What Do Students Have to Say About Ecology and Evolution? Using Podcasting to Apply Integrative Biology Themes Across the Tree of Life Amy M
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Analysis of Tardigrade Damage Suppressor Protein (Dsup) Expressed in Tobacco
Analysis of Tardigrade Damage Suppressor Protein (Dsup) Expressed in Tobacco by Justin Kirke A Thesis Submitted to the Faculty of The Charles E. Schmidt College of Science In Partial Fulfillment of the Requirements for the Degree of Master of Science Florida Atlantic University Boca Raton, FL December 2019 Copyright 2019 by Justin Kirke ii Abstract Author: Justin Kirke Title: Analysis of Tardigrade Damage Suppressor Protein (Dsup) Expressed in Tobacco Institution: Florida Atlantic University Thesis Advisor: Dr. Xing-Hai Zhang Degree: Master of Science Year: 2019 DNA damage is one of the most harmful stress inducers in living organisms. Studies have shown that exposure to high doses of various types of radiation cause DNA sequence changes (mutation) and disturb protein synthesis, hormone balance, leaf gas exchange and enzyme activity. Recent discovery of a protein called Damage Suppressor Protein (Dsup), found in the tardigrade species Ramazzotius varieornatus, has shown to reduce the effects of radiation damage in human cell lines. We have generated multiple lines of tobacco plants expressing the Dsup gene and preformed numerous tests to show viability and response of these transgenic plants when exposed to mutagenic chemicals, UV radiation and ionizing radiation. We have also investigated Dsup function in association to DNA damage and repair in plants by analyzing the expression of related genes using RT-qPCR. We have also analyzed DNA damage from X-ray and UV treatments using an Alkaline Comet Assay. This project has the potential to help generate plants that are tolerant to more extreme stress environments, particularly DNA damage and iv mutation, unshielded by our atmosphere. -
Molecular Genetic Characteristics of Nepalese Ephedra Plants (Ephedraceae)
J. Jpn. Bot. 86: 303–313 (2011) Molecular Genetic Characteristics of Nepalese Ephedra Plants (Ephedraceae) a a a Emi HAMANAKA , Keisuke OHKUBO , Masayuki MIKAGE and Nobuko b, KAKIUCHI * a Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192 JAPAN b Department of Pharmacognosy, School of Pharmaceutical Sciences, Kyusyu University of Health and Welfare, 1714-1, Yoshino-cho, Nobeoka, 882-8508 JAPAN * Corresponding author: [email protected] (Accepted on June 28, 2011) The aerial part of Ephedra plants is a staple crude drug worldwide. With the aim of developing new Ephedra resources, we investigated Nepalese wild Ephedra plants, E. gerardiana Wall. ex Stapf and E. pachyclada Boiss., and analyzed their molecular genetic features by DNA analysis. Ephedra gerardiana were distributed on the sub-Himalayan steppes at high altitudes, 3100–4500 m, and E. pachyclada were found along the Kali Gandaki River Valley in the Mustang region at relatively lower altitudes, 2000–3500 m. Ephedra gerardiana specimens from western collection sites shared an identical ITS1 sequence, while that of specimens from eastern collection sites at higher altitudes was 1–12 bases different from western specimens. Ephedra pachyclada specimens showed complex ITS1 signals by the overlapping of two type sequences. By cloning of ITS1 sequences of four E. pachyclada specimens from around the 400th nucleotide to separate these overlapping sequences, they were confirmed to contain sequences either monophyletic with E. intermedia Schrenk & C. A. Mey. or E. gerardiana. The ratio of clones with these two types varied among the specimens. Both Nepalese Ephedra plants, especially E. pachyclada, had a markedly heterogeneous ITS1 sequence that may be caused by harsh environmental pressure at high altitudes. -
The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants
SUPPLEMENTARY INFORMATIONARTICLES https://doi.org/10.1038/s41559-020-1221-7 In the format provided by the authors and unedited. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Linzhou Li1,2,13, Sibo Wang1,3,13, Hongli Wang1,4, Sunil Kumar Sahu 1, Birger Marin 5, Haoyuan Li1, Yan Xu1,4, Hongping Liang1,4, Zhen Li 6, Shifeng Cheng1, Tanja Reder5, Zehra Çebi5, Sebastian Wittek5, Morten Petersen3, Barbara Melkonian5,7, Hongli Du8, Huanming Yang1, Jian Wang1, Gane Ka-Shu Wong 1,9, Xun Xu 1,10, Xin Liu 1, Yves Van de Peer 6,11,12 ✉ , Michael Melkonian5,7 ✉ and Huan Liu 1,3 ✉ 1State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. 2Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. 3Department of Biology, University of Copenhagen, Copenhagen, Denmark. 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. 5Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany. 6Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium. 7Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany. 8School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China. 9Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada. 10Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China. 11College of Horticulture, Nanjing Agricultural University, Nanjing, China. 12Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. -
Diapause in Tardigrades: a Study of Factors Involved in Encystment
2296 The Journal of Experimental Biology 211, 2296-2302 Published by The Company of Biologists 2008 doi:10.1242/jeb.015131 Diapause in tardigrades: a study of factors involved in encystment Roberto Guidetti1,*, Deborah Boschini2, Tiziana Altiero2, Roberto Bertolani2 and Lorena Rebecchi2 1Department of the Museum of Paleobiology and Botanical Garden, Via Università 4, 41100, Modena, Italy and 2Department of Animal Biology, University of Modena and Reggio Emilia, Via Campi 213/D, 41100, Modena, Italy *Author for correspondence (e-mail: [email protected]) Accepted 12 May 2008 SUMMARY Stressful environmental conditions limit survival, growth and reproduction, or these conditions induce resting stages indicated as dormancy. Tardigrades represent one of the few animal phyla able to perform both forms of dormancy: quiescence and diapause. Different forms of cryptobiosis (quiescence) are widespread and well studied, while little attention has been devoted to the adaptive meaning of encystment (diapause). Our goal was to determine the environmental factors and token stimuli involved in the encystment process of tardigrades. The eutardigrade Amphibolus volubilis, a species able to produce two types of cyst (type 1 and type 2), was considered. Laboratory experiments and long-term studies on cyst dynamics of a natural population were conducted. Laboratory experiments demonstrated that active tardigrades collected in April produced mainly type 2 cysts, whereas animals collected in November produced mainly type 1 cysts, indicating that the different responses are functions of the physiological state at the time they were collected. The dynamics of the two types of cyst show opposite seasonal trends: type 2 cysts are present only during the warm season and type 1 cysts are present during the cold season. -
And Thermo-Adaptation in Hyperthermophilic Archaea: Identification of Compatible Solutes, Accumulation Profiles, and Biosynthetic Routes in Archaeoglobus Spp
Universidade Nova de Lisboa Osmo- andInstituto thermo de Tecnologia-adaptation Química e Biológica in hyperthermophilic Archaea: Subtitle Subtitle Luís Pedro Gafeira Gonçalves Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. OH OH OH CDP c c c - CMP O O - PPi O3P P CTP O O O OH OH OH OH OH OH O- C C C O P O O P i Dissertation presented to obtain the Ph.D degree in BiochemistryO O- Instituto de Tecnologia Química e Biológica | Universidade Nova de LisboaP OH O O OH OH OH Oeiras, Luís Pedro Gafeira Gonçalves January, 2008 2008 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. This dissertation was presented to obtain a Ph. D. degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. By Luís Pedro Gafeira Gonçalves Supervised by Prof. Dr. Helena Santos Oeiras, January, 2008 Apoio financeiro da Fundação para a Ciência e Tecnologia (POCI 2010 – Formação Avançada para a Ciência – Medida IV.3) e FSE no âmbito do Quadro Comunitário de apoio, Bolsa de Doutoramento com a referência SFRH / BD / 5076 / 2001. ii ACKNOWNLEDGMENTS The work presented in this thesis, would not have been possible without the help, in terms of time and knowledge, of many people, to whom I am extremely grateful. Firstly and mostly, I need to thank my supervisor, Prof. Helena Santos, for her way of thinking science, her knowledge, her rigorous criticism, and her commitment to science. -
Introduction to the Body-Plan of Onychophora and Tardigrada
Joakim Eriksson, 02.12.13 Animal bodyplans Onychophora Tardigrada Bauplan, bodyplan • A Bauplan is a set of conservative characters that are typical for one group but distinctively different from a Bauplan of another group Arthropoda Bauplan 2 Bauplan 3 Bauplan 4 Tardigrada Onychophora Euarthropoda/Arthropoda Insects Chelicerates Myriapods Crustaceans Arthropoda/Panarthropoda Bauplan 1 Arthropod characters • Body segmented, with limbs on several segments • Adult body cavity a haemocoel that extends into the limbs • Cuticle of α-chitin which is molted regularly • Appendages with chitinous claws, and mixocoel with metanephridia and ostiate heart (absent in tardigrades) • Engrailed gene expressed in posterior ectoderm of each segment • Primitively possess a terminal mouth, a non-retractable proboscis, and a thick integument of diverse plates Phylogenomics and miRNAs suggest velvets worm are the sister group to the arthropods within a monophyletic Panarthropoda. Campbell L I et al. PNAS 2011;108:15920-15924 Fossil arthropods, the Cambrian explosion Aysheaia An onychophoran or phylum of its own? Anomalocaris A phylum on its own? Crown group and stem group Arthropoda Bauplan 2 Bauplan 3 Bauplan 4 Tardigrada Onychophora Euarthropoda/Arthropoda Arthropoda/Panarthropoda Bauplan 1 How do arthropods relate to other animal groups Articulata Georges Cuvier, 1817 Characters uniting articulata: •Segmentation •Ventral nerv cord •Teloblastic growth zone Ecdysozoa Aguinaldo et al 1997 Ecdysozoa Character uniting ecdysozoa: •Body covered by cuticle of α-chitin -
The Impact of Tourists on Antarctic Tardigrades: an Ordination-Based Model
J. Limnol., 2013; 72(s1): 128-135 DOI: 10.4081/jlimnol.2013.s1.e16 The impact of tourists on Antarctic tardigrades: an ordination-based model Sandra J. McINNES,1* Philip J.A. PUGH2 1British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK; 2Department of Life Sciences, Anglia Ruskin University, East Road, Cambridge, CB1 1PT, UK *Corresponding author: [email protected] ABSTRACT Tardigrades are important members of the Antarctic biota yet little is known about their role in the soil fauna or whether they are affected by anthropogenic factors. The German Federal Environment Agency commissioned research to assess the impact of human activities on soil meiofauna at 14 localities along the Antarctic peninsula during the 2009/2010 and 2010/2011 austral summers. We used ordination techniques to re-assess the block-sampling design used to compare areas of high and low human impact, to identify which of the sampled variables were biologically relevant and/or demonstrated an anthropogenic significance. We found the most sig- nificant differences between locations, reflecting local habitat and vegetation factor, rather than within-location anthropogenic impact. We noted no evidence of exotic imports but report on new maritime Antarctic sample sites and habitatsonly. Key words: Tardigrada, soil, alien introduction, maritime Antarctic. INTRODUCTION The German Federal Environment Agency commis- sioned a studyuse into the impact of ship-based tourism on The introduction of exotic taxa is regarded as a major Antarctic terrestrial soil ecosystems, focusing on a range threat to native species even in Antarctica (Chown et al., of taxa including Tardigrada. -
Tardigrade Reproduction and Food
Glime, J. M. 2017. Tardigrade Reproduction and Food. Chapt. 5-2. In: Glime, J. M. Bryophyte Ecology. Volume 2. Bryological 5-2-1 Interaction. Ebook sponsored by Michigan Technological University and the International Association of Bryologists. Last updated 18 July 2020 and available at <http://digitalcommons.mtu.edu/bryophyte-ecology2/>. CHAPTER 5-2 TARDIGRADE REPRODUCTION AND FOOD TABLE OF CONTENTS Life Cycle and Reproductive Strategies .............................................................................................................. 5-2-2 Reproductive Strategies and Habitat ............................................................................................................ 5-2-3 Eggs ............................................................................................................................................................. 5-2-3 Molting ......................................................................................................................................................... 5-2-7 Cyclomorphosis ........................................................................................................................................... 5-2-7 Bryophytes as Food Reservoirs ........................................................................................................................... 5-2-8 Role in Food Web ...................................................................................................................................... 5-2-12 Summary .......................................................................................................................................................... -
Being Aquifex Aeolicus: Untangling a Hyperthermophile's Checkered Past
GBE Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past Robert J.M. Eveleigh1,2, Conor J. Meehan1,2,JohnM.Archibald1, and Robert G. Beiko2,* 1Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada 2Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada *Corresponding author: E-mail: [email protected]. Accepted: November 22, 2013 Abstract Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyper- thermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Downloaded from Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a http://gbe.oxfordjournals.org/ minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria. -
The Thermal Limits to Life on Earth
International Journal of Astrobiology 13 (2): 141–154 (2014) doi:10.1017/S1473550413000438 © Cambridge University Press 2014. The online version of this article is published within an Open Access environment subject to the conditions of the Creative Commons Attribution licence http://creativecommons.org/licenses/by/3.0/. The thermal limits to life on Earth Andrew Clarke1,2 1British Antarctic Survey, Cambridge, UK 2School of Environmental Sciences, University of East Anglia, Norwich, UK e-mail: [email protected] Abstract: Living organisms on Earth are characterized by three necessary features: a set of internal instructions encoded in DNA (software), a suite of proteins and associated macromolecules providing a boundary and internal structure (hardware), and a flux of energy. In addition, they replicate themselves through reproduction, a process that renders evolutionary change inevitable in a resource-limited world. Temperature has a profound effect on all of these features, and yet life is sufficiently adaptable to be found almost everywhere water is liquid. The thermal limits to survival are well documented for many types of organisms, but the thermal limits to completion of the life cycle are much more difficult to establish, especially for organisms that inhabit thermally variable environments. Current data suggest that the thermal limits to completion of the life cycle differ between the three major domains of life, bacteria, archaea and eukaryotes. At the very highest temperatures only archaea are found with the current high-temperature limit for growth being 122 °C. Bacteria can grow up to 100 °C, but no eukaryote appears to be able to complete its life cycle above *60 °C and most not above 40 °C. -
Educator's Guide
Educator’s Guide INSIDE • Map of the Exhibition • Essential Questions • Teaching in the Exhibition • Come Prepared Checklist • Correlation to Standards • Glossary ONLINE • Science & Literacy Activities • Additional Resources amnh.org/lal/educators ESSENTIAL QUESTIONS Use the Essential Questions below to connect the exhibition’s themes to your curriculum. Identify key points that you’d like your students to learn. Bolded text are science concepts that are addressed in this exhibition. Words in blue are defined in the Glossary. What do all living things need to do? • KEEP SAFE: Animals won’t get eaten if predators can’t Basic biological processes o!en include ge"ing oxygen, find them. Camouflage and finding food, moving around, taking in information, staying mimicry protect species safe, and above all, reproducing. that range from ants to The mimic octopus imitates octopodes, including the diferent animals—here, a flatfish moving along the ocean floor. What are some of the unexpected ways in harlequin jawfish, which which life survives and thrives? mimics the arm of the mimic octopus and eats its scraps; Living things have responded to the fundamental challenge and the treehopper, an insect that resembles an enormous of surviving and reproducing in extremely inventive ways: venomous ant. Because protective armor is such an effective defense, it has evolved again and again in countless plants • REPRODUCE: Every organism on Earth has a way to bring and animals, from the scales of a snake to the shell of a new life into the world and maximize its offspring’s conch. chance of survival. Some animals, like corals, • SENSE: release billions of tiny eggs and sperm at a In order to carry out all these life processes, time. -
Tardigrades: an Imaging Approach, a Record of Occurrence, and A
TARDIGRADES: AN IMAGING APPROACH, A RECORD OF OCCURRENCE, AND A BIODIVERSITY INVENTORY By STEVEN LOUIS SCHULZE A thesis submitted to the Graduate School-Camden Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Master of Science Graduate Program in Biology Written under the direction of Dr. John Dighton And approved by ____________________________ Dr. John Dighton ____________________________ Dr. William Saidel ____________________________ Dr. Emma Perry ____________________________ Dr. Jennifer Oberle Camden, New Jersey May 2020 THESIS ABSTRACT Tardigrades: An Imaging Approach, A Record of Occurrence, and a Biodiversity Inventory by STEVEN LOUIS SCHULZE Thesis Director: Dr. John Dighton Three unrelated studies that address several aspects of the biology of tardigrades— morphology, records of occurrence, and local biodiversity—are herein described. Chapter 1 is a collaborative effort and meant to provide supplementary scanning electron micrographs for a forthcoming description of a genus of tardigrade. Three micrographs illustrate the structures that will be used to distinguish this genus from its confamilials. An In toto lateral view presents the external structures relative to one another. A second micrograph shows a dentate collar at the distal end of each of the fourth pair of legs, a posterior sensory organ (cirrus E), basal spurs at the base of two of four claws on each leg, and a ventral plate. The third micrograph illustrates an appendage on the second leg (p2) of the animal and a lateral appendage (C′) at the posterior sinistral margin of the first paired plate (II). This image also reveals patterning on the plate margin and the leg.