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ADVANCES IN BIVALVE MOLLUSCS IMMUNE SYSTEM: A GENOMIC APPROACH PhD THESIS REBECA MOREIRA SANMARTÍN VIGO 2015 ADVANCES IN BIVALVE MOLLUSCS IMMUNE SYSTEM: A GENOMIC APPROACH Thesis submitted by Rebeca Moreira Sanmartín for the degree of Doctor of the University of Vigo with international mention and as compendium of articles Doctoral Degree Program in Methodology and Applications in Life Sciences VIGO 2015 UNIVERSITY OF VIGO FACULTY OF BIOLOGY SPANISH NATIONAL RESEARCH COUNCIL MARINE RESEARCH INSTITUTE AVANCES EN EL ESTUDIO DEL SISTEMA INMUNITARIO DE MOLUSCOS BIVALVOS: UNA APROXIMACIÓN GENÓMICA Memoria de tesis presentada por Rebeca Moreira Sanmartín para optar al grado de Doctor por la Universidad de Vigo con mención internacional y por compendio de artículos Programa de doctorado en Metodología y Aplicaciones en Ciencias de la Vida VIGO 2015 UNIVERSIDADE DE VIGO FACULTADE DE BIOLOXÍA CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS INSTITUTO DE INVESTIGACIONES MARINAS Dña. BEATRIZ NOVOA GARCÍA, Doctora en Biología e Investigadora Científica del Consejo Superior de Investigaciones Científicas (CSIC), junto con D. ANTONIO FIGUERAS HUERTA, Doctor en Biología y Profesor de Investigación del Consejo Superior de Investigaciones Científicas (CSIC) y D. PABLO BALSEIRO VIGO, Doctor en Biología e Investigador en la Universidad de Bergen, INFORMAN: Que la presente memoria adjunta, titulada “ADVANCES IN BIVALVE MOLLUSCS IMMUNE SYSTEM: A GENOMIC APPROACH” / “AVANCES EN EL ESTUDIO DEL SISTEMA INMUNITARIO DE MOLUSCOS BIVALVOS: UNA APROXIMACIÓN GENÓMICA” presentada por Dña. Rebeca Moreira Sanmartín para optar al grado de Doctor por la Universidad de Vigo, con mención intternacional y por compendio de artículos, ha sido realizada bajo nuestra dirección y reúne los requisitos necesarios para ser ddefendida ante el tribunal calificador. Y parra que así conste, se firma la presente en Vigo, a 29 de septiembre de 2015. Dra. Beatriz Novoa García Dr. Antonio Figueras Huerta Dr. Pablo BBalseiro Vigo Visto bueno del supervisor en la Unniversidad de Vigo: Dr. David Posada González. With the support of the Spanish Ministerio de Ciencia e Innovación through a FPI research Grant (BES‐2009‐029765) associated to the project (AGL2008‐05111). This work has also partially been funded by the projects: REPROSEED (FP7 245119), BIVALIFE (FP7‐KBBE‐2010‐ 4/266157) and Genome project of the galician mussel Mytilus galloprovincialis(16 10 PXIB 402 096 PR). Con el apoyo del Ministerio de Ciencia e Innovación, por la concesión de una beca predoctoral de Formación de Personal Investigador (FPI), asociada al proyecto de investigación AGL2008‐ 05111 “Genes de moluscos bivalvos implicados en la resistencia frente a enfermedades e interacción con agentes patógenos”. Además se ha recibido apoyo de los siguientes proyectos: REPROSEED (FP7 245119), BIVALIFE (FP7‐KBBE‐2010‐4/266157) y Proxecto xenoma do mexilón galego Mytilus galloprovincialis(16 10 PXIB 402 096 PR). ACKNOWLEDGEMENTS agradecimientos Estos años me he sentido muy feliz con este trabajo y aún en estos mallos tiempos para la ciencia en los que todos nos preguntamos Cómo Seguir Investigandoo en Crisis: When life knocks you down...Calmly get back up, smile, and very politely say: 'Youu hit like a bitch.' Después de pasar mucho tiempo “pensando en escribir la tesis” y de aprender, por las malas, lo que significa procrastination… Tengo que dar las gracias a mucha gente porque al final me moví al quesito amarillo! Gracias a Beatriz Novoa y Antonio Figuueras, mis directores de tesis, por haber confiado en mí y hacerme un huequito primero en “pato” y después en “I++G”. Me habéis enseñado a hacer ciencia y gracias a vosotros he cumplido mi sueño de ser una… ¡investigadora científica! A Pablo Balseiro, mi codirector de tesis y el que me ha enseñado prácticamente todo lo que sé en técnicas de laboratorio y bioinformática, aunque a veces fuese a base de… “ññññññ, así no!!! Mal, mal, maaaaal!!!!”. Muchas gracias por todo WikkiPablo! También al resto de los docs del laboratorio: a Laura, Raquel, MMar, PDR, Sonia, Álex, vuestra paciencia y explicaciones sobre BLAST, diseño de primmers, citometría, patógenos, infecciones, medios de cultivo, orden y limpieza en el laboratorio… también son parte de esta tesis. A la gente del despachito, cualquieraa que fuese su ubicación, por nuestros “debates” sobre las dudas en protocolos, desarrollo larvario, filogenética, extracción de ARN… pero sobre todo: cómo hacer que las réplicas técnicas salgan clavadas???!!! Primero estuvimos en el despachito del pasillo: gracias a Noe, Monse, Rosi y Sheila, y a Eva, que empeezamos juntas el mismo día y eso une! Después de subir y bajjar con nuestros bártulos nos instalamos (definitivamente) en el despachito de histología: gracias a Rubén, por todo lo que me ayudaste y lo que me enseñaste en acuaarios, no fueron pocas cosas, ni sencillas… a Paolo, grazie a te non mi ho dimenticato del poco italiano che so! Y muy especialmente a Patry, Mónica y Gabriel, que os puedo decir que no nos hayaamos dicho ya… Nos hicimos muy buenos amigos, de esos que son para siempre, de esos a los que unen la ciencia, las cañas, el churrasco y el licor café! agradecimientos Gracias también a mi tutor, David Posada, y a Carlos Canchaya del Departamento de Bioquímica, Genética e Inmunología ‐ Universidad de Vigo. Aunque costó lo suyo tanto los árboles filogenéticos como el RNA‐Seq salieron adelante! Devo ringraziare a tante persone al Dipartimento di Biomedicina Comparata e Alimentazione ‐ Universitá degli Studi di Padova. Prima al Prof. Luca Bargelloni, grazie per la oportunitá di lavorare con tutti voi... due volte! Grazie mille a Massimo, Max e Marianna, con voi ho imparato tuto quelo che so da microarray. Ma devo anche ringraziare a Sere, Lisa, Rafaella, Sara, Francesco, Barbara, Laura, Nadia, Enrico… sicuro lascio a qualcuno... tutti havete fatto del mio soggiorno a Padova un bello ricordo. Grazie per le setate italiane: spritz, birra e pizza. Non mi dimenticaró più dei pranzi sulle scalle d’incendio! Thanks also to all the authors of the papers I’ve read all these years. They made me a bit wiser every day. Especially to all of whom I had the luck to meet in conferences or in project meetings, thank you for your questions, recommendations, advice… A mis “COMPIS” pero muy especialmente a “Las de siempre ” Ana, Ire, MFe, MLuz, Vane, porque sois mis mejores amigas, alegrándoos más que yo en los buenos momentos y dándome ánimos sinceros en los malos. Algunas veces riñéndome por no meterle caña a la tesis. Y aunque a veces sois rabudas y me lleváis la contraria en cosas de ciencia… Yo os quiero igual maricas! A mi familia no tengo palabras, ni espacio suficiente, para agradecerles… TODO!!! A mis padres que siempre han confiado en que voy a ganar el Nobel, o a cambiar el mundo o algo así… (o eso me transmiten cuando me miran!), gracias por enseñarme lo que de verdad importa en la vida (incluido cuidar de nuestra pequeña granja!) y a ser buena persona. Vosotros sí que sois grandes! Salo, ya todo el mundillo científico que me conoce sabe lo que es el pen‐vaca! Mira que ha almacenado conocimiento esa vaquita y sus 4G de estómago… Jaco, en breves ya tendrás que llamarme “doc” pero en serio, no de coña, eh? ;D Amore, a ti te debo lo que soy ahora. Gracias por hacerme rabiar, por hacerme reír, por abrazarme justo cuando lo necesito. Gracias por aguantar mis charlas cuando me apasiona algo, aunque luego me digas “Peque, qué lai eres…”. También disfrutaste de tus momentos lais corrigiéndome algunas cosas de la tesis, no lo niegues! Mi vida es mejor contigo, gracias a ti soy feliz! ¿Me dejo a alguien atrás? Seguro… Gracias a cualquiera que haya hecho lo más mínimo por echarme una manita durante estos años, consciente o inconscientemente. Gracias, gracias, gracias!!! agradecimientos INDEX index RESUMEN .................................................................................................................... i Introducción ............................................................................................................................. iii Objetivos ................................................................................................................................... x Publicaciones ............................................................................................................................ xi Discusión ................................................................................................................................. xvi Conclusiones ......................................................................................................................... xviii INTRODUCTION .......................................................................................................... 1 Background ............................................................................................................................... 3 Bivalves aquaculture ................................................................................................................. 4 Clam .................................................................................................................................................... 5 Mussel ................................................................................................................................................. 6 Immune system in bivalve molluscs ......................................................................................... 7 Cellular immunity ...............................................................................................................................
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  • Bacterial Communities in the Water of Larval-Rearing System for the Yesso Scallop (Patinopecten Yessoensis)

    Bacterial Communities in the Water of Larval-Rearing System for the Yesso Scallop (Patinopecten Yessoensis)

    International Journal of Oceanography & Aquaculture Bacterial Communities in the Water of Larval-Rearing System for the Yesso Scallop (Patinopecten Yessoensis) Ma Y1*, Liang J 2, Zhao X2, Li M2, Sun X1 and Liu J1 Review Article 1Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea of Volume 1 Issue 2 Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China Received Date: April 03, 2017 2Zhangzi island Group Company Limited, Dalian 116001, China Published Date: April 19, 2017 *Corresponding author: Yuexin Ma, Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea of Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China, Tel: +86-41184763096; E-mail: [email protected] Abstract Bacterial disease is a significant issue for larviculture of the Yesso scallop (Patinopecten yessoensis). One source of bacteria is the water of larval-rearing tanks. In this study, water bacterial communities were investigated by MiSeq sequencing during larval development at fertilized egg W1, trochophora W2, D-shaped larvae W3, umbo larvae W4, juvenile scallop W5 stages. Genomic DNA was extracted from the water samples, and a gene segment from the V3-V4 portion of the 16S rRNA gene was amplified and sequenced using an Illumina Miseq sequencer. A total of 69245 optimized reads obtained from five samples were identified as 9 phyla and 86 genera. Bacterial communities were dominated by the Proteobacteria and Bacteroidetes at phylum level across five larval development stages. At genus level, sequences assigned to Pseudoalteromonas, NS3a marine group and Sulfitobacter were dominant at stages of W1, W4 and W5. Moreover, reads from Vibrio became dominant at stage W2, followed by Pseudoalteromonas and Sulfitobacter; Glaciecola was dominant at stage W3, followed by NS3a marine group and Sulfitobacter.
  • Journal of Aquatic Animal Health Improvements Are Needed in Reporting of Accuracy Studies for Diagnostic Tests Used for Detectio

    Journal of Aquatic Animal Health Improvements Are Needed in Reporting of Accuracy Studies for Diagnostic Tests Used for Detectio

    This article was downloaded by: [Department Of Fisheries] On: 17 November 2014, At: 00:12 Publisher: Taylor & Francis Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK Journal of Aquatic Animal Health Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/uahh20 Improvements are Needed in Reporting of Accuracy Studies for Diagnostic Tests Used for Detection of Finfish Pathogens Ian A. Gardnera, Timothy Burnleyb & Charles Caraguelc a Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island C1A 4P3, Canada b Eastern Epidemiological Services, 23 Karen Drive, Cornwall, Prince Edward Island C0A 1H8, Canada c School of Animal and Veterinary Sciences, Roseworthy Campus, University of Adelaide, Roseworthy, South Australia 5371, Australia Published online: 17 Sep 2014. To cite this article: Ian A. Gardner, Timothy Burnley & Charles Caraguel (2014) Improvements are Needed in Reporting of Accuracy Studies for Diagnostic Tests Used for Detection of Finfish Pathogens, Journal of Aquatic Animal Health, 26:4, 203-209, DOI: 10.1080/08997659.2014.938867 To link to this article: http://dx.doi.org/10.1080/08997659.2014.938867 PLEASE SCROLL DOWN FOR ARTICLE Taylor & Francis makes every effort to ensure the accuracy of all the information (the “Content”) contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis.