
Spermatogenesis and Spermatozoon Ultrastructure in Dugesia Sicula Lepori, 1948 (Platyhelminthes, Tricladida, Paludicola)
Belg. J. Zool., 140 (Suppl.): 118-125 July 2010 Spermatogenesis and spermatozoon ultrastructure in Dugesia sicula Lepori, 1948 (Platyhelminthes, Tricladida, Paludicola) Mohamed Charni1, Aouatef Ben Ammar2, Mohamed Habib Jaafoura2, Fathia Zghal1 and Saïda Tekaya1 1Université de Tunis El-Manar, Faculté des Sciences, Campus Universitaire, 2092 El-Manar Tunis, Tunisie. 2 Service commun pour la recherche en microscopie électronique à transmission, Faculté de Médecine de Tunis, 15, Rue Djebel Lakhdar La Rabta, 1007, Tunis. Corresponding author: Mohammed Charni; e-mail: [email protected] ABSTRACT. We examine for the first time spermatogenesis, spermiogenesis and spermatozoon ultrastructure in Dugesia sicula Lepori, 1948 a sexual and diploid planarian living in Tunisian springs. This TEM-study shows that early spermatids joined by cytophores have rounded nuclei. During spermiogenesis, a row of microtubules appears in the differentiation zone beneath the plasma membrane and close to the intercentriolar body, which consists of several dense bands connected by filaments. Two free flagella (9+1 configuration) grow out- side the spermatid. An apical layer of dense nucleoplasm develops and the flagellum appear, facing in opposite directions before rotating to lie parallel to each other after the intercentriolar body splits into two halves. Mitochondria are closely packed around the spermatocyte nucleus before fusing during spermiogenesis, to form a long mitochondrion, which lies parallel to the elongated nucleus along the ripe spermatozoon. The latter is thread-shaped and consists of two regions: the proximal process and a distal part. The former contains the nucleus and a part of the mitochondrion. The latter contains the rest of the mitochondrion and a tapering tail of the nucleus. -
R E S E a R C H / M a N a G E M E N T Aquatic and Terrestrial Flatworm (Platyhelminthes, Turbellaria) and Ribbon Worm (Nemertea)
RESEARCH/MANAGEMENT FINDINGSFINDINGS “Put a piece of raw meat into a small stream or spring and after a few hours you may find it covered with hundreds of black worms... When not attracted into the open by food, they live inconspicuously under stones and on vegetation.” – BUCHSBAUM, et al. 1987 Aquatic and Terrestrial Flatworm (Platyhelminthes, Turbellaria) and Ribbon Worm (Nemertea) Records from Wisconsin Dreux J. Watermolen D WATERMOLEN Bureau of Integrated Science Services INTRODUCTION The phylum Platyhelminthes encompasses three distinct Nemerteans resemble turbellarians and possess many groups of flatworms: the entirely parasitic tapeworms flatworm features1. About 900 (mostly marine) species (Cestoidea) and flukes (Trematoda) and the free-living and comprise this phylum, which is represented in North commensal turbellarians (Turbellaria). Aquatic turbellari- American freshwaters by three species of benthic, preda- ans occur commonly in freshwater habitats, often in tory worms measuring 10-40 mm in length (Kolasa 2001). exceedingly large numbers and rather high densities. Their These ribbon worms occur in both lakes and streams. ecology and systematics, however, have been less studied Although flatworms show up commonly in invertebrate than those of many other common aquatic invertebrates samples, few biologists have studied the Wisconsin fauna. (Kolasa 2001). Terrestrial turbellarians inhabit soil and Published records for turbellarians and ribbon worms in leaf litter and can be found resting under stones, logs, and the state remain limited, with most being recorded under refuse. Like their freshwater relatives, terrestrial species generic rubric such as “flatworms,” “planarians,” or “other suffer from a lack of scientific attention. worms.” Surprisingly few Wisconsin specimens can be Most texts divide turbellarians into microturbellarians found in museum collections and a specialist has yet to (those generally < 1 mm in length) and macroturbellari- examine those that are available. -
Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms
RESEARCH ARTICLE Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms Eduard Solà1☯, Marta Álvarez-Presas1☯, Cristina Frías-López1, D. Timothy J. Littlewood2, Julio Rozas1, Marta Riutort1* 1 Institut de Recerca de la Biodiversitat and Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain, 2 Department of Life Sciences, Natural History Museum, Cromwell Road, London, United Kingdom ☯ These authors contributed equally to this work. * [email protected] (MR) Abstract Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of mo- lecular data to explore and understand the evolutionary history and relationships of eukary- OPEN ACCESS otic organisms across diverse taxonomic levels. The availability of complete mitogenomes Citation: Solà E, Álvarez-Presas M, Frías-López C, from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms Littlewood DTJ, Rozas J, Riutort M (2015) (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms. PLoS ONE 10(3): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly e0120081. doi:10.1371/journal.pone.0120081 complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have rea- Academic Editor: Hector Escriva, Laboratoire notated the published mitogenome of the species Dugesia japonica (Dugesiidae). This con- Arago, FRANCE tribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich Received: September 18, 2014 group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living Accepted: January 19, 2015 and selected parasitic flatworms in order to gain insights into the putative effect of life cycle Published: March 20, 2015 on nucleotide composition through mutation and natural selection. -
The First Subterranean Freshwater Planarians
A.H. Harrath, R. Sluys, A. Ghlala, and S. Alwasel – The first subterranean freshwater planarians from North Africa, with an analysis of adenodactyl structure in the genus Dendrocoelum (Platyhelminthes, Tricladida, Dendrocoelidae). Journal of Cave and Karst Studies, v. 74, no. 1, p. 48–57. DOI: 10.4311/2011LSC0215 THE FIRST SUBTERRANEAN FRESHWATER PLANARIANS FROM NORTH AFRICA, WITH AN ANALYSIS OF ADENODACTYL STRUCTURE IN THE GENUS DENDROCOELUM (PLATYHELMINTHES, TRICLADIDA, DENDROCOELIDAE) ABDUL HALIM HARRATH1,2*,RONALD SLUYS3,ADNEN GHLALA4, AND SALEH ALWASEL1 Abstract: The paper describes the first species of freshwater planarians collected from subterranean localities in northern Africa, represented by three new species of Dendrocoelum O¨ rsted, 1844 from Tunisian springs. Each of the new species possesses a well-developed adenodactyl, resembling similar structures in other species of Dendrocoelum, notably those from southeastern Europe. Comparative studies revealed previously unreported details and variability in the anatomy of these structures, particularly in the composition of the musculature. An account of this variability is provided, and it is argued that the anatomical structure of adenodactyls may provide useful taxonomic information. INTRODUCTION have been reported (Porfirjeva, 1977). The Holarctic range of the Dendrocoelidae includes the northwestern section of The French zoologists C. Alluaud and R. Jeannel were North Africa, based on the records of Dendrocoelum among the first workers to research in some detail the vaillanti De Beauchamp, 1955 from the Grande Kabylie subterranean fauna of Africa (see, Jeannel and Racovitza, Mountains in Algeria and Acromyadenium moroccanum De 1914). Subsequently, an increasing number of groundwater Beauchamp, 1931 from Bekrit in the Atlas Mountains of species were reported from African caves (Messana, 2004). -
Planarians, a Neglected Component of Biodiversity in Groundwaters
diversity Article Planarians, a Neglected Component of Biodiversity in Groundwaters Benedetta Barzaghi 1,2,* , Davide De Giorgi 1, Roberta Pennati 1 and Raoul Manenti 1,2 1 Department of Environmental Science and Policy, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy; [email protected] (D.D.G.); [email protected] (R.P.); [email protected] (R.M.) 2 Laboratorio di Biologia Sotterranea “Enrico Pezzoli”, Parco Regionale del Monte Barro, Località Eremo, 23851 Galbiate, Italy * Correspondence: [email protected] Abstract: Underground waters are still one of the most important sources of drinking water for the planet. Moreover, the fauna that inhabits these waters is still little known, even if it could be used as an effective bioindicator. Among cave invertebrates, planarians are strongly suited to be used as a study model to understand adaptations and trophic web features. Here, we show a systematic literature review that aims to investigate the studies done so far on groundwater-dwelling planarians. The research was done using Google Scholar and Web of Science databases. Using the key words “Planarian cave” and “Flatworm Cave” we found 2273 papers that our selection reduced to only 48, providing 113 usable observations on 107 different species of planarians from both groundwaters and springs. Among the most interesting results, it emerged that planarians are at the top of the food chain in two thirds of the reported caves, and in both groundwaters and springs they show a high variability of morphological adaptations to subterranean environments. This is a first attempt to review the phylogeny of the groundwater-dwelling planarias, focusing on the online literature. -
Schmidtea Mediterranea Thesis
Open Research Online The Open University’s repository of research publications and other research outputs Epidermis and Re-epithelialization in Schmidtea mediterranea Thesis How to cite: Gumbrys, Aurimas (2017). Epidermis and Re-epithelialization in Schmidtea mediterranea. PhD thesis The Open University. For guidance on citations see FAQs. c 2016 The Author https://creativecommons.org/licenses/by-nc-nd/4.0/ Version: Version of Record Link(s) to article on publisher’s website: http://dx.doi.org/doi:10.21954/ou.ro.0000c71c Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online’s data policy on reuse of materials please consult the policies page. oro.open.ac.uk Epidermis and re-epithelialization in Schmidtea mediterranea Aurimas Gumbrys, B.Sc., M.Sc. A thesis submitted in fulfillment of the requirements of the Open University for the Degree of Doctor of Philosophy The Stowers Institute for Medical Research Kansas City, USA an Affiliated Research Center of the Open University, UK 31 Decemer 2016 Abstract Epidermal layer is crucial for organism’s survival as its ability to close the wound is essential for tissue recovery. Planarian epidermis enables animal recovery and survival after virtually any body part amputation. Nevertheless, neither the epidermis nor the mechanisms endowing such a remarkable wound healing capacity is described in detail in planarians. Our work introduces live imaging methodology, which allows following epidermal cells and their response to tissue damage or tissue loss for extended time (hours) and in high resolution. -
Dugesia Japonica Is the Best Suited of Three Planarian Species for High-Throughput
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.23.917047; this version posted January 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Dugesia japonica is the best suited of three planarian species for high-throughput 2 toxicology screening 3 Danielle Irelanda, Veronica Bocheneka, Daniel Chaikenb, Christina Rabelera, Sumi Onoeb, Ameet 4 Sonib, and Eva-Maria S. Collinsa,c* 5 6 a Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of 7 America 8 b Department of Computer Science, Swarthmore College, Swarthmore, Pennsylvania, United 9 States of America 10 c Department of Physics, University of California San Diego, La Jolla, California, United States of 11 America 12 13 14 15 16 * Corresponding author 17 Email: [email protected] (E-MSC) 18 Address: Martin Hall 202, 500 College Avenue, Swarthmore College, Swarthmore, PA 19081 19 Phone number: 610-690-5380 20 21 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.23.917047; this version posted January 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 23 Abstract 24 High-throughput screening (HTS) using new approach methods is revolutionizing 25 toxicology. Asexual freshwater planarians are a promising invertebrate model for neurotoxicity 26 HTS because their diverse behaviors can be used as quantitative readouts of neuronal function. -
The Effects of Fluoride Ions on Neuromuscular Activity and Regeneration in Dugesia Tigrina," Georgia Journal of Science, Vol
Georgia Journal of Science Volume 75 No. 2 Scholarly Contributions from the Article 5 Membership and Others 2017 The ffecE ts of Fluoride Ions on Neuromuscular Activity and Regeneration in Dugesia tigrina John Williams Jr. Albany State University, [email protected] Follow this and additional works at: http://digitalcommons.gaacademy.org/gjs Part of the Cellular and Molecular Physiology Commons, Environmental Health Commons, and the Zoology Commons Recommended Citation Williams, John Jr. (2017) "The Effects of Fluoride Ions on Neuromuscular Activity and Regeneration in Dugesia tigrina," Georgia Journal of Science, Vol. 75, No. 2, Article 5. Available at: http://digitalcommons.gaacademy.org/gjs/vol75/iss2/5 This Research Articles is brought to you for free and open access by Digital Commons @ the Georgia Academy of Science. It has been accepted for inclusion in Georgia Journal of Science by an authorized editor of Digital Commons @ the Georgia Academy of Science. The ffecE ts of Fluoride Ions on Neuromuscular Activity and Regeneration in Dugesia tigrina Cover Page Footnote The iW lliams Laboratory would like to thank the Albany State University Department of Natural and Forensic Sciences for providing resources and laboratory space to conduct this research. The al boratory would also like to thank the Florida Georgia Alliance for Minority Participation for support and funding. Dr. Williams would also like to thank Qurat Ain and Kimberly Gaines for technical support in conducting these experiments. This research articles is available in Georgia Journal of Science: http://digitalcommons.gaacademy.org/gjs/vol75/iss2/5 Williams: Negative Effects of Fluoride on Planaria Nervous/Muscular Systems THE EFFECTS OF FLUORIDE IONS ON NEUROMUSCULAR ACTIVITY AND REGENERATION IN Dugesia tigrina John Williams, Ph.D.