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DISEASES OF AQUATIC ORGANISMS Vol. 80: 241–258, 2008 Published August 7 Dis Aquat Org COMBINED AUTHOR AND TITLE INDEX (Volumes 71 to 80, 2006–2008) A (2006) Persistence of Piscirickettsia salmonis and detection of serum antibodies to the bacterium in white seabass Atrac- Aarflot L, see Olsen AB et al. (2006) 72:9–17 toscion nobilis following experimental exposure. 73:131–139 Abreu PC, see Eiras JC et al. (2007) 77:255–258 Arunrut N, see Kiatpathomchai W et al. (2007) 79:183–190 Acevedo C, see Silva-Rubio A et al. (2007) 79:27–35 Arzul I, see Carrasco N et al. (2007) 79:65–73 Adams A, see McGurk C et al. (2006) 73:159–169 Arzul I, see Corbeil S et al. (2006) 71:75–80 Adkison MA, see Arkush KD et al. (2006) 73:131–139 Arzul I, see Corbeil S et al. (2006) 71:81–85 Aeby GS, see Work TM et al. (2007) 78:255–264 Ashton KJ, see Kriger KM et al. (2006) 71:149–154 Aguirre WE, see Félix F et al. (2006) 75:259–264 Ashton KJ, see Kriger KM et al. (2006) 73:257–260 Aguirre-Macedo L, see Gullian-Klanian M et al. (2007) 79: Atkinson SD, see Bartholomew JL et al. (2007) 78:137–146 237–247 Aubard G, see Quillet E et al. (2007) 76:7–16 Aiken HM, see Hayward CJ et al. (2007) 79:57–63 Audemard C, Carnegie RB, Burreson EM (2008) Shellfish tis- Aishima N, see Maeno Y et al. (2006) 71:169–173 sues evaluated for Perkinsus spp. using the Ray’s fluid Akiyama K, see Yoshinaga T et al. (2007) 78:155–160 thioglycollate medium culture assay can be used for Alcaide E, Herraiz S, Esteve C (2006) Occurrence of Edward- downstream molecular assays 80:233–237 siella tarda in wild European eels Anguilla anguilla from Austin FW, see Ostland VE et al. (2007) 79:107–118 Mediterranean Spain. 73:77–81 Avendaño-Herrera R, Toranzo AE, Magariños B (2006) Tena- Alday Sanz V, see Escobedo-Bonilla CM et al. (2006) 74: cibaculosis infection in marine fish caused by Tenacibacu- 85–94 lum maritimum: a review. 71:255–266 Alday-Sanz V, see Rahman MM et al. (2007) 79:191–198 Avendaño-Herrera R, see Silva-Rubio A et al. (2007) 79:27–35 Alford RA, see Cashins SD et al. (2008) 80:63–67 Azad IS, see Al-Marzouk A (2007) 76:49–56 Alford RA, see Rowley JJL (2007) 77:1–9 Azad IS, Shekhar MS, Thirunavukkarasu AR, Jithendran KP Alford RA, see Rowley JJL et al. (2006) 74:7–12 (2006) Viral nerve necrosis in hatchery-produced fry of Alford RA, see Rowley JJL et al. (2007) 78:87–95 Asian seabass Lates calcarifer: sequential microscopic Al-Hussinee L, see Lumsden JS et al. (2007) 76:99–111 analysis of histopathology. 73:123–130 Alishahi M, Buchmann K (2006) Temperature-dependent pro- Azevedo C, Conchas RF, Tajdari J, Montes J (2006) Ultra- tection against Ichthyophthirius multifiliis following structural description of new Rickettsia-like organisms in immunisation of rainbow trout using live theronts. 72: the commercial abalone Haliotis tuberculata (Gastropoda: 269–273 Haliotidae) from the NW of Spain. 71:233–237 Allam B, see Qian H et al. (2007) 77:159–168 Azevedo C, see Gestal C (2006) 71:25–31 Aller-Gancedo JM, see Fregeneda-Grandes JM et al. (2006) 74:107–111 Al-Marzouk A, Azad IS (2007) Growth kinetics, protease B activity and histophagous capability of Uronema sp. infesting cultured silver pomfret Pampus argenteus in Bain N, see López-Vázquez C et al. (2006) 73:23–31 Kuwait. 76:49–56 Bakke HG, see Glover KA et al. (2007) 76:57–65 Al-Samman A, see Székely C et al. (2006) 74:127–137 Baldi Salas M, see Walker SF et al. (2007) 77:105–112 Ammassari LL, see Natale GS et al. (2006) 72:261–267 Baldwin CA, see Gray MJ et al. (2007) 77:97–103 Amorena M, see Perugini M et al. (2006) 71:155–161 Bandín I, see López-Vázquez C et al. (2006) 73:23–31 An EJ, see Cha SJ et al. (2007) 77:181–189 Barandela T, see Ramos MF et al. (2006) 74:249–253 Anderson CW, see Kirshtein JD et al. (2007) 77:11–15 Barber BJ, see Maloy AP et al. (2007) 76:151–161 Anderson RC, see Mather JA (2006) 75:119–129 Barrionuevo S, Mangione S (2006) Chytridiomycosis in two Angelidis P, Karagiannis D, Crump EM (2006) Efficacy of a species of Telmatobius (Anura: Leptodactylidae) from Listonella anguillarum (syn. Vibrio anguillarum) vaccine Argentina. 73:171–174 for juvenile sea bass Dicentrarchus labrax. 71:19–24 Bartholomew JL, Atkinson SD, Hallett SL, Zielinski CM, Foott Anil TM, see Patil R et al. (2007) 79:157–161 JS (2007) Distribution and abundance of the salmonid par- Anthony R, see Lund V et al. (2006) 75:109–118 asite Parvicapsula minibicornis (Myxozoa) in the Klamath Aoki T (2007) In Memoriam Syuzo Egusa. 78:179 River basin (Oregon-California, USA). 78:137–146 Aoki T, see Matsuyama T et al. (2006) 75:79–83 Bartholomew JL, see Hallett SL (2006) 71:109–118 Arias-Bañuelos E, see Huchin-Mian JP et al. (2007) 79: Bartholomew JL, see Roberts JF et al. (2008) 80:199–207 153–156 Basso NG, see Natale GS et al. (2006) 72:261–267 Arias-Fernández C, see Crespo-González C et al. (2007) 79: Bateman K, see Verner-Jeffreys DW et al. (2007) 79:207–218 83–86 Bateman KS, Stentiford GD (2007) Cancer pagurus bacilli- Arikan H, see Saglam N (2006) 72:253–260 form virus (CpBV) infecting juvenile European edible Arkush KD, Edes HL, McBride AM, Adkison MA, Hedrick RP crabs C. pagurus from UK waters. 79:147–151 © Inter-Research 2008 · www.int-res.com 242 Dis Aquat Org 80: 241–258, 2008 Bateman KS, see Stentiford GD (2006) 75:73–78 Branson EJ, see Graham DA et al. (2006) 74:191–197 Bateman KS, see Stentiford GD et al. (2006) 75:61–72 Bremont M, see Romero A et al. (2008) 80:123–135 Batts WN, see Groocock GH et al. (2007) 76:187–192 Bresciani J, see Jørgensen TR et al. (2006) 73:235–244 Bebak J, see Draghi A II et al. (2007) 76:27–38 Bricknell IR, Dalesman SJ, O’Shea B, Pert CC, Mordue Luntz Becker JA, see Jones MA et al. (2007) 78:29–36 AJ (2006) Effect of environmental salinity on sea lice Lep- Becker P, Gillan DC, Eeckhaut I (2007) Microbiological study eophtheirus salmonis settlement success. 71:201–212 of the body wall lesions of the echinoid Tripneustes Bricknell IR, see McBeath AJA et al. (2006) 73:141–150 gratilla. 77:73–82 Bright Singh IS, see Preetha R et al. (2006) 74:243–247 Bégout ML, see Durieux EDH et al. (2006) 75:221–228 Briones-Fourzán P, see Huchin-Mian JP et al. (2007) 79: Behringer DC, see Butler MJ et al. (2007) 79:173–182 153–156 Bekoff M (2006) Aquatic animals, cognitive ethology, and Briones-Fourzán P, see Lozano-Álvarez E et al. (2008) 80: ethics: questions about sentience and other troubling 95–104 issues that lurk in turbid water. 75:87–98 Britt KL, see Groocock GH et al. (2007) 76:187–192 Bendorf CM, see Kelley GO et al. (2007) 77:29–40 Broadhurst MK, Butcher PA, Brand CP, Porter M (2006) Inges- Berger L, see Hyatt AD et al. (2006) 73:175–192 tion and ejection of hooks: effects on long-term health and Berger L, see Skerratt LF et al. (2008) 80:85–94 mortality of angler-caught yellowfin bream Acanthopa- Berger L, see Voyles J et al. (2007) 77:113–118 grus australis. 74:27–36 Berger L, see Webb R et al. (2006) 74:13–16 Broadhurst MK, Millar RB, Brand CP, Uhlmann SS (2008) Bergh Ø (2006) The dual myths of the healthy wild fish and Mortality of discards from southeastern Australian beach the unhealthy farmed fish. 75:159–164 seines and gillnets. 80:51–61 Bergh Ø, see Engelsen AR et al. (2008) 80:13–20 Broadhurst MK, see Butcher PA et al. (2006) 74:17–26 Bergh Ø, see Patel S et al. (2007) 77:169–173 Broadhurst MK, see Uhlmann SS (2007) 76:173–186 Bergh Ø, see Samuelsen OB et al. (2006) 71:239–254 Broom DM (2006) Cognitive ability and sentience: Which Bermingham M, see Hanajavanit C et al. (2008) 80:145–156 aquatic animals should be protected? 75:99–108 Bermingham ML, Mulcahy MF (2007) Neoparamoeba sp. and Browman HI, see Fields DM et al. (2007) 78:161–168 other protozoans on the gills of Atlantic salmon Salmo Browman HI, Skiftesvik AB (2006) Moral, ethical and scien- salar smolts in seawater. 76:231–240 tific aspects of welfare in aquatic organisms. 75:85 Berthe FCJ, see Carrasco N et al. (2007) 79:65–73 Brown GD, see Moss JA et al. (2007) 77:207–223 Berthe FCJ, see Choi DL et al. (2006) 72:65–69 Browne RK, Li H, Vaughan M (2006) Sexually mediated shed- Berthe FCJ, see Corbeil S et al. (2006) 71:75–80 ding of Myxobolus fallax spores during spermiation of Berthe FCJ, see Corbeil S et al. (2006) 71:81–85 Litoria fallax (Anura). 72:71–75 Besnard-Cochennec N, see Corbeil S et al. (2006) 71:81–85 Bruheim T, see Sterud E et al. (2007) 77:191–198 Birkbeck TH, see Olsen AB et al.
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    Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay George Tsipas SCHOOL OF ECONOMICS, BUSINESS ADMINISTRATION & LEGAL STUDIES A thesis submitted for the degree of Master of Science (MSc) in Bioeconomy Law, Regulation and Management May, 2019 Thessaloniki – Greece George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ Student Name: George Tsipas SID: 268186037282 Supervisor: Prof. Dr. Savvas Genitsaris I hereby declare that the work submitted is mine and that where I have made use of another’s work, I have attributed the source(s) according to the Regulations set in the Student’s Handbook. May, 2019 Thessaloniki - Greece Page 2 of 63 George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ 1. Abstract The present research investigates through metagenomics sequencing the unicellular protistan communities in Thermaikos Gulf. This research analyzes the diversity, composition and abundance in this marine environment. Water samples were collected monthly from April 2017 to February 2018 in the port of Thessaloniki (Harbor site, 40o 37’ 55 N, 22o 56’ 09 E). The extraction of DNA was completed as well as the sequencing was performed, before the downstream read processing and the taxonomic classification that was assigned using PR2 database. A total of 1248 Operational Taxonomic Units (OTUs) were detected but only 700 unicellular eukaryotes were analyzed, excluding unclassified OTUs, Metazoa and Streptophyta. In this research-based study the most abundant and diverse taxonomic groups were Dinoflagellata and Protalveolata. Specifically, the most abundant groups of all samples are Dinoflagellata with 190 OTUs (27.70%), Protalveolata with 139 OTUs (20.26%) Ochrophyta with 73 OTUs (10.64%), Cercozoa with 67 OTUs (9.77%) and Ciliophora with 64 OTUs (9.33%).
  • Respiratory Disorders of Fish

    Respiratory Disorders of Fish

    This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Author's personal copy Disorders of the Respiratory System in Pet and Ornamental Fish a, b Helen E. Roberts, DVM *, Stephen A. Smith, DVM, PhD KEYWORDS Pet fish Ornamental fish Branchitis Gill Wet mount cytology Hypoxia Respiratory disorders Pathology Living in an aquatic environment where oxygen is in less supply and harder to extract than in a terrestrial one, fish have developed a respiratory system that is much more efficient than terrestrial vertebrates. The gills of fish are a unique organ system and serve several functions including respiration, osmoregulation, excretion of nitroge- nous wastes, and acid-base regulation.1 The gills are the primary site of oxygen exchange in fish and are in intimate contact with the aquatic environment. In most cases, the separation between the water and the tissues of the fish is only a few cell layers thick. Gills are a common target for assault by infectious and noninfectious disease processes.2 Nonlethal diagnostic biopsy of the gills can identify pathologic changes, provide samples for bacterial culture/identification/sensitivity testing, aid in fungal element identification, provide samples for viral testing, and provide parasitic organisms for identification.3–6 This diagnostic test is so important that it should be included as part of every diagnostic workup performed on a fish.
  • Detection and Identification of Fish Pathogens: What Is the Future?

    Detection and Identification of Fish Pathogens: What Is the Future?

    The Israeli Journal of Aquaculture – Bamidgeh 60(4), 2008, 213-229. 213 Detection and Identification of Fish Pathogens: What is the Future? A Review I. Frans1,2†, B. Lievens1,2*†, C. Heusdens1,2 and K.A. Willems1,2 1 Scientia Terrae Research Institute, B-2860 Sint-Katelijne-Waver, Belgium 2 Research Group Process Microbial Ecology and Management, Department Microbial and Molecular Systems, Katholieke Universiteit Leuven Association, De Nayer Campus, B-2860 Sint-Katelijne-Waver, Belgium, and Leuven Food Science and Nutrition Research Centre (LfoRCe), Katholieke Universiteit Leuven, B-3001 Heverlee-Leuven, Belgium (Received 1.8.08, Accepted 20.8.08) Key words: biosecurity, diagnosis, DNA array, multiplexing, real-time PCR Abstract Fish diseases pose a universal threat to the ornamental fish industry, aquaculture, and public health. They can be caused by many organisms, including bacteria, fungi, viruses, and protozoa. The lack of rapid, accurate, and reliable means of detecting and identifying fish pathogens is one of the main limitations in fish pathogen diagnosis and disease management and has triggered the search for alternative diagnostic techniques. In this regard, the advent of molecular biology, especially polymerase chain reaction (PCR), provides alternative means for detecting and iden- tifying fish pathogens. Many techniques have been developed, each requiring its own protocol, equipment, and expertise. A major challenge at the moment is the development of multiplex assays that allow accurate detection, identification, and quantification of multiple pathogens in a single assay, even if they belong to different superkingdoms. In this review, recent advances in molecular fish pathogen diagnosis are discussed with an emphasis on nucleic acid-based detec- tion and identification techniques.