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RNA Detection Technology for Applications in Marine Science: Microbes to Fish Robert Michael Ulrich University of South Florida, [email protected]
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 6-25-2014 RNA Detection Technology for Applications in Marine Science: Microbes to Fish Robert Michael Ulrich University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Biology Commons, and the Molecular Biology Commons Scholar Commons Citation Ulrich, Robert Michael, "RNA Detection Technology for Applications in Marine Science: Microbes to Fish" (2014). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/5321 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. RNA Detection Technology for Applications in Marine Science: Microbes to Fish by Robert M. Ulrich A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy College of Marine Science University of South Florida Major Professor: John H. Paul, Ph.D. Valerie J. Harwood, Ph.D. Mya Breitbart, Ph.D. Christopher D. Stallings, Ph.D. David E. John, Ph.D. Date of Approval June 25, 2014 Keywords: NASBA, grouper, Karenia mikimotoi, Enterococcus Copyright © 2014, Robert M. Ulrich DEDICATION This dissertation is dedicated to my fiancée, Dr. Shannon McQuaig for inspiring my return to graduate school and her continued support over the last four years. On no other porch in our little town have there been more impactful scientific discussions, nor more words of encouragement. ACKNOWLEDGMENTS I gratefully acknowledge the many people who have encouraged and advised me throughout my graduate studies. -
Parasites of Coral Reef Fish: How Much Do We Know? with a Bibliography of Fish Parasites in New Caledonia
Belg. J. Zool., 140 (Suppl.): 155-190 July 2010 Parasites of coral reef fish: how much do we know? With a bibliography of fish parasites in New Caledonia Jean-Lou Justine (1) UMR 7138 Systématique, Adaptation, Évolution, Muséum National d’Histoire Naturelle, 57, rue Cuvier, F-75321 Paris Cedex 05, France (2) Aquarium des lagons, B.P. 8185, 98807 Nouméa, Nouvelle-Calédonie Corresponding author: Jean-Lou Justine; e-mail: [email protected] ABSTRACT. A compilation of 107 references dealing with fish parasites in New Caledonia permitted the production of a parasite-host list and a host-parasite list. The lists include Turbellaria, Monopisthocotylea, Polyopisthocotylea, Digenea, Cestoda, Nematoda, Copepoda, Isopoda, Acanthocephala and Hirudinea, with 580 host-parasite combinations, corresponding with more than 370 species of parasites. Protozoa are not included. Platyhelminthes are the major group, with 239 species, including 98 monopisthocotylean monogeneans and 105 digeneans. Copepods include 61 records, and nematodes include 41 records. The list of fish recorded with parasites includes 195 species, in which most (ca. 170 species) are coral reef associated, the rest being a few deep-sea, pelagic or freshwater fishes. The serranids, lethrinids and lutjanids are the most commonly represented fish families. Although a list of published records does not provide a reliable estimate of biodiversity because of the important bias in publications being mainly in the domain of interest of the authors, it provides a basis to compare parasite biodiversity with other localities, and especially with other coral reefs. The present list is probably the most complete published account of parasite biodiversity of coral reef fishes. -
Updated Checklist of Marine Fishes (Chordata: Craniata) from Portugal and the Proposed Extension of the Portuguese Continental Shelf
European Journal of Taxonomy 73: 1-73 ISSN 2118-9773 http://dx.doi.org/10.5852/ejt.2014.73 www.europeanjournaloftaxonomy.eu 2014 · Carneiro M. et al. This work is licensed under a Creative Commons Attribution 3.0 License. Monograph urn:lsid:zoobank.org:pub:9A5F217D-8E7B-448A-9CAB-2CCC9CC6F857 Updated checklist of marine fishes (Chordata: Craniata) from Portugal and the proposed extension of the Portuguese continental shelf Miguel CARNEIRO1,5, Rogélia MARTINS2,6, Monica LANDI*,3,7 & Filipe O. COSTA4,8 1,2 DIV-RP (Modelling and Management Fishery Resources Division), Instituto Português do Mar e da Atmosfera, Av. Brasilia 1449-006 Lisboa, Portugal. E-mail: [email protected], [email protected] 3,4 CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. E-mail: [email protected], [email protected] * corresponding author: [email protected] 5 urn:lsid:zoobank.org:author:90A98A50-327E-4648-9DCE-75709C7A2472 6 urn:lsid:zoobank.org:author:1EB6DE00-9E91-407C-B7C4-34F31F29FD88 7 urn:lsid:zoobank.org:author:6D3AC760-77F2-4CFA-B5C7-665CB07F4CEB 8 urn:lsid:zoobank.org:author:48E53CF3-71C8-403C-BECD-10B20B3C15B4 Abstract. The study of the Portuguese marine ichthyofauna has a long historical tradition, rooted back in the 18th Century. Here we present an annotated checklist of the marine fishes from Portuguese waters, including the area encompassed by the proposed extension of the Portuguese continental shelf and the Economic Exclusive Zone (EEZ). The list is based on historical literature records and taxon occurrence data obtained from natural history collections, together with new revisions and occurrences. -
Serranidae), in the Southeastern Adriatic Sea by Branko GLAMUZINA, Pero TUTMAN, Valter KO∏UL, Nik≈A GLAVI¶ & Bo≈Ko SKARAMUCA (1
NOTE ICHTYOLOGIQUE - ICHTHYOLOGICAL NOTE THE FIRST RECORDED OCCURRENCE OF THE MOTTLED GROUPER, MYCTEROPERCA RUBRA (SERRANIDAE), IN THE SOUTHEASTERN ADRIATIC SEA by Branko GLAMUZINA, Pero TUTMAN, Valter KO∏UL, Nik≈a GLAVI¶ & Bo≈ko SKARAMUCA (1) RÉSUMÉ. - Premier spécimen de badèche rouge, Mycteroperca The specimen in question, examined at the Biological Institute, rubra (Serranidae), signalé en mer Adriatique du sud-est. had a total length of 327 mm; a wet mass of 381.5 g; and was Le premier exemplaire de badèche rouge, Mycteroperca rubra, estimated to be 3 years old by scale reading under binocular micro- (poids = 381,5 g ; LT = 327 mm) a été capturé en mer Adriatique scope (Fig. 2). du sud-est, au large de Dubrovnik, Croatie (42,5°N), en septembre The main feature that distinguishes M. rubra from groupers of 2001. La présence de la badèche rouge dans les eaux de la mer the genus Epinephelus, especially the very similar E. caninus, is Adriatique conforte l’hypothèse du réchauffement actuel des eaux the number of soft anal fin rays: from 10 to 13, usually 11-12, for de la Méditerranée septentrionale. M. rubra; 7 to 10 for Epinephelus and 8 for E. caninus (Heemstra and Randall, 1993). Key words. - Serranidae - Mycteroperca rubra - MED - Adriatic All other important morphological characteristics of the cap- Sea - First record. tured specimen fit well with the species description provided by Heemstra and Randall (1993) (Table I). For example, the caudal- The proposition of Francour et al. (1994) that the Mediterranean fin margin is truncated, as is typical in this genus for fish from Sea is warming is supported, at least circumstantially, by the accu- 20-50 cm SL. -
Species of Pseudorhabdosynochus (Monogenea, Diplectanidae) From
RESEARCH ARTICLE Species of Pseudorhabdosynochus (Monogenea, Diplectanidae) from Groupers (Mycteroperca spp., Epinephelidae) in the Mediterranean and Eastern Atlantic Ocean, with Special Reference to the ‘ ’ a11111 Beverleyburtonae Group and Description of Two New Species Amira Chaabane1*, Lassad Neifar1, Delphine Gey2, Jean-Lou Justine3 1 Laboratoire de Biodiversité et Écosystèmes Aquatiques, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia, 2 UMS 2700 Service de Systématique moléculaire, Muséum National d'Histoire Naturelle, OPEN ACCESS Sorbonne Universités, Paris, France, 3 ISYEB, Institut Systématique, Évolution, Biodiversité, UMR7205 (CNRS, EPHE, MNHN, UPMC), Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France Citation: Chaabane A, Neifar L, Gey D, Justine J-L (2016) Species of Pseudorhabdosynochus * [email protected] (Monogenea, Diplectanidae) from Groupers (Mycteroperca spp., Epinephelidae) in the Mediterranean and Eastern Atlantic Ocean, with Special Reference to the ‘Beverleyburtonae Group’ Abstract and Description of Two New Species. PLoS ONE 11 (8): e0159886. doi:10.1371/journal.pone.0159886 Pseudorhabdosynochus Yamaguti, 1958 is a species-rich diplectanid genus, mainly restricted to the gills of groupers (Epinephelidae) and especially abundant in warm seas. Editor: Gordon Langsley, Institut national de la santé et de la recherche médicale - Institut Cochin, Species from the Mediterranean are not fully documented. Two new and two previously FRANCE known species from the gills of Mycteroperca spp. (M. costae, M. rubra, and M. marginata) Received: April 28, 2016 in the Mediterranean and Eastern Atlantic Ocean are described here from new material and slides kept in collections. Identifications of newly collected fish were ascertained by barcod- Accepted: July 8, 2016 ing of cytochrome c oxidase subunit I (COI) sequences. -
A Parasite of Deep-Sea Groupers (Serranidae) Occurs Transatlantic
Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts ( Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic Amira Chaabane, Jean-Lou Justine, Delphine Gey, Micah Bakenhaster, Lassad Neifar To cite this version: Amira Chaabane, Jean-Lou Justine, Delphine Gey, Micah Bakenhaster, Lassad Neifar. Pseudorhab- dosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts ( Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic. PeerJ, PeerJ, 2016, 4, pp.e2233. 10.7717/peerj.2233. hal- 02557717 HAL Id: hal-02557717 https://hal.archives-ouvertes.fr/hal-02557717 Submitted on 16 Aug 2020 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. Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), -
Islnad Grouper Status Review 2015
Island Grouper (Mycteroperca fusca) Status Review Report Photo Credit: Philippe Burnel © July 2015 Ronald J. Salz Fishery Biologist National Marine Fisheries Service National Oceanic and Atmospheric Administration Silver Spring, MD Acknowledgements I thank João Pedro Barreiros, Claudia Ribeiro, and Fernando Tuya for providing their time, expertise, and insights as external peer reviewers of this report. I also thank the following NMFS co-workers who provided valuable information and feedback as internal reviewers: Dwayne Meadows, Maggie Miller, Marta Nammack, Angela Somma, and Chelsea Young. Other helpful sources of information were George Sedberry, Carlos Ferreira Santos, Albertino Martins, Rui Freitas, and the Portugal National Institute of Statistics. I also thank NOAA librarian Caroline Woods for quickly responding to article requests, and Philippe Burnel for allowing me to use his island grouper photograph on the cover page. This document should be cited as: Salz, R. J. 2015. Island Grouper (Mycteroperca fusca) Draft Status Review Report. Report to National Marine Fisheries Service, Office of Protected Resources. July 2015, 69 pp. 2 Executive Summary On July 15, 2013, NMFS received a petition to list 81 species of marine organisms as endangered or threatened species under the Endangered Species Act (ESA). If an ESA petition is found to present substantial scientific or commercial information that the petitioned action may be warranted, a status review shall be promptly commenced (16 U.S.C. 1533(b)(3)(A)). NMFS determined that for 27 of the 81 species, including the island grouper (Mycteroperca fusca), the petition had sufficient merit for consideration and that a status review was warranted (79 FR 10104, February 24, 2014). -
Activity, Habitat Use, Feeding Behavior, and Diet of Four Sympatric Species of Serranidae (Actinopterygii: Perciformes) in Southeastern Brazil
Neotropical Ichthyology, 5(3):387-398, 2007 Copyright © 2007 Sociedade Brasileira de Ictiologia Activity, habitat use, feeding behavior, and diet of four sympatric species of Serranidae (Actinopterygii: Perciformes) in southeastern Brazil Fernando Zaniolo Gibran Diplectrum formosum (the sand perch), Diplectrum radiale (the aquavina), Epinephelus marginatus (the dusky grouper) and Mycteroperca acutirostris (the comb grouper) are four sympatric serranid of remarkable ecological and commercial importance. This study investigated the feeding of these four species in the São Sebastião Channel, São Paulo State (southeastern Brazil), comparing their diet, habitat utilization and morphological features related to foraging. These four serranids are opportunistic visual predators that use a total of nine different tactics to capture their preys, feed mostly on crustaceans during the day and twilight, and keep stationary and quiescent at night. The ecomorphological study was conducted to test its predictive value to infer lifestyles. It was verified that such analysis should be used carefully and must be complemented by field observations. Although morphologically and behaviorally very similar, D. formosum and D. radiale showed different preferences to the substratum type used by large individuals, which are exclusively sit-and-wait predators. On the other hand, E. marginatus displayed more sedentary habits than M. acutirostris, the most versatile predator from the studied species. The studied species of Diplectrum and E. marginatus can be regarded as benthic serranids, while M. acutirostris could be viewed as a nektobenthic species. Diplectrum formosum, Diplectrum radiale (micholes-da-areia), Epinephelus marginatus (garoupa-verdadeira) e Mycteroperca acutirostris (badejo-mira) são quatro espécies simpátricas que pertencem à família Serranidae, de reconhecida importância ecológica e comercial. -
Ensuring Seafood Identity: Grouper Identification by Real-Time Nucleic
Food Control 31 (2013) 337e344 Contents lists available at SciVerse ScienceDirect Food Control journal homepage: www.elsevier.com/locate/foodcont Ensuring seafood identity: Grouper identification by real-time nucleic acid sequence-based amplification (RT-NASBA) Robert M. Ulrich a, David E. John b, Geran W. Barton c, Gary S. Hendrick c, David P. Fries c, John H. Paul a,* a College of Marine Science, MSL 119, University of South Florida, 140 Seventh Ave. South, St. Petersburg, FL 33701, USA b Department of Biological Sciences, University of South Florida St. Petersburg, 140 Seventh Ave. S., St. Petersburg, FL 33701, USA c EcoSystems Technology Group, College of Marine Science, University of South Florida, 140 Seventh Ave. S., St. Petersburg, FL 33701, USA article info abstract Article history: Grouper are one of the most economically important seafood products in the state of Florida and their Received 19 September 2012 popularity as a high-end restaurant dish is increasing across the U.S. There is an increased incidence rate Accepted 3 November 2012 of the purposeful, fraudulent mislabeling of less costly and more readily available fish species as grouper in the U.S., particularly in Florida. This is compounded by commercial quotas on grouper becoming Keywords: increasingly more restrictive, which continues to drive both wholesale and restaurant prices higher each RT-NASBA year. Currently, the U.S. Food and Drug Administration recognize 56 species of fish that can use “grouper” FDA seafood list as an acceptable market name for interstate commerce. This group of fish includes species from ten Grouper fi fi Mislabeling different genera, making accurate taxonomic identi cation dif cult especially if distinguishing features such as skin, head, and tail have been removed. -
Redalyc.Reproductive Cycle of The
Red de Revistas Científicas de América Latina, el Caribe, España y Portugal Sistema de Información Científica JA Estrada-Godínez, M Maldonado-García, V Gracia-López, M Carrillo Reproductive cycle of the leopard grouper Mycteroperca rosacea in La Paz Bay, Mexico Ciencias Marinas, vol. 37, núm. 4A, diciembre, 2011, pp. 425-441, Universidad Autónoma de Baja California México Available in: http://www.redalyc.org/articulo.oa?id=48020747005 Ciencias Marinas, ISSN (Printed Version): 0185-3880 [email protected], [email protected] Universidad Autónoma de Baja California México How to cite Complete issue More information about this article Journal's homepage www.redalyc.org Non-Profit Academic Project, developed under the Open Acces Initiative Ciencias Marinas (2011), 37(4): 425–441 C M Reproductive cycle of the leopard grouper Mycteroperca rosacea in La Paz Bay, Mexico Ciclo reproductivo de la cabrilla sardinera Mycteroperca rosacea en la bahía de La Paz, México JA Estrada-Godínez1, M Maldonado-García1*, V Gracia-López1, M Carrillo2 1 Centro de Investigaciones Biológicas del Noroeste, Mar Bermejo No. 195, Col. Playa Palo de Santa Rita, CP 23090, La Paz, Baja California Sur, México. 2 Instituto de Acuicultura de Torre de la Sal, Castellón, España. * Corresponding author. E-mail: [email protected] ABSTRACT. The leopard grouper Mycteroperca rosacea is an endemic species from the northwestern coast of Mexico and, like other serranid fishes, it has a high commercial value; hence, it is a good candidate for cultivation. This study aimed to describe the reproductive cycle of the leopard grouper in the wild as a step toward evaluating its aquaculture and restocking potential. -
And Cabo De Gata (Spain) Medtek: the Mediterranean Traditional Ecological Knowledge on Small-Scale Fisheries
A snapshot from Malta, Pantelleria Island (Italy) and Cabo de Gata (Spain) MedTEK: The Mediterranean Traditional Ecological Knowledge on Small-Scale Fisheries. A snapshot from Malta, Pantelleria Island (Italy) and Cabo de Gata (Spain) AUTHORS Alicia Said, Iuri Peri, Macarena Molina COORDINATION AND EDITING Marta Cavallé Mediterranean Coordinator Low Impact Fishers of Europe (LIFE) Credits Authors: Alicia Said, Iuri Peri, Macarena Molina Coordination and Editing: Marta Cavallé - Information was gathered while working with small-scale fishing communities of the different sites mentioned from January to December 2019. This report is one of the outcomes of the project Mainstreaming Small-scale Fisheries in the Mediterranean, carried out by the Low Impact Fishers of Europe, supported by the MAVA Foundation within 2018-2020. - Recommended Citation: Said, A., Peri, I. and Molina, M., 2020. MedTEK: Traditional Ecological Knowledge of Mediterranean Small-scale Fishing Communities. Preliminary Findings in Cabo de Gata (Spain), Malta and Pantelleria island (Italy) sites. Published by Low Imapct Fishers of Europe. Contact e-mail: [email protected] - DECEMBER - 2020 Executive Summary MedTEK report is a contribution resulting from a project within and for fishing communities aimed at the collection, recognition and recording of Mediterranean Traditional Ecological Knowledge (TEK). We consider TEK to be the cumulative body of knowledge, 6 practice and beliefs accumulated over time and passed to subsequent through generations. This report compiled by the Low Impact Fishers of Europe deciphers and explicates part of the local and indigenous knowledge about small-scale fisheries as perceived and lived by local fishing communities. Our lens is deployed over the Mediterranean region where we compile the MedTEK of fishing community in Pantelleria islands of Italy, the Maltese Islands, and Cabo de Gata Marine Reserve area of influence in North Alboran Sea, in the south-west of Spain. -
ASFIS ISSCAAP Fish List February 2007 Sorted on Scientific Name
ASFIS ISSCAAP Fish List Sorted on Scientific Name February 2007 Scientific name English Name French name Spanish Name Code Abalistes stellaris (Bloch & Schneider 1801) Starry triggerfish AJS Abbottina rivularis (Basilewsky 1855) Chinese false gudgeon ABB Ablabys binotatus (Peters 1855) Redskinfish ABW Ablennes hians (Valenciennes 1846) Flat needlefish Orphie plate Agujón sable BAF Aborichthys elongatus Hora 1921 ABE Abralia andamanika Goodrich 1898 BLK Abralia veranyi (Rüppell 1844) Verany's enope squid Encornet de Verany Enoploluria de Verany BLJ Abraliopsis pfefferi (Verany 1837) Pfeffer's enope squid Encornet de Pfeffer Enoploluria de Pfeffer BJF Abramis brama (Linnaeus 1758) Freshwater bream Brème d'eau douce Brema común FBM Abramis spp Freshwater breams nei Brèmes d'eau douce nca Bremas nep FBR Abramites eques (Steindachner 1878) ABQ Abudefduf luridus (Cuvier 1830) Canary damsel AUU Abudefduf saxatilis (Linnaeus 1758) Sergeant-major ABU Abyssobrotula galatheae Nielsen 1977 OAG Abyssocottus elochini Taliev 1955 AEZ Abythites lepidogenys (Smith & Radcliffe 1913) AHD Acanella spp Branched bamboo coral KQL Acanthacaris caeca (A. Milne Edwards 1881) Atlantic deep-sea lobster Langoustine arganelle Cigala de fondo NTK Acanthacaris tenuimana Bate 1888 Prickly deep-sea lobster Langoustine spinuleuse Cigala raspa NHI Acanthalburnus microlepis (De Filippi 1861) Blackbrow bleak AHL Acanthaphritis barbata (Okamura & Kishida 1963) NHT Acantharchus pomotis (Baird 1855) Mud sunfish AKP Acanthaxius caespitosa (Squires 1979) Deepwater mud lobster Langouste