What Is a Lab Animal? Small but Dedicated Communities Are Bringing the Earliest Lineages of the Animal Kingdom Into the Lab
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Freshwater Sponges (Porifera: Spongillida) of Tennessee
Freshwater Sponges (Porifera: Spongillida) of Tennessee Authors: John Copeland, Stan Kunigelis, Jesse Tussing, Tucker Jett, and Chase Rich Source: The American Midland Naturalist, 181(2) : 310-326 Published By: University of Notre Dame URL: https://doi.org/10.1674/0003-0031-181.2.310 BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Complete website, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/terms-of-use. Usage of BioOne Complete content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Downloaded From: https://bioone.org/journals/The-American-Midland-Naturalist on 18 Sep 2019 Terms of Use: https://bioone.org/terms-of-use Access provided by United States Fish & Wildlife Service National Conservation Training Center Am. Midl. Nat. (2019) 181:310–326 Notes and Discussion Piece Freshwater Sponges (Porifera: Spongillida) of Tennessee ABSTRACT.—Freshwater sponges (Porifera: Spongillida) are an understudied fauna. Many U.S. state and federal conservation agencies lack fundamental information such as species lists and distribution data. Such information is necessary for management of aquatic resources and maintaining biotic diversity. -
Freshwater Sponge Hosts and Their Green Algae Symbionts
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.12.247908; this version posted August 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Freshwater sponge hosts and their green algae 2 symbionts: a tractable model to understand intracellular 3 symbiosis 4 5 Chelsea Hall2,3, Sara Camilli3,4, Henry Dwaah2, Benjamin Kornegay2, Christine A. Lacy2, 6 Malcolm S. Hill1,2§, April L. Hill1,2§ 7 8 1Department of Biology, Bates College, Lewiston ME, USA 9 2Department of Biology, University of Richmond, Richmond VA, USA 10 3University of Virginia, Charlottesville, VA, USA 11 4Princeton University, Princeton, NJ, USA 12 13 §Present address: Department of Biology, Bates College, Lewiston ME USA 14 Corresponding author: 15 April L. Hill 16 44 Campus Ave, Lewiston, ME 04240, USA 17 Email address: [email protected] 18 19 20 21 22 23 24 25 26 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.12.247908; this version posted August 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 27 Abstract 28 In many freshwater habitats, green algae form intracellular symbioses with a variety of 29 heterotrophic host taxa including several species of freshwater sponge. These sponges perform 30 important ecological roles in their habitats, and the poriferan:green algae partnerships offers 31 unique opportunities to study the evolutionary origins and ecological persistence of 32 endosymbioses. -
Animal Evolution: Looking for the First Nervous System
Dispatch R655 cellular or symbiotic functions, cannot genome reduction in the symbiont, 10. Nakabachi, A., Ishida, K., Hongoh, Y., Ohkuma, M., and Miyagishima, S. (2014). be lost without harmful or fatal results. HGT from various sources to the host Aphid gene of bacterial origin encodes a But these genes can be replaced, genome to maintain symbiont function, protein transported to an obligate and perhaps ever more easily as and now the targeting of protein endosymbiont. Curr. Biol. 24, R640–R641. 11. Moran, N.A., and Jarvik, T. (2010). Lateral the interaction networks of the products from host to symbiont has transfer of genes from fungi underlies endosymbiont reduce in complexity, even been found [4,10]. These make carotenoid production in aphids. Science 328, 624–627. thus reducing pressures on proteins clean separation of endosymbiont from 12. Jorgenson, M.A., Chen, Y., Yahashiri, A., to co-evolve. In a sense, when genes organelle more difficult to see, Popham, D.L., and Weiss, D.S. (2014). The are transferred from symbiont or prompting us not to look for the point bacterial septal ring protein RlpA is a lytic transglycosylase that contributes to rod organelle to the host nuclear genome when a symbiont ‘becomes’ an shape and daughter cell separation in and their proteins targeted back, this is organelle, but rather to ask, ‘Is there Pseudomonas aeruginosa. Mol. Microbiol. 93, 113–128. a compensatory change [4,9,14,17]. really anything so special about 13. Acuna, R., Padilla, B.E., Florez-Ramos, C.P., But other compensatory transfers that organelles?’ Rubio, J.D., Herrera, J.C., Benavides, P., affect a symbiont or organelle can also Lee, S.J., Yeats, T.H., Egan, A.N., Doyle, J.J., et al. -
Basal Metazoans - Dirk Erpenbeck, Simion Paul, Michael Manuel, Paulyn Cartwright, Oliver Voigt and Gert Worheide
EVOLUTION OF PHYLOGENETIC TREE OF LIFE - Basal Metazoans - Dirk Erpenbeck, Simion Paul, Michael Manuel, Paulyn Cartwright, Oliver Voigt and Gert Worheide BASAL METAZOANS Dirk Erpenbeck Ludwig-Maximilians Universität München, Germany Simion Paul and Michaël Manuel Université Pierre et Marie Curie in Paris, France. Paulyn Cartwright University of Kansas USA. Oliver Voigt and Gert Wörheide Ludwig-Maximilians Universität München, Germany Keywords: Metazoa, Porifera, sponges, Placozoa, Cnidaria, anthozoans, jellyfishes, Ctenophora, comb jellies Contents 1. Introduction on ―Basal Metazoans‖ 2. Phylogenetic relationships among non-bilaterian Metazoa 3. Porifera (Sponges) 4. Placozoa 5. Ctenophora (Comb-jellies) 6. Cnidaria 7. Cultural impact and relevance to human welfare Glossary Bibliography Biographical Sketch Summary Basal metazoans comprise the four non-bilaterian animal phyla Porifera (sponges), Cnidaria (anthozoans and jellyfishes), Placozoa (Trichoplax) and Ctenophora (comb jellies). The phylogenetic position of these taxa in the animal tree is pivotal for our understanding of the last common metazoan ancestor and the character evolution all Metazoa,UNESCO-EOLSS but is much debated. Morphological, evolutionary, internal and external phylogenetic aspects of the four phyla are highlighted and discussed. SAMPLE CHAPTERS 1. Introduction on “Basal Metazoans” In many textbooks the term ―lower metazoans‖ still refers to an undefined assemblage of invertebrate phyla, whose phylogenetic relationships were rather undefined. This assemblage may contain both bilaterian and non-bilaterian taxa. Currently, ―Basal Metazoa‖ refers to non-bilaterian animals only, four phyla that lack obvious bilateral symmetry, Porifera, Placozoa, Cnidaria and Ctenophora. ©Encyclopedia of Life Support Systems (EOLSS) EVOLUTION OF PHYLOGENETIC TREE OF LIFE - Basal Metazoans - Dirk Erpenbeck, Simion Paul, Michael Manuel, Paulyn Cartwright, Oliver Voigt and Gert Worheide These four phyla have classically been known as ―diploblastic‖ Metazoa. -
Animal Evolution: Trichoplax, Trees, and Taxonomic Turmoil
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Dispatch R1003 Dispatches Animal Evolution: Trichoplax, Trees, and Taxonomic Turmoil The genome sequence of Trichoplax adhaerens, the founding member of the into the same major classes (C, E/F enigmatic animal phylum Placozoa, has revealed that a surprising level of and B) as do those described from genetic complexity underlies its extremely simple body plan, indicating either Amphimedon [4]. Consistent with that placozoans are secondarily simple or that there is an undiscovered a more derived position, however, morphologically complex life stage. Trichoplax has a number of Antp superclass Hox genes that are absent David J. Miller1 and Eldon E. Ball2 but no other axial differentiation, from the sponge Amphimedon. resembling an amoeba. Grell [3] who These include the ‘ParaHox’ gene With the recent or imminent release formally described these common but Trox-2 [5] and the extended Hox of the whole genome sequences of inconspicuous marine organisms as family gene Not [6] known from a number of key animal species, this belonging to a new phylum, assumed previous work. Particularly intriguing is an exciting time for the ‘evo-devo’ that their simplicity is primary, and is the discovery in Trichoplax of many community. In the last twelve months, that they therefore must represent genes associated with neuroendocrine whole genome analyses of the a key stage in animal evolution. This function across the Bilateria; in cnidarian Nematostella vectensis, view is still held by several prominent common with Amphimedon [7], many the choanoflagellate Monosiga Trichoplax biologists, but has always elements of the post-synaptic scaffold brevicollis and the cephalochordate been contentious; the view that it is are present, but so too are channel Branchiostoma floridae (commonly derived from a more complex ancestor and receptor proteins not known from known as amphioxus) have been has recently been gaining momentum sponges. -
Implications for Proteasome Nuclear Localization Revealed by the Structure of the Nuclear Proteasome Tether Protein Cut8
Implications for proteasome nuclear localization revealed by the structure of the nuclear proteasome tether protein Cut8 Kojiro Takedaa, Nam K. Tonthatb, Tiffany Gloverc, Weijun Xuc, Eugene V. Koonind, Mitsuhiro Yanagidaa, and Maria A. Schumacherb,1 aG0 Cell Unit; Okinawa Institute of Science and Technology (OIST); 1919-1 Tancha, Onna, Okinawa, Japan; bDepartment of Biochemistry, Duke University Medical Center, Room 243A Nanaline H. Duke Building, Box 3711, Durham, NC 27710; cDepartment of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Unit 1000, Houston, TX 77030; and dNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892 Edited by Axel T. Brunger, Stanford University, Stanford, CA, and approved August 29, 2011 (received for review March 7, 2011) Degradation of nuclear proteins by the 26S proteasome is essential ultimately found to be a delay in the destruction of the mitotic for cell viability. In yeast, the nuclear envelope protein Cut8 med- cyclin and securin (13). However, the polyubiquitination of these iates nuclear proteasomal sequestration by an uncharacterized proteins was normal, suggesting a role for the proteasome. Sub- mechanism. Here we describe structures of Schizosaccharomyces sequent studies showed that Cut8 is responsible for sequestering pombe Cut8, which shows that it contains a unique, modular the 26S proteasome to the nucleus (10, 11). Cut8 was found to be fold composed of an extended N-terminal, lysine-rich segment localized to the nuclear envelope and overlapping the location that when ubiquitinated binds the proteasome, a dimer domain of the proteasome (17–21). An interaction between Cut8 and followed by a six-helix bundle connected to a flexible C tail. -
Understanding Animal Evolution: the Added Value of Sponge Transcriptomics and Genomics the Disconnect Between Gene Content and Body Plan Evolution
PROBLEMS AND PARADIGMS Prospects & Overviews www.bioessays-journal.com Understanding Animal Evolution: The Added Value of Sponge Transcriptomics and Genomics The disconnect between gene content and body plan evolution Emmanuelle Renard,* Sally P. Leys, Gert Wörheide, and Carole Borchiellini 1. Introduction Sponges are important but often-neglected organisms. The absence of Bilaterians represent the majority of extant classical animal traits (nerves, digestive tract, and muscles) makes sponges animal species and unsurprisingly are challenging for non-specialists to work with and has delayed getting high highly represented with fully sequenced quality genomic data compared to other invertebrates. Yet analyses of sponge genomes. There is particular interest, genomes and transcriptomes currently available have radically changed our however, in studying non-bilaterian taxa understanding of animal evolution. Sponges are of prime evolutionary (Placozoa, Cnidaria, Ctenophora, and Por- importance as one of the best candidates to form the sister group of all other ifera) because they hold the key to understanding the origin of major tran- animals, and genomic data are essential to understand the mechanisms that sitions in animal body plans.[1,2] Sequenc- control animal evolution and diversity. Here we review the most significant ing and analyzing the genomes of non- outcomes of current genomic and transcriptomic analyses of sponges, and bilaterians will help determine the origins discuss limitations and future directions of sponge transcriptomic and of major features of Bilaterians such as genomic studies. axial polarity, symmetry, nervous systems, muscles, and even the origin of germ layers and the gut. Many fewer genomes are available for non-bilaterians, but one of the most poorly represented phyla is also one of the earliest branching of animals, and one with widespread ecological and evolutionary importance: Porifera (sponges). -
Full Issue, Vol. 57 No. 2
Great Basin Naturalist Volume 57 Number 2 Article 14 5-7-1997 Full Issue, Vol. 57 No. 2 Follow this and additional works at: https://scholarsarchive.byu.edu/gbn Recommended Citation (1997) "Full Issue, Vol. 57 No. 2," Great Basin Naturalist: Vol. 57 : No. 2 , Article 14. Available at: https://scholarsarchive.byu.edu/gbn/vol57/iss2/14 This Full Issue is brought to you for free and open access by the Western North American Naturalist Publications at BYU ScholarsArchive. It has been accepted for inclusion in Great Basin Naturalist by an authorized editor of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. T H E GREATG R E A T BASINBAS I1 naturalistnaturalist A VOLUME 57 NQ 2 APRIL 1997 br16hamBRIGHAM YOUNG university GREAT BASIN naturalist editor assistant editor RICHARD W BAUMANN NATHAN M SMITH 290 MLBM 190 MLBM PO box 20200 PO box 26879 brigham young university brigham young university provo UT 84602020084602 0200 provo UT 84602687984602 6879 801378soisol8013785053801 378 5053 8013786688801 378 6688 FAX 8013783733801 378 3733 emailE mail nmshbll1byuedu associate editors J R CALLAHAN PAUL C MARSH museum of southwestern biology university of center for environmental studies arizona new mexico albuquerque NM state university tempe AZ 85287 mailing address box 3140 hemet CA 92546 STANLEY D SMITH BRUCE D ESHELMAN department of biology department of biological sciences university of university of nevada las vegas wisconsin whitewater whitewater wlWI 53190 las vegas NV 89154400489154 -
Expression of Immunoproteasome Genes Is Regulated by Cell-Intrinsic
www.nature.com/scientificreports OPEN Expression of immunoproteasome genes is regulated by cell-intrinsic and –extrinsic factors in human Received: 06 April 2016 Accepted: 06 September 2016 cancers Published: 23 September 2016 Alexandre Rouette1,2,*, Assya Trofimov1,2,3,*, David Haberl1, Geneviève Boucher1, Vincent-Philippe Lavallée1,2,4,5, Giovanni D’Angelo4,5, Josée Hébert1,2,4,5, Guy Sauvageau1,2,4,5, Sébastien Lemieux1,3 & Claude Perreault1,2,4 Based on transcriptomic analyses of thousands of samples from The Cancer Genome Atlas, we report that expression of constitutive proteasome (CP) genes (PSMB5, PSMB6, PSMB7) and immunoproteasome (IP) genes (PSMB8, PSMB9, PSMB10) is increased in most cancer types. In breast cancer, expression of IP genes was determined by the abundance of tumor infiltrating lymphocytes and high expression of IP genes was associated with longer survival. In contrast, IP upregulation in acute myeloid leukemia (AML) was a cell-intrinsic feature that was not associated with longer survival. Expression of IP genes in AML was IFN-independent, correlated with the methylation status of IP genes, and was particularly high in AML with an M5 phenotype and/or MLL rearrangement. Notably, PSMB8 inhibition led to accumulation of polyubiquitinated proteins and cell death in IPhigh but not IPlow AML cells. Co-clustering analysis revealed that genes correlated with IP subunits in non-M5 AMLs were primarily implicated in immune processes. However, in M5 AML, IP genes were primarily co-regulated with genes involved in cell metabolism and proliferation, mitochondrial activity and stress responses. We conclude that M5 AML cells can upregulate IP genes in a cell-intrinsic manner in order to resist cell stress. -
The Phylogeography of the Placozoa Suggests a Taxonrich Phylum In
Molecular Ecology (2010) 19, 2315–2327 doi: 10.1111/j.1365-294X.2010.04617.x The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical waters M. EITEL* and B. SCHIERWATER*† *Tiera¨rztliche Hochschule Hannover, ITZ, Ecology and Evolution, Bu¨nteweg 17d, D-30559 Hannover, Germany, †American Museum of Natural History, New York, Division of Invertebrate Zoology, 79 St at Central Park West, New York, NY 10024, USA Abstract Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. -
Biophysical Analyses of the Oxygen Sensing Prolyl Hydroxylase from the Simplest Animal Trichoplax Adhaerens
Journal name: Hypoxia Article Designation: Original Research Year: 2018 Volume: 6 Hypoxia Dovepress Running head verso: Lippl et al Running head recto: Biophysical analyses of the oxygen sensing PHDs from the simplest animal T. adhaerens open access to scientific and medical research DOI: http://dx.doi.org/10.2147/HP.S174655 Open Access Full Text Article ORIGINAL RESEARCH Born to sense: biophysical analyses of the oxygen sensing prolyl hydroxylase from the simplest animal Trichoplax adhaerens Kerstin Lippl Background: In humans and other animals, the chronic hypoxic response is mediated by Anna Boleininger hypoxia inducible transcription factors (HIFs) which regulate the expression of genes that Michael A McDonough counteract the effects of limiting oxygen. Prolyl hydroxylases (PHDs) act as hypoxia sensors Martine I Abboud for the HIF system in organisms ranging from humans to the simplest animal Trichoplax Hanna Tarhonskaya adhaerens. We report structural and biochemical studies on the T. adhaerens HIF prolyl hydroxy- Rasheduzzaman Chowdhury Methods: lase (TaPHD) that inform about the evolution of hypoxia sensing in animals. Christoph Loenarz Results: High resolution crystal structures (≤1.3 Å) of TaPHD, with and without its HIFα Christopher J Schofield substrate, reveal remarkable conservation of key active site elements between T. adhaerens and Chemistry Research Laboratory, human PHDs, which also manifest in kinetic comparisons. University of Oxford, Oxford, UK Conclusion: Conserved structural features of TaPHD and human PHDs include those appar- ently enabling the slow binding/reaction of oxygen with the active site Fe(II), the formation of a stable 2-oxoglutarate complex, and a stereoelectronically promoted change in conformation of the hydroxylated proline-residue. -
Isolating the Targets of Six Transcription Factor in Ephydatia Muelleri and Identifying the Role Of
University of the Pacific Scholarly Commons University of the Pacific Theses and Dissertations Graduate School 2017 ISOLATING THE TARGETS OF SIX TRANSCRIPTION FACTOR IN EPHYDATIA MUELLERI AND IDENTIFYING THE ROLE OF THE SUPEROXIDE DISMUTASE 6 IN HOST IMMUNE RESPONSE TO TRICHOMONAS VAGINALIS Gurbir Kaur Gudial University of the Pacific Follow this and additional works at: https://scholarlycommons.pacific.edu/uop_etds Part of the Biology Commons Recommended Citation Gudial, Gurbir Kaur. (2017). ISOLATING THE TARGETS OF SIX TRANSCRIPTION FACTOR IN EPHYDATIA MUELLERI AND IDENTIFYING THE ROLE OF THE SUPEROXIDE DISMUTASE 6 IN HOST IMMUNE RESPONSE TO TRICHOMONAS VAGINALIS. University of the Pacific, Thesis. https://scholarlycommons.pacific.edu/uop_etds/2972 This Thesis is brought to you for free and open access by the Graduate School at Scholarly Commons. It has been accepted for inclusion in University of the Pacific Theses and Dissertations by an authorized administrator of Scholarly Commons. For more information, please contact [email protected]. 1 ISOLATING THE TARGETS OF SIX TRANSCRIPTION FACTOR IN EPHYDATIA MUELLERI AND IDENTIFYING THE ROLE OF THE SUPEROXIDE DISMUTASE 6 IN HOST IMMUNE RESPONSE TO TRICHOMONAS VAGINALIS by Gurbir K. Gudial A Thesis Submitted to the Office of Research and Graduate Studies In Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE College of the Pacific Department of Biological Sciences University of the Pacific Stockton, CA 2017 2 ISOLATING THE TARGETS OF SIX TRANSCRIPTION FACTOR IN EPHYDATIA MUELLERI AND IDENTIFYING THE ROLE OF THE SUPEROXIDE DISMUTASE 6 IN HOST IMMUNE RESPONSE TO TRICHOMONAS VAGINALIS by Gurbir K. Gudial APPROVED BY: Thesis Advisor: Lisa Wrischnik, Ph.D.