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Toubanaki DK, Efstathiou A, Tzortzatos OP, Valsamidis MA, Papaharisis L, Bakopoulos V, Karagouni E. Nervous Necrosis Virus Modulation of European Sea Bass ( Dicentrarchus labrax, L.) Immune Genes and Transcriptome towards Establishment of Virus Carrier State. Int J Mol Sci 2023; 24:16613. [PMID: 38068937 PMCID: PMC10706053 DOI: 10.3390/ijms242316613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Viral infections of teleost fish have great environmental and economic implications in aquaculture. Nervous necrosis virus (NNV) is a pathogen affecting more than 120 different species, causing high mortality and morbidity. Herein, we studied the course of NNV experimental infection of D. labrax, focusing on survivors which indicated viral carrier state. To determine the carrier state of D. labrax head kidney, we performed a gene expression analysis of selected immune-related genes and we profiled its transcriptome 14 days post infection (dpi). All tested genes showed clear differentiations in expression levels while most of them were up-regulated 14 dpi suggesting that their role is not limited in early antiviral responses, but they are also implicated in disease persistence. To gain a better understanding of the fish that survived the acute infection but still maintained a high viral load, we studied the differential expression of 124 up-regulated and 48 down-regulated genes in D. labrax head kidney, at 14 dpi. Concluding, the NNV virus persistent profile was assessed in D. labrax, where immune-related gene modification was intense (14 dpi) and the head kidney transcriptome profile at this time point offered a glimpse into host attempts to control the infection in asymptomatic carriers.
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Affiliation(s)
- Dimitra K. Toubanaki
- Immunology of Infection Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.K.T.); (A.E.); (O.-P.T.)
| | - Antonia Efstathiou
- Immunology of Infection Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.K.T.); (A.E.); (O.-P.T.)
| | - Odysseas-Panagiotis Tzortzatos
- Immunology of Infection Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.K.T.); (A.E.); (O.-P.T.)
| | - Michail-Aggelos Valsamidis
- Department of Marine Sciences, School of the Environment, University of the Aegean, University Hill, Lesvos, 81100 Mytilene, Greece; (M.-A.V.); (V.B.)
| | | | - Vasileios Bakopoulos
- Department of Marine Sciences, School of the Environment, University of the Aegean, University Hill, Lesvos, 81100 Mytilene, Greece; (M.-A.V.); (V.B.)
| | - Evdokia Karagouni
- Immunology of Infection Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.K.T.); (A.E.); (O.-P.T.)
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2
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Zafeiropoulos H, Gioti A, Ninidakis S, Potirakis A, Paragkamian S, Angelova N, Antoniou A, Danis T, Kaitetzidou E, Kasapidis P, Kristoffersen JB, Papadogiannis V, Pavloudi C, Ha QV, Lagnel J, Pattakos N, Perantinos G, Sidirokastritis D, Vavilis P, Kotoulas G, Manousaki T, Sarropoulou E, Tsigenopoulos CS, Arvanitidis C, Magoulas A, Pafilis E. 0s and 1s in marine molecular research: a regional HPC perspective. Gigascience 2021; 10:6353916. [PMID: 34405237 PMCID: PMC8371273 DOI: 10.1093/gigascience/giab053] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 01/23/2023] Open
Abstract
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade's experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility's future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
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Affiliation(s)
- Haris Zafeiropoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013, Heraklion, Crete, Greece
| | - Anastasia Gioti
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Stelios Ninidakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Antonis Potirakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Savvas Paragkamian
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013, Heraklion, Crete, Greece
| | - Nelina Angelova
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Aglaia Antoniou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Theodoros Danis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,School of Medicine, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Eliza Kaitetzidou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Panagiotis Kasapidis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Jon Bent Kristoffersen
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Vasileios Papadogiannis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Christina Pavloudi
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Quoc Viet Ha
- Bull SAS, Rue du Gros Caillou, 78340 Les Clayes-sous-Bois, France
| | - Jacques Lagnel
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche Provence-Alpes-Côte d'Azur, Domaine Saint Maurice, CS60094, 84143 Montfavet Cedex, France
| | - Nikos Pattakos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Giorgos Perantinos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Dimitris Sidirokastritis
- Hellenic Centre for Marine Research, Network Operation Center, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Panagiotis Vavilis
- Hellenic Centre for Marine Research, Network Operation Center, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Tereza Manousaki
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Elena Sarropoulou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Costas S Tsigenopoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Christos Arvanitidis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,LifeWatch European Research Infrastructure Consortium, Sector II-III Plaza de España, 41071, Seville, Spain
| | - Antonios Magoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Evangelos Pafilis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
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3
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Pontigo JP, Espinoza C, Hernandez M, Nourdin G, Oliver C, Avendaño-Herrera R, Figueroa J, Rauch C, Troncoso JM, Vargas-Chacoff L, Yáñez AJ. Protein-Based Vaccine Protect Against Piscirickettsia salmonis in Atlantic Salmon ( Salmo salar). Front Immunol 2021; 12:602689. [PMID: 33679740 PMCID: PMC7927424 DOI: 10.3389/fimmu.2021.602689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/22/2021] [Indexed: 11/25/2022] Open
Abstract
An effective and economical vaccine against the Piscirickettsia salmonis pathogen is needed for sustainable salmon farming and to reduce disease-related economic losses. Consequently, the aquaculture industry urgently needs to investigate efficient prophylactic measures. Three protein-based vaccine prototypes against Piscirickettsia salmonis were prepared from a highly pathogenic Chilean isolate. Only one vaccine effectively protected Atlantic salmon (Salmo salar), in correlation with the induction of Piscirickettsia-specific IgM antibodies and a high induction of transcripts encoding pro-inflammatory cytokines (i.e., Il-1β and TNF-α). In addition, we studied the proteome fraction protein of P. salmonis strain Austral-005 using multidimensional protein identification technology. The analyzes identified 87 proteins of different subcellular origins, such as the cytoplasmic and membrane compartment, where many of them have virulence functions. The other two prototypes activated only the innate immune responses, but did not protect Salmo salar against P. salmonis. These results suggest that the knowledge of the formulation of vaccines based on P. salmonis proteins is useful as an effective therapy, this demonstrates the importance of the different research tools to improve the study of the different immune responses, resistance to diseases in the Atlantic salmon. We suggest that this vaccine can help prevent widespread infection by P. salmonis, in addition to being able to be used as a booster after a primary vaccine to maintain high levels of circulating protective antibodies, greatly helping to reduce the economic losses caused by the pathogen.
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Affiliation(s)
- Juan Pablo Pontigo
- Laboratorio de Biotecnología Aplicada, Facultad de Medicina Veterianaria, Universidad San Sebastián, Puerto Montt, Chile
| | - Carla Espinoza
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Mauricio Hernandez
- Proteogenomics Laboratory, Molecular Epidemiology for Life of Science reseArch (MELISA) Institute, San Pedro de Paz, Chile
| | - Guillermo Nourdin
- Proteogenomics Laboratory, Molecular Epidemiology for Life of Science reseArch (MELISA) Institute, San Pedro de Paz, Chile
| | - Cristian Oliver
- Laboratorio de Biotecnología Acuática, Facultad de Ciencias Veterinarias. Universidad Austral de Chile, Valdivia, Chile
| | - Rubén Avendaño-Herrera
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile.,Laboratorio de Patología de Organismos Acuaticos y Biotecnologia Acuicola, Facultad de Ciencias Biologicas, Universidad Andres Bello, Viña del Mar, Chile
| | - Jaime Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
| | - Cecilia Rauch
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Luis Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile.,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Alejandro J Yáñez
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile.,Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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4
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Moreno P, Gemez-Mata J, Garcia-Rosado E, Bejar J, Labella AM, Souto S, Alonso MC. Differential immunogene expression profile of European sea bass (Dicentrarchus labrax, L.) in response to highly and low virulent NNV. FISH & SHELLFISH IMMUNOLOGY 2020; 106:56-70. [PMID: 32702480 DOI: 10.1016/j.fsi.2020.06.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
European sea bass is highly susceptible to the nervous necrosis virus, RGNNV genotype, whereas natural outbreaks caused by the SJNNV genotype have not been recorded. The onset and severity of an infectious disease depend on pathogen virulence factors and the host immune response. The importance of RGNNV capsid protein amino acids 247 and 270 as virulence factors has been previously demonstrated in European sea bass; however, sea bass immune response against nodaviruses with different levels of virulence has been poorly characterized. Knowing the differences between the immune response against both kinds of isolates may be key to get more insight into the host mechanisms responsible for NNV virulence. For this reason, this study analyses the transcription of immunogenes differentially expressed in European sea bass inoculated with nodaviruses with different virulence: a RGNNV virus obtained by reverse genetics (rDl956), highly virulent to sea bass, and a mutated virus (Mut247+270Dl956, RGNNV virus displaying SJNNV-type amino acids at positions 247 and 270 of the capsid protein), presenting lower virulence. This study has been performed in brain and head kidney, and the main differences between the immunogene responses triggered by both viruses have been observed in brain. The immunogene response in this organ is stronger after inoculation with the most virulent virus, and the main differences involved genes related with IFN I system, inflammatory response, cell-mediated response, and apoptosis. The lower virulence of Mut247+270Dl956 to European sea bass can be associated with a delayed IFN I response, as well as an early and transitory inflammation and cell-mediated responses, suggesting that those can be pivotal elements in controlling the viral infection, and therefore, their functional activity could be analysed in future studies. In addition, this study supports the role of capsid amino acids at positions 247 and 270 as important determinants of RGNNV virulence to European sea bass.
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Affiliation(s)
- Patricia Moreno
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul, IBYDA, Departamento de Microbiología, Facultad de Ciencias, 29071, Málaga, Spain
| | - Juan Gemez-Mata
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul, IBYDA, Departamento de Microbiología, Facultad de Ciencias, 29071, Málaga, Spain
| | - Esther Garcia-Rosado
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul, IBYDA, Departamento de Microbiología, Facultad de Ciencias, 29071, Málaga, Spain
| | - Julia Bejar
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul, IBYDA, Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, 29071, Málaga, Spain
| | - Alejandro M Labella
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul, IBYDA, Departamento de Microbiología, Facultad de Ciencias, 29071, Málaga, Spain
| | - Sandra Souto
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - M Carmen Alonso
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul, IBYDA, Departamento de Microbiología, Facultad de Ciencias, 29071, Málaga, Spain.
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5
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Potential Involvement of lncRNAs in the Modulation of the Transcriptome Response to Nodavirus Challenge in European Sea Bass ( Dicentrarchus labrax L.). BIOLOGY 2020; 9:biology9070165. [PMID: 32679770 PMCID: PMC7407339 DOI: 10.3390/biology9070165] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) are being increasingly recognised as key modulators of various biological mechanisms, including the immune response. Although investigations in teleosts are still lagging behind those conducted in mammals, current research indicates that lncRNAs play a pivotal role in the response of fish to a variety of pathogens. During the last several years, interest in lncRNAs has increased considerably, and a small but notable number of publications have reported the modulation of the lncRNA profile in some fish species after pathogen challenge. This study was the first to identify lncRNAs in the commercial species European sea bass. A total of 12,158 potential lncRNAs were detected in the head kidney and brain. We found that some lncRNAs were not common for both tissues, and these lncRNAs were located near coding genes that are primarily involved in tissue-specific processes, reflecting a degree of cellular specialisation in the synthesis of lncRNAs. Moreover, lncRNA modulation was analysed in both tissues at 24 and 72 h after infection with nodavirus. Enrichment analysis of the neighbouring coding genes of the modulated lncRNAs revealed many terms related to the immune response and viral infectivity but also related to the stress response. An integrated analysis of the lncRNAs and coding genes showed a strong correlation between the expression of the lncRNAs and their flanking coding genes. Our study represents the first systematic identification of lncRNAs in European sea bass and provides evidence regarding the involvement of these lncRNAs in the response to nodavirus.
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6
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Lama R, Pereiro P, Valenzuela-Muñoz V, Gallardo-Escárate C, Tort L, Figueras A, Novoa B. RNA-Seq analysis of European sea bass (Dicentrarchus labrax L.) infected with nodavirus reveals powerful modulation of the stress response. Vet Res 2020; 51:64. [PMID: 32398117 PMCID: PMC7218500 DOI: 10.1186/s13567-020-00784-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/16/2020] [Indexed: 12/15/2022] Open
Abstract
Nodavirus, or nervous necrosis virus (NNV), is the causative agent of viral encephalopathy and retinopathy (VER), a severe disease affecting numerous fish species worldwide. European sea bass, a cultured species of great economic importance, is highly susceptible to the disease. To better understand the response of this organism to NNV, we conducted RNA-Seq analysis of the brain and head kidney from experimentally infected and uninfected sea bass juveniles at 24 and 72 hours post-infection (hpi). Contrary to what was expected, we observed modest modulation of immune-related genes in the brain, the target organ of this virus, and some of these genes were even downregulated. However, genes involved in the stress response showed extremely high modulation. Accordingly, the genes encoding the enzymes implicated in the synthesis of cortisol were almost the only overexpressed genes in the head kidney at 24 hpi. This stress response was attenuated after 72 h in both tissues, and a progressive immune response against the virus was mounted. Moreover, experiments were conducted to determine how stress activation could impact NNV replication. Our results show the complex interplay between viral activity, the stress reaction and the immune response.
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Affiliation(s)
- Raquel Lama
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Patricia Pereiro
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain.,Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160, Concepción, Chile
| | - Valentina Valenzuela-Muñoz
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160, Concepción, Chile
| | - Lluis Tort
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona, 08193, Barcelona, Spain
| | - Antonio Figueras
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Beatriz Novoa
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain.
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7
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Sarropoulou E, Kaitetzidou E, Papandroulakis N, Tsalafouta A, Pavlidis M. Inventory of European Sea Bass ( Dicentrarchus labrax) sncRNAs Vital During Early Teleost Development. Front Genet 2019; 10:657. [PMID: 31404269 PMCID: PMC6670005 DOI: 10.3389/fgene.2019.00657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/21/2019] [Indexed: 01/25/2023] Open
Abstract
During early animal ontogenesis, a plethora of small non-coding RNAs (sncRNAs) are greatly expressed and have been shown to be involved in several regulatory pathways vital to proper development. The rapid advancements in sequencing and computing methodologies in the last decade have paved the way for the production of sequencing data in a broad range of organisms, including teleost species. Consequently, this has led to the discovery of sncRNAs as well as the potentially novel roles of sncRNA in gene regulation. Among the several classes of sncRNAs, microRNAs (miRNAs) have, in particular, been shown to play a key role in development. The present work aims to identify the miRNAs that play important roles during early European sea bass (Dicentrarchus labrax) development. The European sea bass is a species of high commercial impact in European and especially Mediterranean aquaculture. This study reports, for the first time, the identification and characterization of small RNAs that play a part in the 10 developmental stages (from morula to all fins) of the European sea bass. From 10 developmental stages, more than 135 million reads, generated by next-generation sequencing, were retrieved from publicly available databases as well as newly generated. The analysis resulted in about 2,000 sample grouped reads, and their subsequently annotation revealed that the majority of transcripts belonged to the class of miRNAs followed by small nuclear RNAs and small nucleolar RNAs. The analysis of small RNA expression among the developmental stages under study revealed that miRNAs are active throughout development, with the main activity occurring after the earlier stages (morula and 50% epiboly) and at the later stages (first feeding, flexion, and all fins). Furthermore, investigating miRNAs exclusively expressed in one of the stages unraveled five miRNAs with a higher abundance only in the morula stage (miR-155, miR-430a, d1, d2, and miR-458), indicating possible important key roles of those miRNAs in further embryonic development. An additional target search showed putative miRNA-mRNA interactions with possible direct and indirect regulatory functions of the identified miRNAs.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Elizabet Kaitetzidou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Nikos Papandroulakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
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8
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Chaves-Pozo E, Bandín I, Olveira JG, Esteve-Codina A, Gómez-Garrido J, Dabad M, Alioto T, Ángeles Esteban M, Cuesta A. European sea bass brain DLB-1 cell line is susceptible to nodavirus: A transcriptomic study. FISH & SHELLFISH IMMUNOLOGY 2019; 86:14-24. [PMID: 30428392 DOI: 10.1016/j.fsi.2018.11.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/15/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Viral diseases are responsible for high rates of mortality and subsequent economic losses in modern aquaculture. The nervous necrosis virus (NNV) produces viral encephalopathy and retinopathy (VER), which affects the fish central nervous system. It is considered one of the most serious viral diseases in marine aquaculture, the European sea bass (Dicentrarchus labrax) being amongst the most susceptible. We have evaluated the European sea bass brain derived cell line (DLB-1) susceptibility to NNV genotypes and evaluated its transcriptomic profile. DLB-1 cells supported NNV gene transcription and replication since strains belonging to the four NNV genotypes produce cytopathic effects. Afterwards, DLB-1 cells were infected with an RGNNV strain, the one which showed the highest replication, for 12 and 72 h and an RNA-seq analysis was performed to identify potential genes involved in the host-NNV interactions. Differential expression analysis showed the up-regulation of many genes related to immunity, heat-shock proteins or apoptosis but not to proteasome or autophagy processes. These data suggest that the immune response, mainly the interferon (IFN) pathway, is not powerful enough to abrogate the infection, and cells finally suffer stress and die by apoptosis liberating infective particles. GO enrichment also revealed, for the first time, the down-regulation of terms related to brain/neuron biology indicating molecular mechanisms causing the pathogenic effect of NNV. This study opens the way to understand key elements in sea bass brain and NNV interactions.
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Affiliation(s)
- Elena Chaves-Pozo
- Centro Oceanográfico de Murcia, Instituto Español de Oceanografía (IEO), Carretera de la Azohía s/n, Puerto de Mazarrón, 30860 Murcia, Spain
| | - Isabel Bandín
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, Spain
| | - José G Olveira
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - M Ángeles Esteban
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - Alberto Cuesta
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain.
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9
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Magnadóttir B, Bragason BT, Bricknell IR, Bowden T, Nicholas AP, Hristova M, Guðmundsdóttir S, Dodds AW, Lange S. Peptidylarginine deiminase and deiminated proteins are detected throughout early halibut ontogeny - Complement components C3 and C4 are post-translationally deiminated in halibut (Hippoglossus hippoglossus L.). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:1-19. [PMID: 30395876 DOI: 10.1016/j.dci.2018.10.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 06/08/2023]
Abstract
Post-translational protein deimination is mediated by peptidylarginine deiminases (PADs), which are calcium dependent enzymes conserved throughout phylogeny with physiological and pathophysiological roles. Protein deimination occurs via the conversion of protein arginine into citrulline, leading to structural and functional changes in target proteins. In a continuous series of early halibut development from 37 to 1050° d, PAD, total deiminated proteins and deiminated histone H3 showed variation in temporal and spatial detection in various organs including yolksac, muscle, skin, liver, brain, eye, spinal cord, chondrocytes, heart, intestines, kidney and pancreas throughout early ontogeny. For the first time in any species, deimination of complement components C3 and C4 is shown in halibut serum, indicating a novel mechanism of complement regulation in immune responses and homeostasis. Proteomic analysis of deiminated target proteins in halibut serum further identified complement components C5, C7, C8 C9 and C1 inhibitor, as well as various other immunogenic, metabolic, cytoskeletal and nuclear proteins. Post-translational deimination may facilitate protein moonlighting, an evolutionary conserved phenomenon, allowing one polypeptide chain to carry out various functions to meet functional requirements for diverse roles in immune defences and tissue remodelling.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Birkir Thor Bragason
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Ian R Bricknell
- Aquaculture Research Institute School of Marine Sciences, University of Maine, Orono, ME, USA.
| | - Timothy Bowden
- Aquaculture Research Institute School of Food & Agriculture, University of Maine, University of Maine, Orono, ME, USA.
| | - Anthony P Nicholas
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Mariya Hristova
- Perinatal Brain Protection and Repair Group, EGA Institute for Women's Health, University College London, London, WC1E 6HX, UK.
| | - Sigríður Guðmundsdóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Alister W Dodds
- MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
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10
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Buonocore F, Nuñez-Ortiz N, Picchietti S, Randelli E, Stocchi V, Guerra L, Toffan A, Pascoli F, Fausto AM, Mazzini M, Scapigliati G. Vaccination and immune responses of European sea bass (Dicentrarchus labrax L.) against betanodavirus. FISH & SHELLFISH IMMUNOLOGY 2019; 85:78-84. [PMID: 29175472 DOI: 10.1016/j.fsi.2017.11.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/18/2017] [Accepted: 11/22/2017] [Indexed: 05/22/2023]
Abstract
This review summarizes the available knowledge on the immune defences of European sea bass against antigenic preparations derived from the viral encephalopathy and retinopathy virus (betanodavirus), which represents a major threat to the health of this fish species. The nodavirus is widely present and differentiates into several strains that infect invertebrates (in insects, alphanodavirus) and teleost fish, and thus may represent a great problem for farmed fish species. Many efforts have been directed to discovering new immunizations to induce protection in sea bass, especially at young stages, and these efforts have included employing diverse betanodavirus strains, antigen preparation, vaccination routes, and the addition of adjuvants and/or immunostimulants. The obtained results showed that inactivated preparations of betanodavirus that were administered intraperitoneally may induce both immune recognition and protection. Attempts at performing mucosal immunization by immersion and/or oral administration, which is a vaccination route that is highly preferred for sea bass, have shown intriguing results, and more studies are necessary for its improvement. Overall, the objective of identifying a reliable vaccine that also cross-protects against different genotypes or reassortant viruses for use in European sea bass against betanodavirus appears to be an attainable goal in the near future.
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Affiliation(s)
- Francesco Buonocore
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy.
| | - Noelia Nuñez-Ortiz
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Simona Picchietti
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Elisa Randelli
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Valentina Stocchi
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Laura Guerra
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Anna Toffan
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Francesco Pascoli
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Anna Maria Fausto
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Massimo Mazzini
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
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11
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Byadgi O, Beraldo P, Volpatti D, Massimo M, Bulfon C, Galeotti M. Expression of infection-related immune response in European sea bass (Dicentrarchus labrax) during a natural outbreak from a unique dinoflagellate Amyloodinium ocellatum. FISH & SHELLFISH IMMUNOLOGY 2019; 84:62-72. [PMID: 30266602 DOI: 10.1016/j.fsi.2018.09.069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/06/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Abstract
In the Mediterranean area, amyloodiniosis represents a major hindrance for marine aquaculture, causing high mortalities in lagoon-type based rearing sites during warm seasons. Amyloodinium ocellatum (AO) is the most common and important dinoflagellate parasitizing fish, and is one of the few fish parasites that can infest several fish species living within its ecological range. In the present study, A. ocellatum was recorded and collected from infected European sea bass (Dicentrarchus labrax) during a summer 2017 outbreak in north east Italy. Histological observation of infected ESB gill samples emphasized the presence of round or pear-shaped trophonts anchored to the oro-pharingeal cavity. Molecular analysis for small subunit (SSU) rDNA of A. ocellatum from gill genomic DNA amplified consistently and yielded 248 bp specific amplicon of A. ocellatum, that was also confirmed using sequencing and NCBI Blast analysis. Histological sections of ESB gill samples were addressed to immunohistochemical procedure for the labelling of ESB igm, inos, tlr2, tlr4, pcna and cytokeratin. Infected gills resulted positive for igm, inos, pcna and cytokeratin but negative to tlr-2 and tlr-4. Furthermore, ESB immune related gene response (innate immunity, adaptive immunity, and stress) in the course of A. ocellatum infection using quantitative polymerase chain reaction (qpcr) for infected gills and head kidney was analysed. Among the twenty three immune related gene molecules tested, cc1, il-8, il-10, hep, cox-2, cla, cat, casp9, and igt were significantly expressed in diseased fish. Altogether, these data on parasite identification and expression of host immune-related genes will allow for a better understanding of immune response in European sea bass against A. ocellatum and could promote the development of effective control measures.
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Affiliation(s)
- Omkar Byadgi
- Section of Animal and Veterinary Sciences, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy.
| | - Paola Beraldo
- Section of Animal and Veterinary Sciences, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Donatella Volpatti
- Section of Animal and Veterinary Sciences, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Michela Massimo
- Section of Animal and Veterinary Sciences, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Chiara Bulfon
- Section of Animal and Veterinary Sciences, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Marco Galeotti
- Section of Animal and Veterinary Sciences, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
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12
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Yaacob EN, De Geest BG, Goethals J, Bajek A, Dierckens K, Bossier P, Vanrompay D. Recombinant ferritin-H induces immunosuppression in European sea bass larvae (Dicentrarchus labrax) rather than immunostimulation and protection against a Vibrio anguillarum infection. Vet Immunol Immunopathol 2018; 204:19-27. [DOI: 10.1016/j.vetimm.2018.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 08/17/2018] [Accepted: 09/04/2018] [Indexed: 11/26/2022]
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13
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Magnadóttir B, Hayes P, Hristova M, Bragason BT, Nicholas AP, Dodds AW, Guðmundsdóttir S, Lange S. Post-translational protein deimination in cod (Gadus morhua L.) ontogeny novel roles in tissue remodelling and mucosal immune defences? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:157-170. [PMID: 29908202 DOI: 10.1016/j.dci.2018.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
Peptidylarginine deiminases (PADs) are calcium dependent enzymes with physiological and pathophysiological roles conserved throughout phylogeny. PADs promote post-translational deimination of protein arginine to citrulline, altering the structure and function of target proteins. Deiminated proteins were detected in the early developmental stages of cod from 11 days post fertilisation to 70 days post hatching. Deiminated proteins were present in mucosal surfaces and in liver, pancreas, spleen, gut, muscle, brain and eye during early cod larval development. Deiminated protein targets identified in skin mucosa included nuclear histones; cytoskeletal proteins such as tubulin and beta-actin; metabolic and immune related proteins such as galectin, mannan-binding lectin, toll-like receptor, kininogen, Beta2-microglobulin, aldehyde dehydrogenase, bloodthirsty and preproapolipoprotein A-I. Deiminated histone H3, a marker for anti-pathogenic neutrophil extracellular traps, was particularly elevated in mucosal tissues in immunostimulated cod larvae. PAD-mediated protein deimination may facilitate protein moonlighting, allowing the same protein to exhibit a range of biological functions, in tissue remodelling and mucosal immune defences in teleost ontogeny.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Polly Hayes
- Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
| | - Mariya Hristova
- Perinatal Brain Protection and Repair Group, EGA Institute for Women's Health, University College London, WC1E 6HX, London, UK.
| | - Birkir Thor Bragason
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Anthony P Nicholas
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Alister W Dodds
- MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Sigríður Guðmundsdóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
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14
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Gao C, Su B, Zhang D, Yang N, Song L, Fu Q, Zhou S, Tan F, Li C. l-rhamnose-binding lectins (RBLs) in turbot (Scophthalmus maximus L.): Characterization and expression profiling in mucosal tissues. FISH & SHELLFISH IMMUNOLOGY 2018; 80:264-273. [PMID: 29886139 DOI: 10.1016/j.fsi.2018.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/29/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Rhamnose-binding lectin (RBL) were mostly identified from egg cortex and ovary cells from vertebrates and invertebrates, with the specific binding activities to l-rhamnose or d-galactose. Previously, we found that a RBL gene was dramatically down-regulated (-11.90 fold at 1 h, -48.95 fold at 4 h, -905.94 fold at 12 h) in the intestine of turbot following Vibrio anguillarum challenge using RNA-seq expression analysis. In this regard, we sought here to identify RBLs in turbot, as well as the analysis of genomic structure, phylogenetic relationships, basal tissue distribution and the expression patterns following different bacteria challenge in mucosal tissues. In this study, two RBLs were captured in turbot with two conserved type 5 CRD5s, which were belong to type IIIc RBL. In phylogenetic tree analysis, turbot RBLs were clustered with tilapia, European sea bass and snakehead. In addition, in comparison of genomic architecture of turbot RBLs with the available published RBL genes revealed a high degree of conservation in the exon/intron organization among the teleost species. Moreover, both RBLs were significantly up-regulated in mucosal tissues following V. anguillarum and Streptococcus iniae challenge, indicated their critical roles in turbot mucosal immunity. Further studies are needed to expand functional characterization of detailed mechanisms of RBLs in fish innate immunity.
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Affiliation(s)
- Chengbin Gao
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- National and Local Joint Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Dongdong Zhang
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ning Yang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Song
- College of Marine Science and Biological Engineering, Qingdao University of Science & Technology, Qingdao, 266011, China
| | - Qiang Fu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shun Zhou
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fenghua Tan
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China.
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15
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Franke A, Roth O, Schryver PD, Bayer T, Garcia-Gonzalez L, Künzel S, Bossier P, Miest JJ, Clemmesen C. Poly-β-hydroxybutyrate administration during early life: effects on performance, immunity and microbial community of European sea bass yolk-sac larvae. Sci Rep 2017; 7:15022. [PMID: 29118332 PMCID: PMC5678127 DOI: 10.1038/s41598-017-14785-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/16/2017] [Indexed: 12/31/2022] Open
Abstract
The reliable production of marine fish larvae is one of the major bottlenecks in aquaculture due to high mortalities mainly caused by infectious diseases. To evaluate if the compound poly-β-hydroxybutyrate (PHB) might be a suitable immunoprophylactic measure in fish larviculture, its capacity to improve immunity and performance in European sea bass (Dicentrarchus labrax) yolk-sac larvae was explored. PHB was applied from mouth opening onwards to stimulate the developing larval immune system at the earliest possible point in time. Larval survival, growth, microbiota composition, gene expression profiles and disease resistance were assessed. PHB administration improved larval survival and, furthermore, altered the larva-associated microbiota composition. The bacterial challenge test using pathogenic Vibrio anguillarum revealed that the larval disease resistance was not influenced by PHB. The expression profiles of 26 genes involved e.g. in the immune response showed that PHB affected the expression of the antimicrobial peptides ferritin (fer) and dicentracin (dic), however, the response to PHB was inconsistent and weaker than previously demonstrated for sea bass post-larvae. Hence, the present study highlights the need for more research focusing on the immunostimulation of different early developmental stages for gaining a more comprehensive picture and advancing a sustainable production of high quality fry.
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Affiliation(s)
- Andrea Franke
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Kiel, Germany.
| | - Olivia Roth
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Kiel, Germany
| | - Peter De Schryver
- Laboratory of Aquaculture and Artemia Reference Center, Ghent University, Ghent, Belgium.,INVE Technologies N.V., Hoogveld 93, Dendermonde, Belgium
| | - Till Bayer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Kiel, Germany
| | | | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Department for Evolutionary Genetics, Plön, Germany
| | - Peter Bossier
- Laboratory of Aquaculture and Artemia Reference Center, Ghent University, Ghent, Belgium
| | - Joanna J Miest
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Kiel, Germany.,University of Greenwich, Department of Life & Sports Sciences, Chatham Maritime, London, United Kingdom
| | - Catriona Clemmesen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Kiel, Germany
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16
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Moreira M, Schrama D, Soares F, Wulff T, Pousão-Ferreira P, Rodrigues P. Physiological responses of reared sea bream (Sparus aurata Linnaeus, 1758) to an Amyloodinium ocellatum outbreak. JOURNAL OF FISH DISEASES 2017; 40:1545-1560. [PMID: 28449283 DOI: 10.1111/jfd.12623] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 06/07/2023]
Abstract
Amyloodiniosis represents a major bottleneck for semi-intensive aquaculture production in Southern Europe, causing extremely high mortalities. Amyloodinium ocellatum is a parasitic dinoflagellate that can infest almost all fish, crustacean and bivalves that live within its ecological range. Fish mortalities are usually attributed to anoxia, associated with serious gill hyperplasia, inflammation, haemorrhage and necrosis in heavy infestations; or with osmoregulatory impairment and secondary microbial infections due to severe epithelial damage in mild infestation. However, physiological information about the host responses to A. ocellatum infestation is scarce. In this work, we analysed the proteome of gilthead sea bream (Sparus aurata) plasma and relate it with haematological and immunological indicators, in order to enlighten the different physiological responses when exposed to an A. ocellatum outbreak. Using 2D-DIGE, immunological and haematological analysis and in response to the A. ocellatum contamination we have identified several proteins associated with acute-phase response, inflammation, lipid transport, homoeostasis, and osmoregulation, wound healing, neoplasia and iron transport. Overall, this preliminary study revealed that amyloodiniosis affects some fish functional pathways as revealed by the changes in the plasma proteome of S. aurata, and that the innate immunological system is not activated in the presence of the parasite.
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Affiliation(s)
- M Moreira
- IPMA - Portuguese Institute for the Ocean and Atmosphere, EPPO - Aquaculture Research Station, Olhão, Portugal
| | - D Schrama
- CCMAR - Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - F Soares
- IPMA - Portuguese Institute for the Ocean and Atmosphere, EPPO - Aquaculture Research Station, Olhão, Portugal
| | - T Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - P Pousão-Ferreira
- IPMA - Portuguese Institute for the Ocean and Atmosphere, EPPO - Aquaculture Research Station, Olhão, Portugal
| | - P Rodrigues
- CCMAR - Centre of Marine Sciences, University of Algarve, Faro, Portugal
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17
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Martínez D, Oyarzún R, Pontigo JP, Romero A, Yáñez AJ, Vargas-Chacoff L. Nutritional Immunity Triggers the Modulation of Iron Metabolism Genes in the Sub-Antarctic Notothenioid Eleginops maclovinus in Response to Piscirickettsia salmonis. Front Immunol 2017; 8:1153. [PMID: 28974951 PMCID: PMC5610722 DOI: 10.3389/fimmu.2017.01153] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/31/2017] [Indexed: 12/21/2022] Open
Abstract
Iron deprivation is a nutritional immunity mechanism through which fish can limit the amount of iron available to invading bacteria. The aim of this study was to evaluate the modulation of iron metabolism genes in the liver and brain of sub-Antarctic notothenioid Eleginops maclovinus challenged with Piscirickettsia salmonis. The specimens were inoculated with two P. salmonis strains: LF-89 (ATCC® VR-1361™) and Austral-005 (antibiotic resistant). Hepatic and brain samples were collected at intervals over a period of 35 days. Gene expression (by RT-qPCR) of proteins involved in iron storage, transport, and binding were statistically modulated in infected fish when compared with control counterparts. Specifically, the expression profiles of the transferrin and hemopexin genes in the liver, as well as the expression profiles of ferritin-M, ferritin-L, and transferrin in the brain, were similar for both experimental groups. Nevertheless, the remaining genes such as ferritin-H, ceruloplasmin, hepcidin, and haptoglobin presented tissue-specific expression profiles that varied in relation to the injected bacterial strain and sampling time-point. These results suggest that nutritional immunity could be an important immune defense mechanism for E. maclovinus against P. salmonis injection. This study provides relevant information for understanding iron metabolism of a sub-Antarctic notothenioid fish.
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Affiliation(s)
- Danixa Martínez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile.,Escuela de Graduados, Programa de Doctorado en Ciencias de la Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile.,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Ricardo Oyarzún
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile.,Escuela de Graduados, Programa de Doctorado en Ciencias de la Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile.,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Juan Pablo Pontigo
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Alex Romero
- Centro Fondap Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Austral de Chile, Valdivia, Chile.,Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
| | - Alejandro J Yáñez
- Centro Fondap Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Austral de Chile, Valdivia, Chile.,Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
| | - Luis Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile.,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
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18
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Martínez D, Oyarzún R, Vargas-Lagos C, Pontigo JP, Soto-Dávila M, Saravia J, Romero A, Núñez JJ, Yáñez AJ, Vargas-Chacoff L. Identification, characterization and modulation of ferritin-H in the sub-Antarctic Notothenioid Eleginops maclovinus challenged with Piscirickettsia salmonis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 73:88-96. [PMID: 28336188 DOI: 10.1016/j.dci.2017.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 03/18/2017] [Accepted: 03/18/2017] [Indexed: 06/06/2023]
Abstract
Ferritin is a major iron storage protein essential not only in the infectious process, but also in any circumstance generating oxidative stress. In this study, the cDNA coding sequence of ferritin-H was obtained from the sub-Antarctic Notothenioid fish Eleginops maclovinus through transcriptomic analysis of the head kidney. This sequence contained a 534 bp open reading frame that coded for a 177 amino acid protein with a molecular weight of 20,786.2 Da and a theoretical pI of 5.56. The protein displayed a region of iron putative response elements in the 5'UTR, two putative ferritin iron-binding region signatures, and seven characteristic amino acids with ferroxidase functions. Phylogenetic analysis related this sequence to ferritin-H sequences of other Antarctic Notothenioid fish, sharing 96.61% similarity. Constitutive gene expression analysis in different organs revealed increased ferritin-H gene expression in the gills, spleen, muscle, and liver. After infection with two bacterial strains of Piscirickettsia salmonis (LF-89 and Austral-005), ferritin-H was differentially expressed depending on bacterial strain and tissue. This study provides relevant information towards understanding the iron metabolism of a sub-Antarctic Notothenioid fish.
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Affiliation(s)
- D Martínez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Escuela de Graduados, Programa de Doctorado en Ciencias de la Acuicultura, Universidad Austral de Chile, Av. Los Pinos s/n Balneario Pelluco, Puerto Montt, Chile; Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile.
| | - R Oyarzún
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Escuela de Graduados, Programa de Doctorado en Ciencias de la Acuicultura, Universidad Austral de Chile, Av. Los Pinos s/n Balneario Pelluco, Puerto Montt, Chile; Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - C Vargas-Lagos
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Escuela de Graduados, Programa de Magister en Microbiología, Universidad Austral de Chile, Valdivia, Chile; Centro Fondap Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Austral de Chile, Valdivia, Chile
| | - J P Pontigo
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - M Soto-Dávila
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - J Saravia
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Escuela de Graduados, Programa de Doctorado en Ciencias de la Acuicultura, Universidad Austral de Chile, Av. Los Pinos s/n Balneario Pelluco, Puerto Montt, Chile
| | - A Romero
- Centro Fondap Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Austral de Chile, Valdivia, Chile; Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
| | - J J Núñez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - A J Yáñez
- Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile; Centro Fondap Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Austral de Chile, Valdivia, Chile
| | - L Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile.
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Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata, by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs. Int J Mol Sci 2017; 18:ijms18020317. [PMID: 28165358 PMCID: PMC5343853 DOI: 10.3390/ijms18020317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/31/2016] [Accepted: 10/08/2016] [Indexed: 12/19/2022] Open
Abstract
This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge. The developed microarray was further validated by analysing monocyte/macrophage activation profiles after challenge with two Gram-negative bacterial pathogen-associated molecular patterns (PAMPs; lipopolysaccharide (LPS) and peptidoglycan (PGN)). Of the approximately 10,000 EST sequenced, we obtained a total of 6837 EST longer than 100 nt, with 3778 and 3059 EST obtained from the bacterial-primed and from the viral-primed cDNA libraries, respectively. Functional classification of contigs from the bacterial- and viral-primed cDNA libraries by Gene Ontology (GO) showed that the top five represented categories were equally represented in the two libraries: metabolism (approximately 24% of the total number of contigs), carrier proteins/membrane transport (approximately 15%), effectors/modulators and cell communication (approximately 11%), nucleoside, nucleotide and nucleic acid metabolism (approximately 7.5%) and intracellular transducers/signal transduction (approximately 5%). Transcriptome analyses using this enriched oligonucleotide platform identified differential shifts in the response to PGN and LPS in macrophage-like cells, highlighting responsive gene-cassettes tightly related to PAMP host recognition. As observed in other fish species, PGN is a powerful activator of the inflammatory response in S. aurata macrophage-like cells. We have developed and validated an oligonucleotide microarray (SAQ) that provides a platform enriched for the study of gene expression in S. aurata with an emphasis upon immunity and the immune response.
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Bazakos C, Manioudaki ME, Sarropoulou E, Spano T, Kalaitzis P. 454 Pyrosequencing of Olive (Olea europaea L.) Transcriptome in Response to Salinity. PLoS One 2015; 10:e0143000. [PMID: 26576008 PMCID: PMC4648586 DOI: 10.1371/journal.pone.0143000] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
Olive (Olea europaea L.) is one of the most important crops in the Mediterranean region. The expansion of cultivation in areas irrigated with low quality and saline water has negative effects on growth and productivity however the investigation of the molecular basis of salt tolerance in olive trees has been only recently initiated. To this end, we investigated the molecular response of cultivar Kalamon to salinity stress using next-generation sequencing technology to explore the transcriptome profile of olive leaves and roots and identify differentially expressed genes that are related to salt tolerance response. Out of 291,958 obtained trimmed reads, 28,270 unique transcripts were identified of which 35% are annotated, a percentage that is comparable to similar reports on non-model plants. Among the 1,624 clusters in roots that comprise more than one read, 24 were differentially expressed comprising 9 down- and 15 up-regulated genes. Respectively, inleaves, among the 2,642 clusters, 70 were identified as differentially expressed, with 14 down- and 56 up-regulated genes. Using next-generation sequencing technology we were able to identify salt-response-related transcripts. Furthermore we provide an annotated transcriptome of olive as well as expression data, which are both significant tools for further molecular studies in olive.
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Affiliation(s)
- Christos Bazakos
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
- Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria E. Manioudaki
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Thodhoraq Spano
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
| | - Panagiotis Kalaitzis
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
- * E-mail:
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Tran NT, Gao ZX, Zhao HH, Yi SK, Chen BX, Zhao YH, Lin L, Liu XQ, Wang WM. Transcriptome analysis and microsatellite discovery in the blunt snout bream (Megalobrama amblycephala) after challenge with Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2015; 45:72-82. [PMID: 25681750 DOI: 10.1016/j.fsi.2015.01.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
The blunt snout bream, Megalobrama amblycephala, is a herbivorous freshwater fish species native to China and a major aquaculture species in Chinese freshwater polyculture systems. In recent years, the bacterium Aeromonas hydrophila has been reported to be its pathogen causing great losses of farmed fish. To understand the immune response of the blunt snout bream to A. hydrophila infection, we used the Solexa/Illumina technology to analyze the transcriptomic profile after artificial bacterial infection. Two nonnormalized cDNA libraries were synthesized from tissues collected from control blunt snout bream or those injected with A. hydrophila. After assembly, 155,052 unigenes (average length 692.8 bp) were isolated. All unigenes were annotated using BLASTX relative to several public databases: the National Center for Biotechnology Information nonreduntant (Nr) database, SwissProt, Eukaryotic Orthologous Groups of proteins (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). The sequence similarity (86%) of the assembled unigenes was to zebrafish based on the Nr database. A number of unigenes (n = 30,482) were assigned to three GO categories: biological processes (25,242 unigenes), molecular functions (26,096 unigenes), and cellular components (22,778 unigenes). 20,909 unigenes were classified into 25 KOG categories and 28,744 unigenes were assigned into 315 specific signaling pathways. In total, 238 significantly differentially expressed unigenes (mapped to 125 genes) were identified: 101 upregulated genes and 24 downregulated genes. Another 303 unigenes were mapped to unknown or novel genes. Among the known expressed genes identified, 53 were immune-related genes and were distributed in 71 signaling pathways. The expression patterns of selected up- and downregulated genes from the control and injected groups were determined with reverse transcription-quantitative PCR (RT-qPCR). Microsatellites (n = 10,877), including di-to pentanucleotide repeat motifs, were also identified in the blunt snout bream transcriptome profiles. This study extends our understanding of the immune defense mechanisms of the blunt snout bream against A. hydrophila and provides useful data for further studies of the immunogenetics of this species.
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Affiliation(s)
- Ngoc Tuan Tran
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Ze-Xia Gao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Hong-Hao Zhao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Shao-Kui Yi
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Bo-Xiang Chen
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Animal Husbandry and Fisheries Research Center of Haid Group Co., Ltd, Guangzhou 511400, China.
| | - Yu-Hua Zhao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Li Lin
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Xue-Qin Liu
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Wei-Min Wang
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Cammarata M, Parisi MG, Benenati G, Vasta GR, Parrinello N. A rhamnose-binding lectin from sea bass (Dicentrarchus labrax) plasma agglutinates and opsonizes pathogenic bacteria. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 44:332-40. [PMID: 24486534 PMCID: PMC4607264 DOI: 10.1016/j.dci.2014.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/19/2014] [Accepted: 01/20/2014] [Indexed: 05/25/2023]
Abstract
The discovery of rhamnose-binding lectins (RBLs) in teleost fish eggs led to the identification of a novel lectin family characterized by a unique sequence motif and a structural fold, and initially proposed to modulate fertilization. Further studies of the RBL tissue localization and gene organization were also suggestive of role(s) in innate immunity. Here we describe the purification, and biochemical and functional characterization of a novel RBL (DlRBL) from sea bass (Dicentrarchus labrax) serum. The purified DlRBL had electrophoretic mobilities corresponding to 24 kDa and 100 kDa under reducing and non-reducing conditions, respectively, suggesting that in plasma the DlRBL is present as a physiological homotetramer. DlRBL subunit transcripts revealed an open reading frame encoding 212 amino acid residues that included two tandemly-arrayed carbohydrate-recognition domains, and an 18-residue signal sequence at the N-terminus. The deduced size of 24.1 kDa for the mature protein was in good agreement with the subunit size of the isolated lectin. Binding activity of DlRBL for rabbit erythrocytes could be inhibited in the presence of rhamnose or galactose, did not require calcium, and was optimal at around 20°C and within the pH 6.5-8.0 range. DlRBL agglutinated Gram positive and Gram negative bacteria, and exposure of formalin-killed Escherichia coli to DlRBL enhanced their phagocytosis by D. labrax peritoneal macrophages relative to the unexposed controls. Taken together, the results suggest that plasma DlRBL may play a role in immune recognition of microbial pathogens and facilitate their clearance by phagocytosis.
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Affiliation(s)
- Matteo Cammarata
- Department of Biological, Chemical, Pharmaceutical Science and Technology, Marine Immunobiology Laboratory, University of Palermo, Via Archirafi 18, Palermo, Italy.
| | - Maria Giovanna Parisi
- Department of Biological, Chemical, Pharmaceutical Science and Technology, Marine Immunobiology Laboratory, University of Palermo, Via Archirafi 18, Palermo, Italy
| | - Gigliola Benenati
- Department of Biological, Chemical, Pharmaceutical Science and Technology, Marine Immunobiology Laboratory, University of Palermo, Via Archirafi 18, Palermo, Italy
| | - Gerardo R Vasta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, UMB, IMET, Suite 236, Columbus Center, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Nicolò Parrinello
- Department of Biological, Chemical, Pharmaceutical Science and Technology, Marine Immunobiology Laboratory, University of Palermo, Via Archirafi 18, Palermo, Italy
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Sarropoulou E, Moghadam HK, Papandroulakis N, De la Gándara F, Ortega Garcia A, Makridis P. The Atlantic Bonito (Sarda sarda, Bloch 1793) transcriptome and detection of differential expression during larvae development. PLoS One 2014; 9:e87744. [PMID: 24503907 PMCID: PMC3913633 DOI: 10.1371/journal.pone.0087744] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/28/2013] [Indexed: 01/06/2023] Open
Abstract
The Atlantic bonito (Sarda sarda, Bloch 1793) belongs to the important marine fish species with a wide geographical distribution covering the Atlantic Ocean, the Mediterranean and its bordering seas. Aquaculture practices for this species are still in their infancies and scientific studies are seldom undertaken, mainly because of difficulties in sampling. Thus for small tuna species like the Atlantic bonito only little is known about its biology and regarding the molecular background even less information is available. In the production of marine fish it is known that the most critical period is the larval stages, as high growth rates as well as significant developmental changes take place. In this study we have investigated the transcriptome of the Atlantic bonito of five larvae stages applying Illumina sequencing technology. For non-model species like aquaculture species, transcriptome analysis of RNA samples from individuals using Illumina sequencing technology is technically efficient and cost effective. In the present study a total number of 169,326,711 paired-end reads with a read length of 100 base pairs were generated resulting in a reference transcriptome of 68,220 contigs with an average length of 2054 base pairs. For differential expression analyses single end reads were obtained from different developmental stages and mapped to the constructed reference transcriptome. Differential expression analyses revealed in total 18,657 differentially expressed transcripts and were assigned to five distinguished groups. Each of the five clusters shows stage specific gene expression. We present for the first time in the Atlantic bonito an extensive RNA-Seq based characterization of its transcriptome as well as significant information on differential expression among five developmental larvae stages. The generated transcripts, including SNP and microsatellite information for candidate molecular markers and gene expression information will be a valuable resource for future genetic and molecular studies.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
- * E-mail:
| | - Hooman K. Moghadam
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Nikos Papandroulakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Fernando De la Gándara
- Instituto Español de Oceanografia (IEO), Centro Oceanografico de Murcia, Carretera de La Azohia, Puerto de Mazarron, Spain
| | - Aurelio Ortega Garcia
- Instituto Español de Oceanografia (IEO), Centro Oceanografico de Murcia, Carretera de La Azohia, Puerto de Mazarron, Spain
| | - Pavlos Makridis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
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Proliferation and resistance difference of a liver-parasitized myxosporean in two different gynogenetic clones of gibel carp. Parasitol Res 2014; 113:1331-41. [DOI: 10.1007/s00436-014-3772-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
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Fernández CG, Roufidou C, Antonopoulou E, Sarropoulou E. Expression of developmental-stage-specific genes in the gilthead sea bream Sparus aurata L. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:313-320. [PMID: 23053055 DOI: 10.1007/s10126-012-9486-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/11/2012] [Indexed: 06/01/2023]
Abstract
The mechanism of early fish development as well as the control of egg quality is of great importance for the ability of the oocyte to develop after fertilization. Embryonic development is initially regulated by maternally provided mRNAs and later by the zygotic genome. Maternal mRNAs have an important role in initiating processes crucial to patterning the developing fish embryo. Furthermore, it has been shown that maternal RNA plays an important role in egg quality. The identification and characterization of candidate maternal genes in non-model fish species with important aquaculture interest like the gilthead sea bream Sparus aurata L. is of importance for future studies related to egg quality. The broodstock of the gilthead sea bream produces large quantities of eggs with a high and non-controllable quality variation. In the present study, we have studied the gene expression of 16 genes (gapdh 1 and 2, cathepsin D, L, S and Z, erk1, jnk1, p38 alpha and p38 delta, ppar alpha, beta and gamma, tubulin beta, ferritin M, cyclinA2) of different functional categories in seven developmental stages. The 16 genes were chosen based on their putative involvement in egg quality and regulation of early development. In total, 11 showed a characteristic gene expression pattern pinpointing to the possible function as maternal genes and thus may function as molecular biomarker for egg quality.
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Affiliation(s)
- Carmen García Fernández
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003, Heraklion, Crete, Greece
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Rajan B, Lokesh J, Kiron V, Brinchmann MF. Differentially expressed proteins in the skin mucus of Atlantic cod (Gadus morhua) upon natural infection with Vibrio anguillarum. BMC Vet Res 2013; 9:103. [PMID: 23672475 PMCID: PMC3666997 DOI: 10.1186/1746-6148-9-103] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 05/08/2013] [Indexed: 12/24/2022] Open
Abstract
Background Vibriosis caused by V. anguillarum is a commonly encountered disease in Atlantic cod farms and several studies indicate that the initiation of infection occurs after the attachment of the pathogen to the mucosal surfaces (gut, skin and gills) of fish. Therefore it is necessary to investigate the role of different mucosal components in fish upon V. anguillarum infection. The present study has two parts; in the first part we analyzed the differential expression of skin mucus proteins from Atlantic cod naturally infected with V. anguillarum using two dimensional gel electrophoresis coupled with mass spectrometry. In the second part, a separate bath challenge experiment with V. anguillarum was conducted to assess the mRNA levels of the genes in skin tissue, corresponding to the selected proteins identified in the first part. Results Comparative proteome analysis of skin mucus of cod upon natural infection with V. anguillarum revealed key immune relevant proteins like calpain small subunit 1, glutathione-S-transferase omega 1, proteasome 26S subunit, 14-kDa apolipoprotein, beta 2-tubulin, cold inducible RNA binding protein, malate dehydrogenase 2 (mitochondrial) and type II keratin that exhibited significant differential expression. Additionally a number of protein spots which showed large variability amongst individual fish were also identified. Some of the proteins identified were mapped to the immunologically relevant JNK (c-Jun N-terminal kinases) signalling pathway that is connected to cellular events associated with pathogenesis. A bath challenge experiment with V. anguillarum showed differential expression of beta 2-tubulin, calpain small subunit 1, cold inducible RNA binding protein, flotillin1, and glutathione S-transferase omega 1 transcripts in the skin tissue of cod during early stages of infection. Conclusions Differentially expressed proteins identified in the cod skin mucus point towards their possible involvement in V. anguillarum pathogenesis. The role of some of these proteins in vibriosis in cod described in this paper can be considered unconventional with respect to their established functions in higher vertebrates. Based on the differential expression of these proteins they are possibly important components of fish defence against bacteria and innate immunity at large. The feasibility of utilizing these proteins/genes as markers of bacterial infection or stress in cod needs to be explored further.
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Affiliation(s)
- Binoy Rajan
- Faculty of Biosciences and Aquaculture, University of Nordland, Bodø 8049, Norway
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Pinto RD, Randelli E, Buonocore F, Pereira PJB, dos Santos NMS. Molecular cloning and characterization of sea bass (Dicentrarchus labrax, L.) MHC class I heavy chain and β2-microglobulin. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:234-254. [PMID: 23116964 DOI: 10.1016/j.dci.2012.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 10/10/2012] [Accepted: 10/11/2012] [Indexed: 06/01/2023]
Abstract
In this work, the gene and cDNA of sea bass (Dicentrarchus labrax) β2-microglobulin (Dila-β2m) and several cDNAs of MHC class I heavy chain (Dila-UA) were characterized. While Dila-β2m is single-copy, numerous Dila-UA transcripts were identified per individual with variability at the peptide-binding domain (PBD), but also with unexpected diversity from the connective peptide (CP) through the 3' untranslated region (UTR). Phylogenetic analysis segregates Dila-β2m and Dila-UA into each subfamily cluster, placing them in the fish class and branching Dila-MHC-I with lineage U. The α1 domains resemble those of the recently proposed L1 trans-species lineage. Although no Dila-specific α1, α2 or α3 sub-lineages could be observed, two highly distinct sub-lineages were identified at the CP/TM/CYT regions. The three-dimensional homology model of sea bass MHC-I complex is consistent with other characterized vertebrate structures. Furthermore, basal tissue-specific expression profiles were determined for both molecules, and expression of β2m was evaluated after poly I:C stimulus. Results suggest these molecules are orthologues of other β2m and teleost classical MHC-I and their basic structure is evolutionarily conserved, providing relevant information for further studies on antigen presentation in this fish species.
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Affiliation(s)
- Rute D Pinto
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, Porto, Portugal.
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Mohd-Padil H, Mohd-Adnan A, Gabaldón T. Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates. Mol Biol Evol 2012; 30:894-905. [PMID: 23258311 PMCID: PMC3603312 DOI: 10.1093/molbev/mss325] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transferrin is a protein super-family involved in iron transport, a central process in cellular homeostasis. Throughout the evolution of vertebrates, transferrin members have diversified into distinct subfamilies including serotransferrin, ovotransferrin, lactoferrin, melanotransferrin, the inhibitor of carbonic anhydrase, pacifastin, and the major yolk protein in sea urchin. Previous phylogenetic analyses have established the branching order of the diverse transferrin subfamilies but were mostly focused on the transferrin repertoire present in mammals. Here, we conduct a comprehensive phylogenetic analysis of transferrin protein sequences in sequenced vertebrates, placing a special focus on the less-studied nonmammalian vertebrates. Our analyses uncover a novel transferrin clade present across fish, sauropsid, and amphibian genomes but strikingly absent from mammals. Our reconstructed scenario implies that this novel class emerged through a duplication event at the vertebrate ancestor, and that it was subsequently lost in the lineage leading to mammals. We detect footprints of accelerated evolution following the duplication event, which suggest positive selection and early functional divergence of this novel clade. Interestingly, the loss of this novel class of transferrin in mammals coincided with the divergence by duplication of lactoferrin and serotransferrin in this lineage. Altogether, our results provide novel insights on the evolution of iron-binding proteins in the various vertebrate groups.
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Affiliation(s)
- Hirzahida Mohd-Padil
- School of Biosciences & Biotechnology, Faculty of Science Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
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29
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Sarropoulou E, Galindo-Villegas J, García-Alcázar A, Kasapidis P, Mulero V. Characterization of European sea bass transcripts by RNA SEQ after oral vaccine against V. anguillarum. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:634-642. [PMID: 22790793 DOI: 10.1007/s10126-012-9466-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 05/05/2012] [Indexed: 06/01/2023]
Abstract
The European sea bass (Dicentrarchus labrax) is, along with the gilthead sea bream (Sparus aurata), one of the most extensively cultured species in European aquaculture productions. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Evaluation of the efficacy of an oral vaccine against Vibrio anguillarum (Aquavac Vibrio Oral) in sea bass revealed specific immune gene expression profiles in the gut as well as protection of fish. In the present study, we performed RNA SEQ in two different tissues: the hind gut and the head kidney. For each tissue, one control sample (where a sample presents a pool of four to five individuals) and one sample after oral vaccine against V. anguillarum were submitted to 454 next-generation sequencing. In total, 269,043 sequences were obtained, 143,007 for head kidney and 125,036 for gut. The read lengths ranged from 40 to 706 bp with an average length of 348 bp. The total number of clustered sequences for head kidney is accounting to 49,089 (∼34 %) and for gut to 71,676 (~57 %). Differential expression was detected for 496 transcripts in head kidney and for 336 in gut. The results not only enrich the present collection of expressed sequence tag sequences including rare transcripts like leukocyte immune-type receptors, cullin, or supervillin but also show the efficacy of oral vaccination against V. anguillarum.
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Affiliation(s)
- E Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece.
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Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes. BMC Vet Res 2012; 8:108. [PMID: 22776770 PMCID: PMC3505460 DOI: 10.1186/1746-6148-8-108] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 06/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Grass carp (Ctenopharyngodon idella) is one of the most economically important freshwater fish, but its production is often affected by diseases that cause serious economic losses. To date, no good breeding varieties have been obtained using the oriented cultivation technique. The ability to identify disease resistance genes in grass carp is important to cultivate disease-resistant varieties of grass carp. RESULTS In this study, we constructed a non-normalized cDNA library of head kidney in grass carp, and, after clustering and assembly, we obtained 3,027 high-quality unigenes. Solexa sequencing was used to generate sequence tags from the transcriptomes of the head kidney in grass carp before and after grass carp reovirus (GCRV) infection. After processing, we obtained 22,144 tags that were differentially expressed by more than 2-fold between the uninfected and infected groups. 679 of the differentially expressed tags (3.1%) mapped to 483 of the unigenes (16.0%). The up-regulated and down-regulated unigenes were annotated using gene ontology terms; 16 were annotated as immune-related and 42 were of unknown function having no matches to any of the sequences in the databases that were used in the similarity searches. Semi-quantitative RT-PCR revealed four unknown unigenes that showed significant responses to the viral infection. Based on domain structure predictions, one of these sequences was found to encode a protein that contained two transmembrane domains and, therefore, may be a transmembrane protein. Here, we proposed that this novel unigene may encode a virus receptor or a protein that mediates the immune signalling pathway at the cell surface. CONCLUSION This study enriches the molecular basis data of grass carp and further confirms that, based on fish tissue-specific EST databases, transcriptome analysis is an effective route to discover novel functional genes.
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31
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Singh A, Sood N, Chauhan U, Mohindra V. EST-based identification of immune-relevant genes from spleen of Indian catfish, Clarias batrachus (Linnaeus, 1758). Gene 2012; 502:53-9. [DOI: 10.1016/j.gene.2012.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/09/2012] [Indexed: 12/23/2022]
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Wu MS, Chen CW, Liu YC, Huang HH, Lin CH, Tzeng CS, Chang CY. Transcriptional analysis of orange-spotted grouper reacting to experimental grouper iridovirus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 37:233-242. [PMID: 22504162 DOI: 10.1016/j.dci.2012.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 03/23/2012] [Accepted: 04/07/2012] [Indexed: 05/31/2023]
Abstract
Disease caused by grouper iridovirus (GIV) has resulted in economic losses due to high mortality in grouper culture. Thirty-eight up- and 48 down-regulated known entities have been identified using a GIV-infected grouper kidney cDNA microarray chip. Further quantitative validation was executed in the head-kidney and spleen for 24 candidate genes and 7 immune factors following GIV inoculation. Significant induction with various patterns could be seen in 30 tested genes in the spleen. However, only 23 genes had induction in the head-kidney and meanwhile 5 genes showed reduction. Transcriptional expression profiles of selected genes in response to lipopolysaccharide (LPS) or polyinosinic:polycytidylic acid (PIC) were also established to compare with the GIV-stimulated expression. The results indicated that the responses of most genes facing GIV invasion have more similarities to PIC treatment than LPS. Seven genes are thought to be interferon-related factors: RNA helicase DHX58, ISG15, viperin, HECT E3 ligase (HECT), CD9, urokinase plasminogen activator surface receptor (PLAUR) and Mx-1. Following immunization with inactivated GIV, significant induction could be seen in DHX58, viperin, IL-1β, IL-8, COX-2, HECT, PLAUR, IgM, Mx-1, very large inducible GTPase-1 (VLIG1) and TNF-α in the head-kidney or spleen, and the latter 6 genes also had a gradual increasing pattern by a boosting immunization. These factors might play important roles in adaptive antiviral protection. Thus, we have characterized the temporal response patterns of virus responsive genes and have also identified several potential immune markers to further investigate host antiviral defense mechanisms.
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Affiliation(s)
- Ming-Shan Wu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, ROC
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Sarropoulou E, Nousdili D, Kotoulas G, Magoulas A. Functional divergences of GAPDH isoforms during early development in two perciform fish species. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:1115-1124. [PMID: 21559871 DOI: 10.1007/s10126-011-9375-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 03/29/2011] [Indexed: 05/30/2023]
Abstract
Glyceraldehyde-3-phospate dehydrogenase (GAPDH) is involved in basic cell catabolic processes and, as it is thought to be continuously expressed, belongs to the group of housekeeping genes. Thus, it is frequently used as an internal control in quantitative gene expression studies. However, the evidence of different expression patterns in a broad range of organisms and tissues, as well as the occurrence of different isoforms, shows that GAPDH has to be reevaluated as an internal control in qPCR studies, and its annotation has to be enriched. GAPDH has been shown to be involved in the pathway of energy and carbon molecule supply as well as in transcription and apoptosis. In the present study, we isolated the two isoforms, GAPDH-1 and GAPDH-2, of the gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax). We inferred the phylogenetic relationships to ten other fish species and gave the gene structure of both genes. We further investigated gene expression analysis in both species for different developmental stages showing divergent gene expression of the two isoforms and the possible function of GAPDH-1 as a maternal gene.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology and Genetics (I.M.B.G.), Hellenic Centre for Marine Research Crete, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
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Xia JH, He XP, Bai ZY, Lin G, Yue GH. Analysis of the Asian seabass transcriptome based on expressed sequence tags. DNA Res 2011; 18:513-22. [PMID: 22086997 PMCID: PMC3223082 DOI: 10.1093/dnares/dsr036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Analysis of transcriptomes is of great importance in genomic studies. Asian seabass is an important fish species. A number of genomic tools in it were developed, while large expressed sequence tag (EST) data are lacking. We sequenced ESTs from nine normalized cDNA libraries and obtained 11 431 high-quality ESTs. We retrieved 8524 ESTs from dbEST database and analyzed all 19 975 ESTs using bioinformatics tools. After clustering, we obtained 8837 unique sequences (2838 contigs and 5999 singletons). The average contig length was 574 bp. Annotation of these unique sequences revealed that 48.9% of them showed significant homology to RNA sequences in GenBank. Functional classification of the unique ESTs identified a broad range of genes involved in different functions. We identified 6114 putative single-nucleotide polymorphisms and 634 microsatellites in ESTs. We discovered different temporal and spatial expression patterns of some immune-related genes in the Asian seabass after challenging with a pathogen Vibrio harveyi. The unique EST sequences are being used in developing a cDNA microarray to examine global gene expression and will also facilitate future whole-genome sequence assembly and annotation of Asian seabass and comparative genomics.
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Affiliation(s)
- Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore
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35
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Millán A, Gómez-Tato A, Fernández C, Pardo BG, Alvarez-Dios JA, Calaza M, Bouza C, Vázquez M, Cabaleiro S, Martínez P. Design and performance of a turbot (Scophthalmus maximus) oligo-microarray based on ESTs from immune tissues. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:452-465. [PMID: 19844759 DOI: 10.1007/s10126-009-9231-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 09/08/2009] [Indexed: 05/28/2023]
Abstract
An expressed sequence tag database from immune tissues was used to design the first high-density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60 mers) were successfully designed for 2,716 out of 3,482 unique sequences of the database. An Agilent custom oligo-microarray 8 x 15 k (five replicates/gene; eight microarrays/slide) was constructed. The performance of the microarray and the sources of variation along microarray analysis were examined on spleen pools of controls and Aeromonas salmonicida-challenged fish at 3 days postinfection. Only 48 out of 2,716 probes did not show signal of hybridization on the 32 microarrays employed, thus demonstrating the consistency of the bioinformatic applications of our database. An asymmetric hierarchical design was employed to ascertain the noise associated with biological and technical (RNA extraction, labeling, hybridization, slide, and dye bias) factors using 1C and 2C labeling approaches. The high correlation coefficient between replicates at most factors tested demonstrated the high reproducibility of the signal. An analysis of random-effects variance revealed that technical variation was mostly negligible, and biological variation represented the main factor, even using pooled samples. One-color approach performed at least as well as 2C, suggesting their usefulness due to its higher design flexibility and lower cost. A relevant proportion of genes turn out to be differentially labeled depending on fluorophore, which alerts for the likely need of swapping replication in 2C experiments. A set of differentially expressed genes and enriched functions related to immune/defense response were detected at 3 days postchallenging.
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Affiliation(s)
- Adrián Millán
- Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain
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Caipang CMA, Lazado CC, Brinchmann MF, Kiron V. Infection-induced changes in expression of antibacterial and cytokine genes in the gill epithelial cells of Atlantic cod, Gadus morhua during incubation with bacterial pathogens. Comp Biochem Physiol B Biochem Mol Biol 2010; 156:319-25. [DOI: 10.1016/j.cbpb.2010.04.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Revised: 04/18/2010] [Accepted: 04/19/2010] [Indexed: 12/28/2022]
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Xia JH, Yue GH. Identification and analysis of immune-related transcriptome in Asian seabass Lates calcarifer. BMC Genomics 2010; 11:356. [PMID: 20525308 PMCID: PMC2893601 DOI: 10.1186/1471-2164-11-356] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 06/04/2010] [Indexed: 01/21/2023] Open
Abstract
Background Fish diseases caused by pathogens are limiting their production and trade, affecting the economy generated by aquaculture. Innate immunity system is the first line of host defense in opposing pathogenic organisms or any other foreign material. For identification of immune-related genes in Asian seabass Lates calcarifer, an important marine foodfish species, we injected bacterial lipopolysaccharide (LPS), a commonly used elicitor of innate immune responses to eight individuals at the age of 35 days post-hatch and applied the suppression subtractive hybridization (SSH) technique to selectively amplify spleen cDNA of differentially expressed genes. Results Sequencing and bioinformatic analysis of 3351 ESTs from two SSH libraries yielded 1692 unique transcripts. Of which, 618 transcripts were unknown/novel genes and the remaining 1074 were similar to 743 known genes and 105 unannotated mRNA sequences available in public databases. A total of 161 transcripts were classified to the category "response to stimulus" and 115 to "immune system process". We identified 25 significantly up-regulated genes (including 2 unknown transcripts) and 4 down-regulated genes associated with immune-related processes upon challenge with LPS. Quantitative real-time PCR confirmed the differential expression of these genes after LPS challenge. Conclusions The present study identified 1692 unique transcripts upon LPS challenge for the first time in Asian seabass by using SSH, sequencing and bioinformatic analysis. Some of the identified transcripts are vertebrate homologues and others are hitherto unreported putative defence proteins. The obtained immune-related genes may allow for a better understanding of immunity in Asian seabass, carrying out detailed functional analysis of these genes and developing strategies for efficient immune protection against infections in Asian seabass.
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Affiliation(s)
- Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, 117604 Republic of Singapore
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Scapigliati G, Buonocore F, Randelli E, Casani D, Meloni S, Zarletti G, Tiberi M, Pietretti D, Boschi I, Manchado M, Martin-Antonio B, Jimenez-Cantizano R, Bovo G, Borghesan F, Lorenzen N, Einer-Jensen K, Adams S, Thompson K, Alonso C, Bejar J, Cano I, Borrego JJ, Alvarez MC. Cellular and molecular immune responses of the sea bass (Dicentrarchus labrax) experimentally infected with betanodavirus. FISH & SHELLFISH IMMUNOLOGY 2010; 28:303-311. [PMID: 19925869 DOI: 10.1016/j.fsi.2009.11.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 11/03/2009] [Accepted: 11/07/2009] [Indexed: 05/28/2023]
Abstract
Naïve sea bass juveniles (38.4 + or - 4.5 g) were intramuscularly infected with a sublethal dose of betanodavirus isolate 378/I03, followed after 43 days by a similar boosting. This infection resulted in an overall mortality of 7.6%. At various intervals, sampling of fish tissues was performed to investigate: i) B and T lymphocyte content in organs and tissues; ii), proliferation of leucocytes re-stimulated in vitro with inactivated virus; iii) presence of serum antibody specific for betanodavirus; iv) expression of genes coding for the following immunoregulatory molecules involved in innate and acquired responses: type I IFN, Mx, IL-1, Cox-2; IL-10, TGF-beta, TCRbeta, CD4, CD8alpha, IgM, by using a quantitative PCR array system developed for sea bass. The obtained results showed a detectable increase of T cells and B cells in PBL during betanodavirus infection. Furthermore, leucocytes obtained from blood, head kidney, and gills showed a detectable "in vitro" increase in viability upon addition of inactivated viral particles, as determined by measuring intracellular ATP concentration. ELISA analysis of sera showed that exposure to nodavirus induced a low, but specific antibody titer measured 43 days after infection, despite the presence of measurable levels of natural antibody. Finally, a strong upregulation of genes coding for type I IFN, Mx, and IgM was identified after both infection and boosting. Interestingly, an upregulation of Cox-2 until boosting, and of TGF-beta and IL-10 after boosting was also observed, while the other tested genes did not show any significant variations with respect to mock-treated fish. Overall, our work represents a first comprehensive analysis of cellular and molecular immune parameters in a fish species exposed to a pathogenic virus.
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Affiliation(s)
- G Scapigliati
- Dipartimento di Scienze Ambientali, Largo dell'Università, Università degli Studi della Tuscia, Viterbo 01100, Italy.
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Sarropoulou E, Fernandes JMO, Mitter K, Magoulas A, Mulero V, Sepulcre MP, Figueras A, Novoa B, Kotoulas G. Evolution of a multifunctional gene: The warm temperature acclimation protein Wap65 in the European seabass Dicentrarchus labrax. Mol Phylogenet Evol 2009; 55:640-9. [PMID: 19853054 DOI: 10.1016/j.ympev.2009.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 09/30/2009] [Accepted: 10/01/2009] [Indexed: 10/20/2022]
Abstract
The warm temperature acclimation protein Wap65 has been shown to be involved in temperature acclimation, in immune response as well as in development. In teleosts, two types of Wap65 proteins, Wap65-1 and Wap65-2 are found, both acting as a multifunctional agent in several biological processes. In the present study we identified both transcripts Wap65-1 and Wap65-2 for the European seabass (Dicentrarchus labrax), examined their evolutionary rate and performed selection tests. The two paralogues were shown to be under moderate positive selection indicating their evolutionary adaptation. This functional diversification was further explored through expression studies. Both transcripts were differentially expressed during development as well as in various tissues and pathogen challenges, showing that Wap65-1 and Wap65-2 have evolved diverse functions. These results direct to the hypothesis that Wap65 proteins may, similarly to heat-shock proteins, have a general role in cell physiology.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, P.O. Box 2214, 710 03 Iraklio, Crete, Greece.
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