2023 |
Meyer, Raïssa; Davies, Neil; Pitz, Kathleen J; Meyer, Chris; Samuel, Robyn; Anderson, Jane; Appeltans, Ward; Barker, Katharine; Chavez, Francisco P; Duffy, Emmett J; Goodwin, Kelly D; Hudson, Maui; Hunter, Margaret E; Karstensen, Johannes; Laney, Christine M; Leinen, Margaret; Mabee, Paula; Macklin, James A; Muller-Karger, Frank; Pade, Nicolas; Pearlman, Jay; Phillips, Lori; Provoost, Pieter; Santi, Ioulia; Schigel, Dmitry; Schriml, Lynn M; Soccodato, Alice; Suominen, Saara; Thibault, Katherine M; Ung, Visotheary; van de Kamp, Jodie; Wallis, Elycia; Walls, Ramona; Buttigieg, Pier Luigi The founding charter of the Omic Biodiversity Observation Network (Omic BON) Journal Article GigaScience, 12 , pp. giad068, 2023, ISSN: 2047-217X. @article{meyer_founding_2022, title = {The founding charter of the Omic Biodiversity Observation Network (Omic BON)}, author = {Raïssa Meyer and Neil Davies and Kathleen J Pitz and Chris Meyer and Robyn Samuel and Jane Anderson and Ward Appeltans and Katharine Barker and Francisco P Chavez and Emmett J Duffy and Kelly D Goodwin and Maui Hudson and Margaret E Hunter and Johannes Karstensen and Christine M Laney and Margaret Leinen and Paula Mabee and James A Macklin and Frank Muller-Karger and Nicolas Pade and Jay Pearlman and Lori Phillips and Pieter Provoost and Ioulia Santi and Dmitry Schigel and Lynn M Schriml and Alice Soccodato and Saara Suominen and Katherine M Thibault and Visotheary Ung and Jodie van de Kamp and Elycia Wallis and Ramona Walls and Pier Luigi Buttigieg}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/09/2023-Meyer-GigaSci-49.pdf https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad068/7252077}, doi = {10.1093/gigascience/giad068}, issn = {2047-217X}, year = {2023}, date = {2023-09-20}, urldate = {2023-09-20}, journal = {GigaScience}, volume = {12}, pages = {giad068}, abstract = {Abstract Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities. |
Lubinevsky, Hadas; Tom, Moshe; Corbera, Jordi; Koulouri, Panayota (Yolanda) Mediterranean Marine Science, 24 (3), pp. 482–490, 2023, ISSN: 1791-6763, 1108-393X. @article{lubinevsky_spatial_2023, title = {Spatial and temporal community composition changes of Cumacea (Crustacea: Malacostraca: Peracarida) from the soft-sediment habitats of the Mediterranean coast of Israel}, author = {Hadas Lubinevsky and Moshe Tom and Jordi Corbera and Panayota (Yolanda) Koulouri}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/09/2023-Lubinevsky-MMS-48.pdf https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/34247}, doi = {10.12681/mms.34247}, issn = {1791-6763, 1108-393X}, year = {2023}, date = {2023-09-15}, urldate = {2023-09-15}, journal = {Mediterranean Marine Science}, volume = {24}, number = {3}, pages = {482--490}, abstract = {The present study provides a zoogeographic and faunistic update on the cumacean species that inhabit the soft substrate habitats of the Israeli waters of the Mediterranean Sea. Published and new unpublished cumacean records are both used to enable an overview of a 74-year period of species composition and distribution, providing a broad perspective of temporal faunistic changes. As a result, 43 cumacean species have now been recorded from the Mediterranean coast of Israel. Previously unpublished results, starting from 2013, were derived from intensified sampling of the continental shelf and slope as well as the bathyal plain, and revealed eight new species records for the eastern part of the Mediterranean Sea. The cumacean community included species primarily of the Mediterranean zoogeographic province with several Mediterranean-Atlantic examples. Three species, postulated to be of Indo-Pacific origin were also previously recorded on the continental shelf of the area. Finally, species composition and structure of the continental shelf indicated spatial and temporal changes between 2010 – 2021, partly due to different sampling methods as well as anthropogenic activities that took place in the area. The continental slope and the bathyal plain seem to remain as relatively stable environments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The present study provides a zoogeographic and faunistic update on the cumacean species that inhabit the soft substrate habitats of the Israeli waters of the Mediterranean Sea. Published and new unpublished cumacean records are both used to enable an overview of a 74-year period of species composition and distribution, providing a broad perspective of temporal faunistic changes. As a result, 43 cumacean species have now been recorded from the Mediterranean coast of Israel. Previously unpublished results, starting from 2013, were derived from intensified sampling of the continental shelf and slope as well as the bathyal plain, and revealed eight new species records for the eastern part of the Mediterranean Sea. The cumacean community included species primarily of the Mediterranean zoogeographic province with several Mediterranean-Atlantic examples. Three species, postulated to be of Indo-Pacific origin were also previously recorded on the continental shelf of the area. Finally, species composition and structure of the continental shelf indicated spatial and temporal changes between 2010 – 2021, partly due to different sampling methods as well as anthropogenic activities that took place in the area. The continental slope and the bathyal plain seem to remain as relatively stable environments. |
Amaral, Raquel; Duci, Damiano; Cotta, Francisco C; Bacellar, Felipe L; Oliveira, Soraia; Verret, Frédéric; Asadi, Kamal; Vandamme, Lode K J; Reis, Nuno M; Bryant, Lee D; Tosh, David; Mouget, Jean-Luc; Perkins, Rupert; Rocha, Paulo R F Ion-driven communication and acclimation strategies in microalgae Journal Article Chemical Engineering Journal, 473 , pp. 144985, 2023, ISSN: 13858947. @article{amaral_ion-driven_2023, title = {Ion-driven communication and acclimation strategies in microalgae}, author = {Raquel Amaral and Damiano Duci and Francisco C Cotta and Felipe L Bacellar and Soraia Oliveira and Frédéric Verret and Kamal Asadi and Lode K J Vandamme and Nuno M Reis and Lee D Bryant and David Tosh and Jean-Luc Mouget and Rupert Perkins and Paulo R F Rocha}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/09/2023-Amaral-R-Chem-Engineer-47.pdf https://linkinghub.elsevier.com/retrieve/pii/S1385894723037166}, doi = {10.1016/j.cej.2023.144985}, issn = {13858947}, year = {2023}, date = {2023-09-11}, urldate = {2023-09-14}, journal = {Chemical Engineering Journal}, volume = {473}, pages = {144985}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rigos, George; Glaropoulos, Alexis; Tzokas, Kostantinos; Gourzioti, Evgenia; Kogiannou, Dimitra; Golomazou, Eleni Journal of Fish Diseases, pp. jfd.13854, 2023, ISSN: 0140-7775, 1365-2761. @article{rigos_field_2023, title = {A field evaluation of orally administered praziquantel against the gill fluke \textit{Sparicotyle chrysophrii} infecting gilthead seabream ( \textit{Sparus aurata} )}, author = {George Rigos and Alexis Glaropoulos and Kostantinos Tzokas and Evgenia Gourzioti and Dimitra Kogiannou and Eleni Golomazou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/09/2023-Rigos-JFD-pre-print-46.pdf https://onlinelibrary.wiley.com/doi/10.1111/jfd.13854}, doi = {10.1111/jfd.13854}, issn = {0140-7775, 1365-2761}, year = {2023}, date = {2023-09-08}, urldate = {2023-09-11}, journal = {Journal of Fish Diseases}, pages = {jfd.13854}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kogiannou, Dimitra; Nikoloudaki, Chrysanthi; Valsamidi, Vasilia; Kotsiri, Mado; Golomazou, Eleni; Rigos, George Pharmacokinetics of praziquantel in gilthead seabream (Sparus aurata) plasma and gills Journal Article Aquaculture, 577 , pp. 739975, 2023, ISSN: 00448486. @article{kogiannou_pharmacokinetics_2023, title = {Pharmacokinetics of praziquantel in gilthead seabream (Sparus aurata) plasma and gills}, author = {Dimitra Kogiannou and Chrysanthi Nikoloudaki and Vasilia Valsamidi and Mado Kotsiri and Eleni Golomazou and George Rigos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/09/2023-Kogiannou-AQUA-pre-print45.pdf https://linkinghub.elsevier.com/retrieve/pii/S0044848623007494}, doi = {10.1016/j.aquaculture.2023.739975}, issn = {00448486}, year = {2023}, date = {2023-09-06}, urldate = {2023-09-07}, journal = {Aquaculture}, volume = {577}, pages = {739975}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul R; Bleidorn, Christoph; Bombarely, Aureliano; Crottini, Angelica; Gallo, Guido R; Godoy, José A; Jentoft, Sissel; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah A; Paez, Sadye; Palsbøll, Per J; Pampoulie, Christophe; Ruiz-López, María J; Secomandi, Simona; Svardal, Hannes; Theofanopoulou, Constantina; Vries, Jan De; Waldvogel, Ann-Marie; Zhang, Guojie; Jarvis, Erich D; Bálint, Miklós; Ciofi, Claudio; Waterhouse, Robert M; Mazzoni, Camila J; Höglund, Jacob; Aghayan, Sargis A; Alioto, Tyler S; Almudi, Isabel; Alvarez, Nadir; Alves, Paulo C; Rosario, Isabel Amorim Do R; Antunes, Agostinho; Arribas, Paula; Baldrian, Petr; Bertorelle, Giorgio; Böhne, Astrid; Bonisoli-Alquati, Andrea; Boštjančić, Ljudevit L; Boussau, Bastien; Breton, Catherine M; Buzan, Elena; Campos, Paula F; Carreras, Carlos; Castro, FIlipe L C; Chueca, Luis J; Čiampor, Fedor; Conti, Elena; Cook-Deegan, Robert; Croll, Daniel; Cunha, Mónica V; Delsuc, Frédéric; Dennis, Alice B; Dimitrov, Dimitar; Faria, Rui; Favre, Adrien; Fedrigo, Olivier D; Fernández, Rosa; Ficetola, Gentile Francesco; Flot, Jean-François; Gabaldón, Toni; Agius, Dolores R; Giani, Alice M; Gilbert, Thomas M P; Grebenc, Tine; Guschanski, Katerina; Guyot, Romain; Hausdorf, Bernhard; Hawlitschek, Oliver; Heintzman, Peter D; Heinze, Berthold; Hiller, Michael; Husemann, Martin; Iannucci, Alessio; Irisarri, Iker; Jakobsen, Kjetill S; Klinga, Peter; Kloch, Agnieszka; Kratochwil, Claudius F; Kusche, Henrik; Layton, Kara K S; Leonard, Jennifer A; Lerat, Emmanuelle; Liti, Gianni; Manousaki, Tereza; Marques-Bonet, Tomas; Matos-Maraví, Pável; Matschiner, Michael; Maumus, Florian; Cartney, Ann Mc M; Meiri, Shai; Melo-Ferreira, José; Mengual, Ximo; Monaghan, Michael T; Montagna, Matteo; Mysłajek, Robert W; Neiber, Marco T; Nicolas, Violaine; Novo, Marta; Ozretić, Petar; Palero, Ferran; Pârvulescu, Lucian; Pascual, Marta; Paulo, Octávio S; Pavlek, Martina; Pegueroles, Cinta; Pellissier, Loïc; Pesole, Graziano; Primmer, Craig R; Riesgo, Ana; Rüber, Lukas; Rubolini, Diego; Salvi, Daniele; Seehausen, Ole; Seidel, Matthias; Studer, Bruno; Theodoridis, Spyros; Thines, Marco; Urban, Lara; Vasemägi, Anti; Vella, Adriana; Vella, Noel; Vernes, Sonja C; Vernesi, Cristiano; Vieites, David R; Wheat, Christopher W; Wörheide, Gert; Wurm, Yannick; Zammit, Gabrielle How genomics can help biodiversity conservation Journal Article Trends in Genetics, 39 (7), pp. 545–559, 2023, ISSN: 01689525. @article{theissinger_how_2023, title = {How genomics can help biodiversity conservation}, author = {Kathrin Theissinger and Carlos Fernandes and Giulio Formenti and Iliana Bista and Paul R Berg and Christoph Bleidorn and Aureliano Bombarely and Angelica Crottini and Guido R Gallo and José A Godoy and Sissel Jentoft and Joanna Malukiewicz and Alice Mouton and Rebekah A Oomen and Sadye Paez and Per J Palsbøll and Christophe Pampoulie and María J Ruiz-López and Simona Secomandi and Hannes Svardal and Constantina Theofanopoulou and Jan De Vries and Ann-Marie Waldvogel and Guojie Zhang and Erich D Jarvis and Miklós Bálint and Claudio Ciofi and Robert M Waterhouse and Camila J Mazzoni and Jacob Höglund and Sargis A Aghayan and Tyler S Alioto and Isabel Almudi and Nadir Alvarez and Paulo C Alves and Isabel R Amorim Do Rosario and Agostinho Antunes and Paula Arribas and Petr Baldrian and Giorgio Bertorelle and Astrid Böhne and Andrea Bonisoli-Alquati and Ljudevit L Boštjančić and Bastien Boussau and Catherine M Breton and Elena Buzan and Paula F Campos and Carlos Carreras and FIlipe L C Castro and Luis J Chueca and Fedor Čiampor and Elena Conti and Robert Cook-Deegan and Daniel Croll and Mónica V Cunha and Frédéric Delsuc and Alice B Dennis and Dimitar Dimitrov and Rui Faria and Adrien Favre and Olivier D Fedrigo and Rosa Fernández and Gentile Francesco Ficetola and Jean-François Flot and Toni Gabaldón and Dolores R Agius and Alice M Giani and Thomas M P Gilbert and Tine Grebenc and Katerina Guschanski and Romain Guyot and Bernhard Hausdorf and Oliver Hawlitschek and Peter D Heintzman and Berthold Heinze and Michael Hiller and Martin Husemann and Alessio Iannucci and Iker Irisarri and Kjetill S Jakobsen and Peter Klinga and Agnieszka Kloch and Claudius F Kratochwil and Henrik Kusche and Kara K S Layton and Jennifer A Leonard and Emmanuelle Lerat and Gianni Liti and Tereza Manousaki and Tomas Marques-Bonet and Pável Matos-Maraví and Michael Matschiner and Florian Maumus and Ann M Mc Cartney and Shai Meiri and José Melo-Ferreira and Ximo Mengual and Michael T Monaghan and Matteo Montagna and Robert W Mysłajek and Marco T Neiber and Violaine Nicolas and Marta Novo and Petar Ozretić and Ferran Palero and Lucian Pârvulescu and Marta Pascual and Octávio S Paulo and Martina Pavlek and Cinta Pegueroles and Loïc Pellissier and Graziano Pesole and Craig R Primmer and Ana Riesgo and Lukas Rüber and Diego Rubolini and Daniele Salvi and Ole Seehausen and Matthias Seidel and Bruno Studer and Spyros Theodoridis and Marco Thines and Lara Urban and Anti Vasemägi and Adriana Vella and Noel Vella and Sonja C Vernes and Cristiano Vernesi and David R Vieites and Christopher W Wheat and Gert Wörheide and Yannick Wurm and Gabrielle Zammit}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/09/2023-Theissinger-Trends-Genetics-44.pdf https://linkinghub.elsevier.com/retrieve/pii/S0168952523000203}, doi = {10.1016/j.tig.2023.01.005}, issn = {01689525}, year = {2023}, date = {2023-08-31}, urldate = {2023-09-01}, journal = {Trends in Genetics}, volume = {39}, number = {7}, pages = {545--559}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kitsoulis, Christos V; Papadogiannis, Vasileios; Kristoffersen, Jon B; Kaitetzidou, Elisavet; Sterioti, Aspasia; Tsigenopoulos, Costas S; Manousaki, Tereza Near-chromosome level genome assembly of devil firefish, Pterois miles Journal Article Peer Community Journal, 3 , pp. e64, 2023, ISSN: 2804-3871. @article{kitsoulis_near-chromosome_2023, title = {Near-chromosome level genome assembly of devil firefish, Pterois miles}, author = {Christos V Kitsoulis and Vasileios Papadogiannis and Jon B Kristoffersen and Elisavet Kaitetzidou and Aspasia Sterioti and Costas S Tsigenopoulos and Tereza Manousaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/08/2023-Kitsoulis-PeerCJ-43.pdf https://peercommunityjournal.org/articles/10.24072/pcjournal.295/}, doi = {10.24072/pcjournal.295}, issn = {2804-3871}, year = {2023}, date = {2023-08-29}, urldate = {2023-08-31}, journal = {Peer Community Journal}, volume = {3}, pages = {e64}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lavecchia, Anna; Manzari, Caterina; Pousis, Chrysovalentinos; Mansi, Luigi; Cox, Sharon N; Mylonas, Constantinos C; Zupa, Rosa; Giudice, Claudio Lo; Virgilio, Caterina De; Picardi, Ernesto; Ventriglia, Gianluca; Pesole, Graziano; Corriero, Aldo Dysregulation of testis mRNA expression levels in hatchery-produced vs wild greater amberjack Seriola dumerili Journal Article Scientific Reports, 13 (1), pp. 13662, 2023, ISSN: 2045-2322. @article{lavecchia_dysregulation_2023, title = {Dysregulation of testis mRNA expression levels in hatchery-produced vs wild greater amberjack Seriola dumerili}, author = {Anna Lavecchia and Caterina Manzari and Chrysovalentinos Pousis and Luigi Mansi and Sharon N Cox and Constantinos C Mylonas and Rosa Zupa and Claudio Lo Giudice and Caterina De Virgilio and Ernesto Picardi and Gianluca Ventriglia and Graziano Pesole and Aldo Corriero}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/08/2023-Lavecchia-SciRep-42.pdf https://www.nature.com/articles/s41598-023-40597-5}, doi = {10.1038/s41598-023-40597-5}, issn = {2045-2322}, year = {2023}, date = {2023-08-28}, urldate = {2023-08-29}, journal = {Scientific Reports}, volume = {13}, number = {1}, pages = {13662}, abstract = {Abstract Reproductive dysfunctions have been recently documented in male greater amberjack Seriola dumerili caught from the wild and reared in captivity. In the present study, we compared testis transcriptome in wild fish (WILD), hatchery-produced fish with apparently normal spermatogenesis (Normal Farmed; NormalF) and hatchery-produced fish with evident reproductive dysfunction (Dysfunctional Farmed; DysF). Gene expression analysis identified 2157, 1985 and 74 differentially expressed genes (DEGs) in DysF vs WILD, NormalF vs DysF and NormalF vs WILD comparisons, respectively. In DysF, a dysregulation of several interconnected biological processes, including cell assembly , steroidogenesis and apoptosis was found. Gene enrichment of progesterone-mediated oocyte maturation , oocyte meiosis and cell cycle pathways were identified in the DysF vs NormalF comparison. Most of the DEGs involved in the enriched pathways were downregulated in DysF. The comparison of NormalF vs WILD showed that most of the DEGs were downregulated in NormalF, including a gene that encodes for a regulatory protein with a protective role in apoptosis regulation ( ptpn 6), indicating that spermatogenesis was dysfunctional also in the apparently “normal” hatchery-produced fish. Hence, rearing of male greater amberjack in captivity, from eggs produced by captive breeders, did not prevent the appearance of reproductive dysfunctions, and these dysfunctions involved several biological processes and metabolic pathways.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Reproductive dysfunctions have been recently documented in male greater amberjack Seriola dumerili caught from the wild and reared in captivity. In the present study, we compared testis transcriptome in wild fish (WILD), hatchery-produced fish with apparently normal spermatogenesis (Normal Farmed; NormalF) and hatchery-produced fish with evident reproductive dysfunction (Dysfunctional Farmed; DysF). Gene expression analysis identified 2157, 1985 and 74 differentially expressed genes (DEGs) in DysF vs WILD, NormalF vs DysF and NormalF vs WILD comparisons, respectively. In DysF, a dysregulation of several interconnected biological processes, including cell assembly , steroidogenesis and apoptosis was found. Gene enrichment of progesterone-mediated oocyte maturation , oocyte meiosis and cell cycle pathways were identified in the DysF vs NormalF comparison. Most of the DEGs involved in the enriched pathways were downregulated in DysF. The comparison of NormalF vs WILD showed that most of the DEGs were downregulated in NormalF, including a gene that encodes for a regulatory protein with a protective role in apoptosis regulation ( ptpn 6), indicating that spermatogenesis was dysfunctional also in the apparently “normal” hatchery-produced fish. Hence, rearing of male greater amberjack in captivity, from eggs produced by captive breeders, did not prevent the appearance of reproductive dysfunctions, and these dysfunctions involved several biological processes and metabolic pathways. |
Alkassar, Mounira; Sanchez-Henao, Andres; Reverté, Jaume; Barreiro, Lourdes; Rambla-Alegre, Maria; Leonardo, Sandra; Mandalakis, Manolis; Peristeraki, Panagiota; Diogène, Jorge; Campàs, Mònica Evaluation of Toxicity Equivalency Factors of Tetrodotoxin Analogues with a Neuro-2a Cell-Based Assay and Application to Puffer Fish from Greece Journal Article Marine Drugs, 21 (8), pp. 432, 2023, ISSN: 1660-3397. @article{alkassar_evaluation_2023, title = {Evaluation of Toxicity Equivalency Factors of Tetrodotoxin Analogues with a Neuro-2a Cell-Based Assay and Application to Puffer Fish from Greece}, author = {Mounira Alkassar and Andres Sanchez-Henao and Jaume Reverté and Lourdes Barreiro and Maria Rambla-Alegre and Sandra Leonardo and Manolis Mandalakis and Panagiota Peristeraki and Jorge Diogène and Mònica Campàs}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/08/2023-Alkassar-marinedrugs-41.pdf https://www.mdpi.com/1660-3397/21/8/432}, doi = {10.3390/md21080432}, issn = {1660-3397}, year = {2023}, date = {2023-08-11}, urldate = {2023-08-17}, journal = {Marine Drugs}, volume = {21}, number = {8}, pages = {432}, abstract = {Tetrodotoxin (TTX) is a potent marine neurotoxin involved in poisoning cases, especially through the consumption of puffer fish. Knowledge of the toxicity equivalency factors (TEFs) of TTX analogues is crucial in monitoring programs to estimate the toxicity of samples analyzed with instrumental analysis methods. In this work, TTX analogues were isolated from the liver of a Lagocephalus sceleratus individual caught on South Crete coasts. A cell-based assay (CBA) for TTXs was optimized and applied to the establishment of the TEFs of 5,11-dideoxyTTX, 11-norTTX-6(S)-ol, 11-deoxyTTX and 5,6,11-trideoxyTTX. Results showed that all TTX analogues were less toxic than the parent TTX, their TEFs being in the range of 0.75–0.011. Then, different tissues of three Lagocephalus sceleratus individuals were analyzed with CBA and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The obtained TEFs were applied to the TTX analogues’ concentrations obtained by LC-MS/MS analysis, providing an indication of the overall toxicity of the sample. Information about the TEFs of TTX analogues is valuable for food safety control, allowing the estimation of the risk of fish products to consumers.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Tetrodotoxin (TTX) is a potent marine neurotoxin involved in poisoning cases, especially through the consumption of puffer fish. Knowledge of the toxicity equivalency factors (TEFs) of TTX analogues is crucial in monitoring programs to estimate the toxicity of samples analyzed with instrumental analysis methods. In this work, TTX analogues were isolated from the liver of a Lagocephalus sceleratus individual caught on South Crete coasts. A cell-based assay (CBA) for TTXs was optimized and applied to the establishment of the TEFs of 5,11-dideoxyTTX, 11-norTTX-6(S)-ol, 11-deoxyTTX and 5,6,11-trideoxyTTX. Results showed that all TTX analogues were less toxic than the parent TTX, their TEFs being in the range of 0.75–0.011. Then, different tissues of three Lagocephalus sceleratus individuals were analyzed with CBA and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The obtained TEFs were applied to the TTX analogues’ concentrations obtained by LC-MS/MS analysis, providing an indication of the overall toxicity of the sample. Information about the TEFs of TTX analogues is valuable for food safety control, allowing the estimation of the risk of fish products to consumers. |
Varamogianni-Mamatsi, Despoina; Anastasiou, Thekla I; Vernadou, Emmanouela; Kouvarakis, Nikos; Kagiampaki, Eirini; Kalogerakis, Nicolas; Dailianis, Thanos; Mandalakis, Manolis Uptake of aquaculture-related dissolved organic pollutants by marine sponges: Kinetics and mechanistic insights from a laboratory study Journal Article Science of The Total Environment, 899 , pp. 165601, 2023, ISSN: 00489697. @article{varamogianni-mamatsi_uptake_2023, title = {Uptake of aquaculture-related dissolved organic pollutants by marine sponges: Kinetics and mechanistic insights from a laboratory study}, author = {Despoina Varamogianni-Mamatsi and Thekla I Anastasiou and Emmanouela Vernadou and Nikos Kouvarakis and Eirini Kagiampaki and Nicolas Kalogerakis and Thanos Dailianis and Manolis Mandalakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/08/2023-Varamogianni-Mamatsi-STEnv-40-preprint.pdf https://linkinghub.elsevier.com/retrieve/pii/S0048969723042249}, doi = {10.1016/j.scitotenv.2023.165601}, issn = {00489697}, year = {2023}, date = {2023-08-01}, urldate = {2023-08-14}, journal = {Science of The Total Environment}, volume = {899}, pages = {165601}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kotsiri, Mado; Panara, Anthi; Koupa, Anastasia; Gourzioti, Evgenia; Thomaidis, Nikolaos S; Rigos, George Preliminary measurements of formaldehyde in seawater and edible tissues of farmed gilthead seabream after formalin immersion Journal Article Mediterranean Marine Science, 24 (2), pp. 384–391, 2023, ISSN: 1791-6763, 1108-393X. @article{kotsiri_preliminary_2023, title = {Preliminary measurements of formaldehyde in seawater and edible tissues of farmed gilthead seabream after formalin immersion}, author = {Mado Kotsiri and Anthi Panara and Anastasia Koupa and Evgenia Gourzioti and Nikolaos S Thomaidis and George Rigos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Kotsiri-MMS-39.pdf https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/33606}, doi = {10.12681/mms.33606}, issn = {1791-6763, 1108-393X}, year = {2023}, date = {2023-07-21}, urldate = {2023-07-21}, journal = {Mediterranean Marine Science}, volume = {24}, number = {2}, pages = {384--391}, abstract = {This study was performed to measure the possible persistence of formaldehyde, the active substance of formalin solution, in seawater and edible gilthead seabream (Sparus aurata) tissues after a formalin bath. The trial was carried out during the summer period as parasitic infestations are of a high frequency. Water samples were taken within or at a short distance from the treatment cages, during and following formalin immersion. Fish fillets were also sampled at the same sampling points. Chromatographic analysis of water and tissue samples was performed with a photodiode array detector (HPLC-PDA). Measured formaldehyde concentrations in gilthead seabream fillets clearly showed no increase due to the immersion or advent of time. Formaldehyde measurements in seawater revealed that after formalin treatments negligible amounts of the substance remain in the aquatic environment and these values seem to be relatively unaffected by depth in the vicinity of the fish cages. Further research is required to investigate the formalin degradation cycle under Mediterranean seawater conditions, including more farm sites and temperature ranges.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study was performed to measure the possible persistence of formaldehyde, the active substance of formalin solution, in seawater and edible gilthead seabream (Sparus aurata) tissues after a formalin bath. The trial was carried out during the summer period as parasitic infestations are of a high frequency. Water samples were taken within or at a short distance from the treatment cages, during and following formalin immersion. Fish fillets were also sampled at the same sampling points. Chromatographic analysis of water and tissue samples was performed with a photodiode array detector (HPLC-PDA). Measured formaldehyde concentrations in gilthead seabream fillets clearly showed no increase due to the immersion or advent of time. Formaldehyde measurements in seawater revealed that after formalin treatments negligible amounts of the substance remain in the aquatic environment and these values seem to be relatively unaffected by depth in the vicinity of the fish cages. Further research is required to investigate the formalin degradation cycle under Mediterranean seawater conditions, including more farm sites and temperature ranges. |
Piferrer, Francesc; Wang, Han-Ping Epigenetics in aquaculture Book First edition, John Wiley & Sons Ltd, Chichester, West Sussex, UK ; Hoboken, 2023, ISBN: 9781119821939 9781119821922, (Sarropoulou E., Fernández I. 2023. Epigenetic regulation of gene expression by non-coding RNAs. In: Epigenetics in Aquaculture, edited by Piferrer F, Wang, Η., Wiley, 512 pp. ). @book{piferrer_epigenetics_2023, title = {Epigenetics in aquaculture}, author = {Francesc Piferrer and Han-Ping Wang}, url = {https://www.wiley.com/en-us/Epigenetics+in+Aquaculture-p-9781119821915}, isbn = {9781119821939 9781119821922}, year = {2023}, date = {2023-07-19}, publisher = {John Wiley & Sons Ltd}, address = {Chichester, West Sussex, UK ; Hoboken}, edition = {First edition}, abstract = {"Epigenetics, as a discipline, started in the 1940s, but with a meaning different from how it is understood today. Initially, it was essentially related to what today is understood as developmental biology and how the phenotype comes into being. The modern concept of epigenetics (i.e., heritable changes in gene expression that are not related to changes in DNA sequence) arose around the turn of this century. The field has largely benefited from the advancements made after the sequence of the human genome and all emerging technologies to interrogate different aspects of the genome. There are three very important aspects to take into account: 1) Epigenetics integrates genomic and environmental influences to bring about the phenotype; 2) There is a large fraction of the phenotypic variance that cannot be explained solely on genetic variation that now we know can be explained by epigenetic variation; and 3) Epigenetic changes can be inherited and, thus, passed from parents to offspring into the following generations. Combined, this has prompted the implementation of epigenetic research into agriculture and livestock for improved food production. Recently, there has been both a clear interest in marine epigenetics and in the application of epigenetics in aquaculture. One of the main reasons is that aquatic, cold-blooded organisms are quite susceptible to environmental cues (e.g., temperature in a cold-blooded animal strongly influences growth rates). Further, in contrast to mammals, fishes seem to have little reprogramming and erasing of the epigenetic marks after fertilization, thus enabling epigenetic transmission of environmental influences on the next generation. Thus, there is a lot of interest for application of epigenetics in aquaculture. However, there are currently no books on epigenetics in aquaculture"--}, note = {Sarropoulou E., Fernández I. 2023. Epigenetic regulation of gene expression by non-coding RNAs. In: Epigenetics in Aquaculture, edited by Piferrer F, Wang, Η., Wiley, 512 pp. }, keywords = {}, pubstate = {published}, tppubtype = {book} } "Epigenetics, as a discipline, started in the 1940s, but with a meaning different from how it is understood today. Initially, it was essentially related to what today is understood as developmental biology and how the phenotype comes into being. The modern concept of epigenetics (i.e., heritable changes in gene expression that are not related to changes in DNA sequence) arose around the turn of this century. The field has largely benefited from the advancements made after the sequence of the human genome and all emerging technologies to interrogate different aspects of the genome. There are three very important aspects to take into account: 1) Epigenetics integrates genomic and environmental influences to bring about the phenotype; 2) There is a large fraction of the phenotypic variance that cannot be explained solely on genetic variation that now we know can be explained by epigenetic variation; and 3) Epigenetic changes can be inherited and, thus, passed from parents to offspring into the following generations. Combined, this has prompted the implementation of epigenetic research into agriculture and livestock for improved food production. Recently, there has been both a clear interest in marine epigenetics and in the application of epigenetics in aquaculture. One of the main reasons is that aquatic, cold-blooded organisms are quite susceptible to environmental cues (e.g., temperature in a cold-blooded animal strongly influences growth rates). Further, in contrast to mammals, fishes seem to have little reprogramming and erasing of the epigenetic marks after fertilization, thus enabling epigenetic transmission of environmental influences on the next generation. Thus, there is a lot of interest for application of epigenetics in aquaculture. However, there are currently no books on epigenetics in aquaculture"-- |
Luoma, Jouni; Nastou, Katerina; Ohta, Tomoko; Toivonen, Harttu; Pafilis, Evangelos; Jensen, Lars Juhl; Pyysalo, Sampo S1000: a better taxonomic name corpus for biomedical information extraction Journal Article Bioinformatics, 39 (6), pp. btad369, 2023, ISSN: 1367-4811. @article{luoma_s1000_2023, title = {S1000: a better taxonomic name corpus for biomedical information extraction}, author = {Jouni Luoma and Katerina Nastou and Tomoko Ohta and Harttu Toivonen and Evangelos Pafilis and Lars Juhl Jensen and Sampo Pyysalo}, editor = {Zhiyong Lu}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Luoma-et-al.-2023-Luoma-37.pdf https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btad369/7192170}, doi = {10.1093/bioinformatics/btad369}, issn = {1367-4811}, year = {2023}, date = {2023-07-14}, urldate = {2023-07-14}, journal = {Bioinformatics}, volume = {39}, number = {6}, pages = {btad369}, abstract = {Abstract Motivation The recognition of mentions of species names in text is a critically important task for biomedical text mining. While deep learning-based methods have made great advances in many named entity recognition tasks, results for species name recognition remain poor. We hypothesize that this is primarily due to the lack of appropriate corpora. Results We introduce the S1000 corpus, a comprehensive manual re-annotation and extension of the S800 corpus. We demonstrate that S1000 makes highly accurate recognition of species names possible (F-score =93.1%), both for deep learning and dictionary-based methods. Availability and implementation All resources introduced in this study are available under open licenses from https://jensenlab.org/resources/s1000/. The webpage contains links to a Zenodo project and three GitHub repositories associated with the study.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Motivation The recognition of mentions of species names in text is a critically important task for biomedical text mining. While deep learning-based methods have made great advances in many named entity recognition tasks, results for species name recognition remain poor. We hypothesize that this is primarily due to the lack of appropriate corpora. Results We introduce the S1000 corpus, a comprehensive manual re-annotation and extension of the S800 corpus. We demonstrate that S1000 makes highly accurate recognition of species names possible (F-score =93.1%), both for deep learning and dictionary-based methods. Availability and implementation All resources introduced in this study are available under open licenses from https://jensenlab.org/resources/s1000/. The webpage contains links to a Zenodo project and three GitHub repositories associated with the study. |
Panteli, Nikolas; Feidantsis, Konstantinos; Demertzioglou, Maria; Paralika, Vasiliki; Karapanagiotis, Stelios; Mylonas, Constantinos C; Kormas, Konstantinos Ar.; Mente, Eleni; Makridis, Pavlos; Antonopoulou, Efthimia Animals, 13 (13), pp. 2154, 2023, ISSN: 2076-2615. @article{panteli_probiotic_2023, title = {The Probiotic Phaeobacter inhibens Provokes Hypertrophic Growth via Activation of the IGF-1/Akt Pathway during the Process of Metamorphosis of Greater Amberjack (Seriola dumerili, Risso 1810)}, author = {Nikolas Panteli and Konstantinos Feidantsis and Maria Demertzioglou and Vasiliki Paralika and Stelios Karapanagiotis and Constantinos C Mylonas and Konstantinos Ar. Kormas and Eleni Mente and Pavlos Makridis and Efthimia Antonopoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Panteli-Animals-36.pdf https://www.mdpi.com/2076-2615/13/13/2154}, doi = {10.3390/ani13132154}, issn = {2076-2615}, year = {2023}, date = {2023-07-07}, urldate = {2023-07-07}, journal = {Animals}, volume = {13}, number = {13}, pages = {2154}, abstract = {Metamorphosis entails hormonally regulated morphological and physiological changes requiring high energy levels. Probiotics as feed supplements generate ameliorative effects on host nutrient digestion and absorption. Thereby, the aim of the present research was to investigate the impact of the probiotic Phaeobacter inhibens as a water additive on cellular signaling pathways in the metamorphosis of greater amberjack (Seriola dumerili). Activation of insulin-like growth factor type 1 receptor (IGF-1R), protein kinase B (Akt), mitogen-activated protein kinases (MAPKs) and AMP-activated protein kinase (AMPK), induction of heat shock proteins (Hsps), and programmed cell death were assessed through SDS-Page/immunoblot analysis, while energy metabolism was determined through enzymatic activities. According to the results, greater amberjack reared in P. inhibens-enriched water entered the metamorphic phase with greater body length, while protein synthesis was triggered to facilitate the hypertrophic growth as indicated by IGF-1/Akt activation and AMPK inhibition. Contrarily, MAPKs levels were reduced, whereas variations in Hsps response were evident in the probiotic treatment. Apoptosis and autophagy were mobilized potentially for the structural remodeling processes. Furthermore, the elevated enzymatic activities of intermediary metabolism highlighted the excess energy demands of metamorphosis. Collectively, the present findings demonstrate that P. inhibens may reinforce nutrient utilization, thus leading greater amberjack to an advanced growth and developmental state.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Metamorphosis entails hormonally regulated morphological and physiological changes requiring high energy levels. Probiotics as feed supplements generate ameliorative effects on host nutrient digestion and absorption. Thereby, the aim of the present research was to investigate the impact of the probiotic Phaeobacter inhibens as a water additive on cellular signaling pathways in the metamorphosis of greater amberjack (Seriola dumerili). Activation of insulin-like growth factor type 1 receptor (IGF-1R), protein kinase B (Akt), mitogen-activated protein kinases (MAPKs) and AMP-activated protein kinase (AMPK), induction of heat shock proteins (Hsps), and programmed cell death were assessed through SDS-Page/immunoblot analysis, while energy metabolism was determined through enzymatic activities. According to the results, greater amberjack reared in P. inhibens-enriched water entered the metamorphic phase with greater body length, while protein synthesis was triggered to facilitate the hypertrophic growth as indicated by IGF-1/Akt activation and AMPK inhibition. Contrarily, MAPKs levels were reduced, whereas variations in Hsps response were evident in the probiotic treatment. Apoptosis and autophagy were mobilized potentially for the structural remodeling processes. Furthermore, the elevated enzymatic activities of intermediary metabolism highlighted the excess energy demands of metamorphosis. Collectively, the present findings demonstrate that P. inhibens may reinforce nutrient utilization, thus leading greater amberjack to an advanced growth and developmental state. |
Polymenakou, Paraskevi N; Nomikou, Paraskevi; Hannington, Mark; Petersen, Sven; Kilias, Stephanos P; Anastasiou, Thekla I; Papadimitriou, Vasiliki; Zaka, Eleutheria; Kristoffersen, Jon Bent; Lampridou, Danai; Wind, Sandra; Heinath, Verena; Lange, Sabine; Magoulas, Antonios Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field Journal Article Frontiers in Microbiology, 14 , pp. 1188544, 2023, ISSN: 1664-302X. @article{polymenakou_taxonomic_2023, title = {Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field}, author = {Paraskevi N Polymenakou and Paraskevi Nomikou and Mark Hannington and Sven Petersen and Stephanos P Kilias and Thekla I Anastasiou and Vasiliki Papadimitriou and Eleutheria Zaka and Jon Bent Kristoffersen and Danai Lampridou and Sandra Wind and Verena Heinath and Sabine Lange and Antonios Magoulas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Polymenakou-FrontMicro-35.pdf https://www.frontiersin.org/articles/10.3389/fmicb.2023.1188544/full}, doi = {10.3389/fmicb.2023.1188544}, issn = {1664-302X}, year = {2023}, date = {2023-07-06}, urldate = {2023-07-06}, journal = {Frontiers in Microbiology}, volume = {14}, pages = {1188544}, abstract = {Introduction Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well. Methods Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis. Results From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas , and Pseudomonas . Discussion In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Introduction Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well. Methods Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis. Results From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas , and Pseudomonas . Discussion In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes. |
Papadogiannis, Vasileios; Manousaki, Tereza; Nousias, Orestis; Tsakogiannis, Alexandros; Kristoffersen, Jon B; Mylonas, Constantinos C; Batargias, Costas; Chatziplis, Dimitrios; Tsigenopoulos, Costas S Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution Journal Article Frontiers in Genetics, 13 , pp. 1081760, 2023, ISSN: 1664-8021. @article{papadogiannis_chromosome_2023b, title = {Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution}, author = {Vasileios Papadogiannis and Tereza Manousaki and Orestis Nousias and Alexandros Tsakogiannis and Jon B Kristoffersen and Constantinos C Mylonas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Papadogiannis-FrontGen-34.pdf https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full}, doi = {10.3389/fgene.2022.1081760}, issn = {1664-8021}, year = {2023}, date = {2023-07-03}, urldate = {2023-07-03}, journal = {Frontiers in Genetics}, volume = {13}, pages = {1081760}, abstract = {The meagre, Argyrosomus regius , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The meagre, Argyrosomus regius , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species. |
Mladineo, Ivona; Volpatti, Donatella; Beraldo, Paola; Rigos, George; Katharios, Pantelis; Padros, Francesc Monogenean Sparicotyle chrysophrii : The major pathogen of the Mediterranean gilthead seabream aquaculture Journal Article Reviews in Aquaculture, pp. raq.12839, 2023, ISSN: 1753-5123, 1753-5131. @article{mladineo_monogenean_2023, title = {Monogenean \textit{Sparicotyle chrysophrii} : The major pathogen of the Mediterranean gilthead seabream aquaculture}, author = {Ivona Mladineo and Donatella Volpatti and Paola Beraldo and George Rigos and Pantelis Katharios and Francesc Padros}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Mladineo-RevAqua-33.pdf https://onlinelibrary.wiley.com/doi/10.1111/raq.12839}, doi = {10.1111/raq.12839}, issn = {1753-5123, 1753-5131}, year = {2023}, date = {2023-06-26}, urldate = {2023-06-26}, journal = {Reviews in Aquaculture}, pages = {raq.12839}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Zirler, Rotem; Leck, Lynn Angele; Farkash, Tamar Feldstein; Holzknecht, Martina; Kroh, Andreas; Gerovasileiou, Vasilis; Huseyinoglu, Mehmet Fatih; Jimenez, Carlos; Resaikos, Vasilis; Yokeş, Mehmet Baki; Bronstein, Omri Frontiers in Marine Science, 10 , pp. 1152584, 2023, ISSN: 2296-7745. @article{zirler_gaining_2023, title = {Gaining a (tube) foothold – trends and status following two decades of the long-spined echinoid Diadema setosum (Leske, 1778) invasion to the Mediterranean Sea}, author = {Rotem Zirler and Lynn Angele Leck and Tamar Feldstein Farkash and Martina Holzknecht and Andreas Kroh and Vasilis Gerovasileiou and Mehmet Fatih Huseyinoglu and Carlos Jimenez and Vasilis Resaikos and Mehmet Baki Yokeş and Omri Bronstein}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Zirler-Frontiers-MarSci-32.pdf https://www.frontiersin.org/articles/10.3389/fmars.2023.1152584/full}, doi = {10.3389/fmars.2023.1152584}, issn = {2296-7745}, year = {2023}, date = {2023-06-21}, urldate = {2023-06-22}, journal = {Frontiers in Marine Science}, volume = {10}, pages = {1152584}, abstract = {The Eastern Mediterranean Sea is an exceptional habitat. Its relative isolation and distinct characteristics create a unique ecosystem recognized as a marine biodiversity hot spot, where one-fifth of the species are endemic. Yet, native Mediterranean biodiversity is under increasing threat, mainly due to massive alien species invasions of Indo-Pacific origin. To date, more than 800 non-indigenous species have been reported in the Eastern Mediterranean Sea, justifying its reputation as one of the most severely affected habitats in the world in terms of marine biological invasions. Here we summarized the Mediterranean invasion dynamics of the long-spined echinoid Diadema setosum (Leske, 1778), one of the most ubiquitous Indo-Pacific sea urchin species. We show an alarming exponential population growth of D. setosum throughout the Eastern Mediterranean since 2018, following more than a decade of ‘invasion lag’ since its first detection in 2006. Molecular analyses illustrate the presence of a single genetic D. setosum clade in the Mediterranean Sea – corresponding to the Arabian Peninsula clade of this species, reinforcing the notion of a Red Sea origin. Our data support the current working hypothesis that the initial introduction of D. setosum occurred in the Northern Levantine Basin from which it gradually expanded in both north-west and south-east trajectories – in contrast to a stepping-stone hypothesis of gradual advancement from the opening of the Suez Canal. Demographic data of D. setosum along the Israeli Mediterranean coastline reveals a well-established population of broad size distributions, from juveniles to adult individuals of remarkably large size. Additionally, we provide evidence of the reproductive capacity of D. setosum in its new environment. Due to the magnitude of Diadema ’s ecological footprint, it poses a severe threat to the entire Eastern Mediterranean Sea, including the Levantine Basin and South Aegean Sea, calling for rapid and coordinated action at both national and regional scales.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Eastern Mediterranean Sea is an exceptional habitat. Its relative isolation and distinct characteristics create a unique ecosystem recognized as a marine biodiversity hot spot, where one-fifth of the species are endemic. Yet, native Mediterranean biodiversity is under increasing threat, mainly due to massive alien species invasions of Indo-Pacific origin. To date, more than 800 non-indigenous species have been reported in the Eastern Mediterranean Sea, justifying its reputation as one of the most severely affected habitats in the world in terms of marine biological invasions. Here we summarized the Mediterranean invasion dynamics of the long-spined echinoid Diadema setosum (Leske, 1778), one of the most ubiquitous Indo-Pacific sea urchin species. We show an alarming exponential population growth of D. setosum throughout the Eastern Mediterranean since 2018, following more than a decade of ‘invasion lag’ since its first detection in 2006. Molecular analyses illustrate the presence of a single genetic D. setosum clade in the Mediterranean Sea – corresponding to the Arabian Peninsula clade of this species, reinforcing the notion of a Red Sea origin. Our data support the current working hypothesis that the initial introduction of D. setosum occurred in the Northern Levantine Basin from which it gradually expanded in both north-west and south-east trajectories – in contrast to a stepping-stone hypothesis of gradual advancement from the opening of the Suez Canal. Demographic data of D. setosum along the Israeli Mediterranean coastline reveals a well-established population of broad size distributions, from juveniles to adult individuals of remarkably large size. Additionally, we provide evidence of the reproductive capacity of D. setosum in its new environment. Due to the magnitude of Diadema ’s ecological footprint, it poses a severe threat to the entire Eastern Mediterranean Sea, including the Levantine Basin and South Aegean Sea, calling for rapid and coordinated action at both national and regional scales. |
Kokoli, Maria; Karatzas, Evangelos; Baltoumas, Fotis A; Schneider, Reinhard; Pafilis, Evangelos; Paragkamian, Savvas; Doncheva, Nadezhda T; Jensen, Lars Juhl; Pavlopoulos, Georgios A NAR Genomics and Bioinformatics, 5 (2), pp. lqad053, 2023, ISSN: 2631-9268. @article{kokoli_arena3dweb_2023, title = {Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration}, author = {Maria Kokoli and Evangelos Karatzas and Fotis A Baltoumas and Reinhard Schneider and Evangelos Pafilis and Savvas Paragkamian and Nadezhda T Doncheva and Lars Juhl Jensen and Georgios A Pavlopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Kokoli-GenBioinformatics-31.pdf https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqad053/7185857}, doi = {10.1093/nargab/lqad053}, issn = {2631-9268}, year = {2023}, date = {2023-06-19}, urldate = {2023-06-19}, journal = {NAR Genomics and Bioinformatics}, volume = {5}, number = {2}, pages = {lqad053}, abstract = {Abstract Arena3Dweb is an interactive web tool that visualizes multi-layered networks in 3D space. In this update, Arena3Dweb supports directed networks as well as up to nine different types of connections between pairs of nodes with the use of Bézier curves. It comes with different color schemes (light/gray/dark mode), custom channel coloring, four node clustering algorithms which one can run on-the-fly, visualization in VR mode and predefined layer layouts (zig-zag, star and cube). This update also includes enhanced navigation controls (mouse orbit controls, layer dragging and layer/node selection), while its newly developed API allows integration with external applications as well as saving and loading of sessions in JSON format. Finally, a dedicated Cytoscape app has been developed, through which users can automatically send their 2D networks from Cytoscape to Arena3Dweb for 3D multi-layer visualization. Arena3Dweb is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Arena3Dweb is an interactive web tool that visualizes multi-layered networks in 3D space. In this update, Arena3Dweb supports directed networks as well as up to nine different types of connections between pairs of nodes with the use of Bézier curves. It comes with different color schemes (light/gray/dark mode), custom channel coloring, four node clustering algorithms which one can run on-the-fly, visualization in VR mode and predefined layer layouts (zig-zag, star and cube). This update also includes enhanced navigation controls (mouse orbit controls, layer dragging and layer/node selection), while its newly developed API allows integration with external applications as well as saving and loading of sessions in JSON format. Finally, a dedicated Cytoscape app has been developed, through which users can automatically send their 2D networks from Cytoscape to Arena3Dweb for 3D multi-layer visualization. Arena3Dweb is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org |
Savin, Andrei; Sini, Maria; Xynogala, Ioanna; Lioupa, Vasiliki; Vougioukalou, Konstantina; Stamatis, Konstantinos; Noè, Simona; Ragkousis, Michail; Gerovasileiou, Vasilis; Dailianis, Thanos; Katsanevakis, Stelios Assessment of macroalgal communities on shallow rocky reefs in the Aegean Sea indicates an impoverished ecological status Journal Article Mediterranean Marine Science, 24 (2), pp. 241–258, 2023, ISSN: 1791-6763. @article{savin_assessment_2023, title = {Assessment of macroalgal communities on shallow rocky reefs in the Aegean Sea indicates an impoverished ecological status}, author = {Andrei Savin and Maria Sini and Ioanna Xynogala and Vasiliki Lioupa and Konstantina Vougioukalou and Konstantinos Stamatis and Simona Noè and Michail Ragkousis and Vasilis Gerovasileiou and Thanos Dailianis and Stelios Katsanevakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Savin-MMS-30.pdf https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/31034}, doi = {10.12681/mms.31034}, issn = {1791-6763}, year = {2023}, date = {2023-06-12}, urldate = {2023-06-14}, journal = {Mediterranean Marine Science}, volume = {24}, number = {2}, pages = {241--258}, abstract = {Mediterranean rocky reefs are undergoing regime shifts, from a structurally complex and diverse state dominated by canopy- forming macroalgae to a degraded one characterised by low-lying turf or encrusting macroalgal species, due to increased anthropogenic pressure and climate change. Using data gathered from 89 sites across the entire Aegean Sea, this study aims to provide the most comprehensive health status assessment of shallow rocky reefs in the area, based on macroalgal community structure. Overall, 2520 benthic images were collected through photoquadrat sampling at 0, 5 and, 15 m depth. Five macroalgal and seven invertebrate morphofunctional groups, along with four substrate categories, were considered for community structure description. Health status was assessed using the reef-EBQI and EEI-c indices. Results indicate turf as the most widespread macroalgal group (36.8% average area cover), followed by encrusting calcareous (16.6%), shrubby (12.7%), articulated calcareous (8.9%), and canopy-forming algae (3.7%). Bare rock also occupied a substantial surface area (9.0%) with highest cover (13.8%) at 5 m. The area cover of canopy-forming algae was particularly low, ranging from 10% at 0 m to 0.1% at 15 m depth, on average. All depths pooled, according to the reef-EBQI index, the ecological status of the Aegean Sea was estimated to be ‘Bad’, mainly due to the bad ecological status of the 5 and 15 m stations. At 0 m depth, the status of the Aegean Sea was ranked ‘Moderate’ according to the reef-EBQI index and ‘Good’ according to the EEI-c index. The results underline the importance of considering a wide depth range when assessing the health status of rocky reef communities.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mediterranean rocky reefs are undergoing regime shifts, from a structurally complex and diverse state dominated by canopy- forming macroalgae to a degraded one characterised by low-lying turf or encrusting macroalgal species, due to increased anthropogenic pressure and climate change. Using data gathered from 89 sites across the entire Aegean Sea, this study aims to provide the most comprehensive health status assessment of shallow rocky reefs in the area, based on macroalgal community structure. Overall, 2520 benthic images were collected through photoquadrat sampling at 0, 5 and, 15 m depth. Five macroalgal and seven invertebrate morphofunctional groups, along with four substrate categories, were considered for community structure description. Health status was assessed using the reef-EBQI and EEI-c indices. Results indicate turf as the most widespread macroalgal group (36.8% average area cover), followed by encrusting calcareous (16.6%), shrubby (12.7%), articulated calcareous (8.9%), and canopy-forming algae (3.7%). Bare rock also occupied a substantial surface area (9.0%) with highest cover (13.8%) at 5 m. The area cover of canopy-forming algae was particularly low, ranging from 10% at 0 m to 0.1% at 15 m depth, on average. All depths pooled, according to the reef-EBQI index, the ecological status of the Aegean Sea was estimated to be ‘Bad’, mainly due to the bad ecological status of the 5 and 15 m stations. At 0 m depth, the status of the Aegean Sea was ranked ‘Moderate’ according to the reef-EBQI index and ‘Good’ according to the EEI-c index. The results underline the importance of considering a wide depth range when assessing the health status of rocky reef communities. |
Zupa, Rosa; Duncan, Neil; Giménez, Ignacio; Mylonas, Constantinos C; Pousis, Chrysovalentinos; Passantino, Letizia; Cuko, Rezart; Corriero, Aldo Scientific Reports, 13 (1), pp. 7013, 2023, ISSN: 2045-2322. @article{zupa_male_2023, title = {Male germ cell proliferation and apoptosis in sexually immature meagre Argyrosomus regius (Asso, 1801) treated with recombinant follicle stimulating hormone}, author = {Rosa Zupa and Neil Duncan and Ignacio Giménez and Constantinos C Mylonas and Chrysovalentinos Pousis and Letizia Passantino and Rezart Cuko and Aldo Corriero}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Zupa-Sci-Reports-29.pdf https://www.nature.com/articles/s41598-023-34102-1}, doi = {10.1038/s41598-023-34102-1}, issn = {2045-2322}, year = {2023}, date = {2023-06-09}, urldate = {2023-06-13}, journal = {Scientific Reports}, volume = {13}, number = {1}, pages = {7013}, abstract = {The meagre Argyrosomus regius (Asso, 1801) is a marine fish species that has an increasing aquaculture production in Europe. Lowering the age at maturity of hatchery-produced juveniles would support meagre aquaculture by reducing time between generations in selective breeding programs and reducing industrial costs for broodstock maintenance. The aim of this work was to assess the effects of a treatment with recombinant follicle stimulating hormone (rFsh), produced in ovarian cells of Chinese hamsters, on male germ cell proliferation and apoptosis in sexually immature meagre. The rFsh-treated fish had higher gonadosomatic index, larger seminiferous tubules, more abundant luminal spermatozoa, a lower density of anti-PCNA positive single A spermatogonia, a higher density of anti-PCNA positive spermatocysts and a lower incidence of germ cell apoptosis than control groups. The present study demonstrated the effectiveness of the produced rFsh in stimulating testis development and spermatogenesis in pre-pubertal meagre. Moreover, the rFsh treatment proved to be highly efficient in removing the apoptotic block of spermatogenesis observed in juvenile meagre, allowing spermatogonial survival and progress towards meiosis. The administration of rFsh did not stimulate spermatogonial self-renewal, a process whose control still needs to be elucidated.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The meagre Argyrosomus regius (Asso, 1801) is a marine fish species that has an increasing aquaculture production in Europe. Lowering the age at maturity of hatchery-produced juveniles would support meagre aquaculture by reducing time between generations in selective breeding programs and reducing industrial costs for broodstock maintenance. The aim of this work was to assess the effects of a treatment with recombinant follicle stimulating hormone (rFsh), produced in ovarian cells of Chinese hamsters, on male germ cell proliferation and apoptosis in sexually immature meagre. The rFsh-treated fish had higher gonadosomatic index, larger seminiferous tubules, more abundant luminal spermatozoa, a lower density of anti-PCNA positive single A spermatogonia, a higher density of anti-PCNA positive spermatocysts and a lower incidence of germ cell apoptosis than control groups. The present study demonstrated the effectiveness of the produced rFsh in stimulating testis development and spermatogenesis in pre-pubertal meagre. Moreover, the rFsh treatment proved to be highly efficient in removing the apoptotic block of spermatogenesis observed in juvenile meagre, allowing spermatogonial survival and progress towards meiosis. The administration of rFsh did not stimulate spermatogonial self-renewal, a process whose control still needs to be elucidated. |
Vasilaki, A; Mente, E; Fountoulaki, E; Henry, M; Nikoloudaki, C; Berillis, P; Kousoulaki, K; Nengas, I Fishmeal, plant protein, and fish oil substitution with single-cell ingredients in organic feeds for European sea bass (Dicentrarchus labrax) Journal Article Frontiers in Physiology, 14 , pp. 1199497, 2023, ISSN: 1664-042X. @article{vasilaki_fishmeal_2023, title = {Fishmeal, plant protein, and fish oil substitution with single-cell ingredients in organic feeds for European sea bass (Dicentrarchus labrax)}, author = {A Vasilaki and E Mente and E Fountoulaki and M Henry and C Nikoloudaki and P Berillis and K Kousoulaki and I Nengas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Vasilaki-Frontiers-Physio-28.pdf https://www.frontiersin.org/articles/10.3389/fphys.2023.1199497/full}, doi = {10.3389/fphys.2023.1199497}, issn = {1664-042X}, year = {2023}, date = {2023-06-06}, urldate = {2023-06-12}, journal = {Frontiers in Physiology}, volume = {14}, pages = {1199497}, abstract = {Single-cell ingredients (SCI) are considered promising nutrient sources which are produced using environmentally friendly biotechnological processes. The aim of the current study was to evaluate the replacement of fishmeal, plant protein sources, and fish oil with SCI in organic feeds for European sea bass ( Dicentrarchus labrax ). Bacterial protein, yeast protein, and microalgae were used to replace fishmeal trimmings, soya bean meal, and fish oil from trimmings. Triplicate groups (30 fish per replicate) of European sea bass (14.4 ± 2.4 g) were fed the experimental diets for 71 days. The results showed that the incorporation of SCI at all levels of inclusion significantly enhanced nutrient digestibility. Additionally, growth performance parameters were not affected by SCI inclusion, exhibiting similar or improved values. Moreover, a tendency for improved anterior and posterior gut structure was observed and a significant increase of lysozyme activity at the two highest inclusion levels of SCI was determined. Overall, the results showed that the inclusion of SCI at 15% (bacterial: yeast: algae—9.4: 4.7: 1) is possible without compromising any of the parameters evaluated. According to these findings, a higher substitution of fishmeal trimmings, plant protein sources, and fish oil from trimmings with SCI in organic diets for European sea bass ( D. labrax ) can be further evaluated in future studies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Single-cell ingredients (SCI) are considered promising nutrient sources which are produced using environmentally friendly biotechnological processes. The aim of the current study was to evaluate the replacement of fishmeal, plant protein sources, and fish oil with SCI in organic feeds for European sea bass ( Dicentrarchus labrax ). Bacterial protein, yeast protein, and microalgae were used to replace fishmeal trimmings, soya bean meal, and fish oil from trimmings. Triplicate groups (30 fish per replicate) of European sea bass (14.4 ± 2.4 g) were fed the experimental diets for 71 days. The results showed that the incorporation of SCI at all levels of inclusion significantly enhanced nutrient digestibility. Additionally, growth performance parameters were not affected by SCI inclusion, exhibiting similar or improved values. Moreover, a tendency for improved anterior and posterior gut structure was observed and a significant increase of lysozyme activity at the two highest inclusion levels of SCI was determined. Overall, the results showed that the inclusion of SCI at 15% (bacterial: yeast: algae—9.4: 4.7: 1) is possible without compromising any of the parameters evaluated. According to these findings, a higher substitution of fishmeal trimmings, plant protein sources, and fish oil from trimmings with SCI in organic diets for European sea bass ( D. labrax ) can be further evaluated in future studies. |
Stavrakidis-Zachou, Orestis; Papandroulakis, Nikos; Lika, Konstadia A bioenergetics approach to modelling tolerance limits under acute thermal stress in farmed finfish Journal Article Frontiers in Marine Science, 10 , pp. 1173358, 2023, ISSN: 2296-7745. @article{stavrakidis-zachou_bioenergetics_2023, title = {A bioenergetics approach to modelling tolerance limits under acute thermal stress in farmed finfish}, author = {Orestis Stavrakidis-Zachou and Nikos Papandroulakis and Konstadia Lika}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Stavrakidis-Zachou-Frontiers-MarSci-27.pdf https://www.frontiersin.org/articles/10.3389/fmars.2023.1173358/full}, doi = {10.3389/fmars.2023.1173358}, issn = {2296-7745}, year = {2023}, date = {2023-06-02}, urldate = {2023-06-09}, journal = {Frontiers in Marine Science}, volume = {10}, pages = {1173358}, abstract = {Pinpointing thermal tolerance thresholds for commercially important species, such as aquaculture finfish, under acute and chronic thermal stress is becoming increasingly relevant in the context of climate change. While experimental research, traditionally quantified by the determination of the Critical Thermal Maximum (CTmax), offers valuable insights, it is necessary to further develop appropriate tools to provide predictions and shed light on the underlying mechanisms of thermal tolerance. Bioenergetic models have long been used to study the effects of temperature on fish metabolism under chronic, but rarely under acute, scales. In this study, we present a modelling approach based on the Dynamic Energy Budget (DEB) theory that describes the tolerance limits of fish under acute thermal stress in bioenergetics terms. It adopts the notion of an energy-dependent tolerance to stress and defines acute tolerance limits at the intersection of fundamental energy fluxes, namely those relating to the mobilization of energy and to maintenance costs. To showcase this approach, DEB models for two finfish, the European sea bass ( Dicentrarchus labrax ) and the meagre ( Argyrosomus regius ) were used to run acute thermal challenge simulations and study shifts in the critical temperature achieved by the fish. The results suggest that the model can adequately capture the general tolerance patterns observed experimentally for the two species as well as pinpoint the parameters that may influence them. In particular, the simulations showed a positive relation between acclimation temperature and tolerance while the opposite stands for the body size of the fish, with smaller fish achieving higher critical temperatures than their larger counterparts. Also, tolerance limits were affected by the state of internal reserves, with well-fed fish exhibiting higher values. Finally, the potential application of this modelling approach on higher taxonomic scales was evaluated, by running simulations on species belonging to major fish orders. The preliminary results suggest that the method can capture differences among groups that are consistent with literature, suggesting it may be a realistic mechanistic approach for studying thermal tolerance in ectotherms.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Pinpointing thermal tolerance thresholds for commercially important species, such as aquaculture finfish, under acute and chronic thermal stress is becoming increasingly relevant in the context of climate change. While experimental research, traditionally quantified by the determination of the Critical Thermal Maximum (CTmax), offers valuable insights, it is necessary to further develop appropriate tools to provide predictions and shed light on the underlying mechanisms of thermal tolerance. Bioenergetic models have long been used to study the effects of temperature on fish metabolism under chronic, but rarely under acute, scales. In this study, we present a modelling approach based on the Dynamic Energy Budget (DEB) theory that describes the tolerance limits of fish under acute thermal stress in bioenergetics terms. It adopts the notion of an energy-dependent tolerance to stress and defines acute tolerance limits at the intersection of fundamental energy fluxes, namely those relating to the mobilization of energy and to maintenance costs. To showcase this approach, DEB models for two finfish, the European sea bass ( Dicentrarchus labrax ) and the meagre ( Argyrosomus regius ) were used to run acute thermal challenge simulations and study shifts in the critical temperature achieved by the fish. The results suggest that the model can adequately capture the general tolerance patterns observed experimentally for the two species as well as pinpoint the parameters that may influence them. In particular, the simulations showed a positive relation between acclimation temperature and tolerance while the opposite stands for the body size of the fish, with smaller fish achieving higher critical temperatures than their larger counterparts. Also, tolerance limits were affected by the state of internal reserves, with well-fed fish exhibiting higher values. Finally, the potential application of this modelling approach on higher taxonomic scales was evaluated, by running simulations on species belonging to major fish orders. The preliminary results suggest that the method can capture differences among groups that are consistent with literature, suggesting it may be a realistic mechanistic approach for studying thermal tolerance in ectotherms. |
Chatziantoniou, Andromachi; Papandroulakis, Nikos; Stavrakidis-Zachou, Orestis; Spondylidis, Spyros; Taskaris, Simeon; Topouzelis, Konstantinos Aquasafe: A Remote Sensing, Web-Based Platform for the Support of Precision Fish Farming Journal Article Applied Sciences, 13 (10), pp. 6122, 2023, ISSN: 2076-3417. @article{chatziantoniou_aquasafe_2023, title = {Aquasafe: A Remote Sensing, Web-Based Platform for the Support of Precision Fish Farming}, author = {Andromachi Chatziantoniou and Nikos Papandroulakis and Orestis Stavrakidis-Zachou and Spyros Spondylidis and Simeon Taskaris and Konstantinos Topouzelis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Chatziantoniou-AppSci-26.pdf https://www.mdpi.com/2076-3417/13/10/6122}, doi = {10.3390/app13106122}, issn = {2076-3417}, year = {2023}, date = {2023-05-31}, urldate = {2023-06-08}, journal = {Applied Sciences}, volume = {13}, number = {10}, pages = {6122}, abstract = {Marine aquaculture has been expanding rapidly in recent years, driven by the growing demand for marine products. However, this expansion has led to increased competition for space and resources with other coastal zone activities, which has resulted in the need for larger facilities and the relocation of operations to offshore areas. Moreover, the complex environment and exposure to environmental conditions and external threats further complicate the sustainable development of the sector. To address these challenges, new and innovative technologies are needed, such as the incorporation of remote sensing and in-situ data for comprehensive and continuous monitoring of aquaculture facilities. This study aims to create an integrated monitoring and decision support system utilizing both satellite and in-situ data to monitor aquaculture facilities on various scales, providing information on water quality, fish growth, and warning signs to alert managers and producers of potential hazards. This study focuses on identifying and estimating parameters that affect aquaculture processes, establishing indicators that can act as warning signs, and evaluating the system’s performance in real-life scenarios. The resulting monitoring tool, called “Aquasafe”, was evaluated for its effectiveness and performance by test users through real-life scenarios. The results of the implemented models showed high accuracy, with an R2 value of 0.67. Additionally, users were generally satisfied with the usefulness of the tool, suggesting that it holds promise for efficient management and decision making in marine aquaculture.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine aquaculture has been expanding rapidly in recent years, driven by the growing demand for marine products. However, this expansion has led to increased competition for space and resources with other coastal zone activities, which has resulted in the need for larger facilities and the relocation of operations to offshore areas. Moreover, the complex environment and exposure to environmental conditions and external threats further complicate the sustainable development of the sector. To address these challenges, new and innovative technologies are needed, such as the incorporation of remote sensing and in-situ data for comprehensive and continuous monitoring of aquaculture facilities. This study aims to create an integrated monitoring and decision support system utilizing both satellite and in-situ data to monitor aquaculture facilities on various scales, providing information on water quality, fish growth, and warning signs to alert managers and producers of potential hazards. This study focuses on identifying and estimating parameters that affect aquaculture processes, establishing indicators that can act as warning signs, and evaluating the system’s performance in real-life scenarios. The resulting monitoring tool, called “Aquasafe”, was evaluated for its effectiveness and performance by test users through real-life scenarios. The results of the implemented models showed high accuracy, with an R2 value of 0.67. Additionally, users were generally satisfied with the usefulness of the tool, suggesting that it holds promise for efficient management and decision making in marine aquaculture. |
Gaudêncio, Susana P; Bayram, Engin; Bilela, Lada Lukić; Cueto, Mercedes; Díaz-Marrero, Ana R; Haznedaroglu, Berat Z; Jimenez, Carlos; Mandalakis, Manolis; Pereira, Florbela; Reyes, Fernando; Tasdemir, Deniz Marine Drugs, 21 (5), pp. 308, 2023, ISSN: 1660-3397. @article{gaudencio_advanced_2023, title = {Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation}, author = {Susana P Gaudêncio and Engin Bayram and Lada Lukić Bilela and Mercedes Cueto and Ana R Díaz-Marrero and Berat Z Haznedaroglu and Carlos Jimenez and Manolis Mandalakis and Florbela Pereira and Fernando Reyes and Deniz Tasdemir}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Gaudencio-Marinedrugs-25.pdf https://www.mdpi.com/1660-3397/21/5/308}, doi = {10.3390/md21050308}, issn = {1660-3397}, year = {2023}, date = {2023-05-30}, urldate = {2023-06-07}, journal = {Marine Drugs}, volume = {21}, number = {5}, pages = {308}, abstract = {Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation. |
Santi, Ioulia; Beluche, Odette; Beraud, Mélanie; Buttigieg, Pier Luigi; Casotti, Raffaella; Cox, Cymon J; Cunliffe, Michael; Davies, Neil; Cerio, Oihane Diaz De; Exter, Katrina; Kervella, Anne Emmanuelle; Kotoulas, Georgios; Lagaisse, Rune; Laroquette, Arnaud; Louro, Bruno; Not, Fabrice; Obst, Matthias; Pavloudi, Christina; Poulain, Julie; Præbel, Kim; Vanaverbeke, Jan; Pade, Nicolas European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation Journal Article Frontiers in Marine Science, 10 , pp. 1118120, 2023, ISSN: 2296-7745. @article{santi_european_2023, title = {European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation}, author = {Ioulia Santi and Odette Beluche and Mélanie Beraud and Pier Luigi Buttigieg and Raffaella Casotti and Cymon J Cox and Michael Cunliffe and Neil Davies and Oihane Diaz De Cerio and Katrina Exter and Anne Emmanuelle Kervella and Georgios Kotoulas and Rune Lagaisse and Arnaud Laroquette and Bruno Louro and Fabrice Not and Matthias Obst and Christina Pavloudi and Julie Poulain and Kim Præbel and Jan Vanaverbeke and Nicolas Pade}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Santi-Frontiers-MarSci-24.pdf https://www.frontiersin.org/articles/10.3389/fmars.2023.1118120/full}, doi = {10.3389/fmars.2023.1118120}, issn = {2296-7745}, year = {2023}, date = {2023-05-29}, urldate = {2023-06-06}, journal = {Frontiers in Marine Science}, volume = {10}, pages = {1118120}, abstract = {Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem’s biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem’s biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address. |
Sánchez-Cueto, Pablo; Stavrakidis-Zachou, Orestis; Clos-Garcia, Marc; Bosch, Montse; Papandroulakis, Nikos; Lladó, Salvador Mediterranean Sea heatwaves jeopardize greater amberjack’s (Seriola dumerili) aquaculture productivity through impacts on the fish microbiota Journal Article ISME Communications, 3 (1), pp. 36, 2023, ISSN: 2730-6151. @article{sanchez-cueto_mediterranean_2023, title = {Mediterranean Sea heatwaves jeopardize greater amberjack’s (Seriola dumerili) aquaculture productivity through impacts on the fish microbiota}, author = {Pablo Sánchez-Cueto and Orestis Stavrakidis-Zachou and Marc Clos-Garcia and Montse Bosch and Nikos Papandroulakis and Salvador Lladó}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Sanchez-Cueto-ISME-23.pdf https://www.nature.com/articles/s43705-023-00243-7}, doi = {10.1038/s43705-023-00243-7}, issn = {2730-6151}, year = {2023}, date = {2023-05-26}, urldate = {2023-06-02}, journal = {ISME Communications}, volume = {3}, number = {1}, pages = {36}, abstract = {Abstract Climate change is dramatically increasing the frequency and severity of marine heatwaves (MHWs) in the Mediterranean basin, strongly affecting marine food production systems. However, how it will shape the ecology of aquaculture systems, and the cascading effects on productivity, is still a major knowledge gap. The present work aims to increase our understanding of future impacts, caused by raising water temperatures, on the interaction between water and fish microbiotas, and consequential effects upon fish growth. Thus, the bacterial communities present in the water tanks, and mucosal tissues (skin, gills and gut), of greater amberjack farmed in recirculatory aquaculture systems (RAS), at three different temperatures (24, 29 and 33 °C), were characterized in a longitudinal study. The greater amberjack ( Seriola dumerili ) is a teleost species with high potential for EU aquaculture diversification due to its fast growth, excellent flesh quality and global market. We show that higher water temperatures disrupt the greater amberjack’s microbiota. Our results demonstrate the causal mediation exerted by this bacterial community shifts on the reduction of fish growth. The abundance of members of the Pseudoalteromonas is positively correlated with fish performance, whereas members of the Psychrobacter, Chryseomicrobium, Paracoccus and Enterovibrio are suggested as biomarkers for dysbiosis, at higher water temperatures. Hence, opening new evidence-based avenues for the development of targeted microbiota-based biotechnological tools, designed to increase the resilience and adaptation to climate change of the Mediterranean aquaculture industry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Climate change is dramatically increasing the frequency and severity of marine heatwaves (MHWs) in the Mediterranean basin, strongly affecting marine food production systems. However, how it will shape the ecology of aquaculture systems, and the cascading effects on productivity, is still a major knowledge gap. The present work aims to increase our understanding of future impacts, caused by raising water temperatures, on the interaction between water and fish microbiotas, and consequential effects upon fish growth. Thus, the bacterial communities present in the water tanks, and mucosal tissues (skin, gills and gut), of greater amberjack farmed in recirculatory aquaculture systems (RAS), at three different temperatures (24, 29 and 33 °C), were characterized in a longitudinal study. The greater amberjack ( Seriola dumerili ) is a teleost species with high potential for EU aquaculture diversification due to its fast growth, excellent flesh quality and global market. We show that higher water temperatures disrupt the greater amberjack’s microbiota. Our results demonstrate the causal mediation exerted by this bacterial community shifts on the reduction of fish growth. The abundance of members of the Pseudoalteromonas is positively correlated with fish performance, whereas members of the Psychrobacter, Chryseomicrobium, Paracoccus and Enterovibrio are suggested as biomarkers for dysbiosis, at higher water temperatures. Hence, opening new evidence-based avenues for the development of targeted microbiota-based biotechnological tools, designed to increase the resilience and adaptation to climate change of the Mediterranean aquaculture industry. |
Ragkousis, Michail; Zenetos, Argyro; Souissi, Jamila Ben; Tsiamis, Konstantinos; Ferrario, Jasmine; Marchini, Agnese; Edelist, Dori; Crocetta, Fabio; Bariche, Michel; Deidun, Alan; Gerovasileiou, Vasilis; Azzurro, Ernesto; Vella, Adriana; Tsirintanis, Konstantinos; Occhipinti-Ambrogi, Anna; Evans, Julian; Kondylatos, Gerasimos; Castriota, Luca; Rizgalla, Jamila; Schembri, Patrick; Kalogirou, Stefanos; Corsini-Foka, Maria; Scannella, Danilo; Tiralongo, Francesco; Bazairi, Hocein; Zava, Bruno; Bilecenoglu, Murat; Çinar, Melih; Kampouris, Thodoros; Dulčić, Jakov; Rilov, Gil; Micu, Dragoș; Katsanevakis, Stelios Unpublished Mediterranean and Black Sea records of marine alien, cryptogenic, and neonative species Journal Article BioInvasions Records, 12 (2), pp. 339–369, 2023, ISSN: 22421300. @article{ragkousis_unpublished_2023, title = {Unpublished Mediterranean and Black Sea records of marine alien, cryptogenic, and neonative species}, author = {Michail Ragkousis and Argyro Zenetos and Jamila Ben Souissi and Konstantinos Tsiamis and Jasmine Ferrario and Agnese Marchini and Dori Edelist and Fabio Crocetta and Michel Bariche and Alan Deidun and Vasilis Gerovasileiou and Ernesto Azzurro and Adriana Vella and Konstantinos Tsirintanis and Anna Occhipinti-Ambrogi and Julian Evans and Gerasimos Kondylatos and Luca Castriota and Jamila Rizgalla and Patrick Schembri and Stefanos Kalogirou and Maria Corsini-Foka and Danilo Scannella and Francesco Tiralongo and Hocein Bazairi and Bruno Zava and Murat Bilecenoglu and Melih Çinar and Thodoros Kampouris and Jakov Dulčić and Gil Rilov and Dragoș Micu and Stelios Katsanevakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2023-Ragkousis-BioInvasions-22.pdf https://www.reabic.net/journals/bir/2023/2/BIR_2023_Ragkousis_etal.pdf}, doi = {10.3391/bir.2023.12.2.01}, issn = {22421300}, year = {2023}, date = {2023-05-25}, urldate = {2023-05-31}, journal = {BioInvasions Records}, volume = {12}, number = {2}, pages = {339--369}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Xirouchakis, S M; Botsidou, P; Baxevani, K; Andreou, G; Tsaparis, D Brood sex ratio variation in a colonial raptor, the Eleonora's falcon, Falco eleonorae Journal Article Animal Behaviour, 195 , pp. 93–106, 2023, ISSN: 00033472. @article{xirouchakis_brood_2023, title = {Brood sex ratio variation in a colonial raptor, the Eleonora's falcon, Falco eleonorae}, author = {S M Xirouchakis and P Botsidou and K Baxevani and G Andreou and D Tsaparis}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0003347222002986 https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2023-Xirouchakis-AniBeh-pre-print-20.pdf}, doi = {10.1016/j.anbehav.2022.11.001}, issn = {00033472}, year = {2023}, date = {2023-05-23}, urldate = {2023-05-23}, journal = {Animal Behaviour}, volume = {195}, pages = {93--106}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kondylatos, Gerasimos; Mavrouleas, Dimitrios; Gratsia, Eirini; Kasapidis, Panagiotis; Corsini-Foka, Maria; Klaoudatos, Dimitris BioInvasions Records, 12 (1), pp. 234–244, 2023, ISSN: 22421300. @article{kondylatos_first_2023, title = {First record of Arcania brevifrons Chen, 1989 (Decapoda; Leucosiidae) and further record of Macrophthalmus (Macrophthalmus) indicus Davie, 2012 (Decapoda; Macrophthalmidae) in Hellenic waters}, author = {Gerasimos Kondylatos and Dimitrios Mavrouleas and Eirini Gratsia and Panagiotis Kasapidis and Maria Corsini-Foka and Dimitris Klaoudatos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Kondylatos-Bioinvasions-21.pdf https://www.reabic.net/journals/bir/2023/1/BIR_2023_Kondylatos_etal.pdf}, doi = {10.3391/bir.2023.12.1.19}, issn = {22421300}, year = {2023}, date = {2023-05-23}, urldate = {2023-06-01}, journal = {BioInvasions Records}, volume = {12}, number = {1}, pages = {234--244}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Plis, Kamila; Niedziałkowska, Magdalena; Borowik, Tomasz; Lang, Johannes; Heddergott, Mike; Tiainen, Juha; Bunevich, Aleksey; Šprem, Nikica; Paule, Ladislav; Danilkin, Aleksey; Kholodova, Marina; Zvychaynaya, Elena; Kashinina, Nadezhda; Pokorny, Boštjan; Flajšman, Katarina; Paulauskas, Algimantas; Djan, Mihajla; Ristić, Zoran; Novák, Luboš; Kusza, Szilvia; Miller, Christine; Tsaparis, Dimitris; Stoyanov, Stoyan; Shkvyria, Maryna; Suchentrunk, Franz; Kutal, Miroslav; Lavadinović, Vukan; Šnjegota, Dragana; Krapal, Ana-Maria; Dănilă, Gabriel; Veeroja, Rauno; Dulko, Elżbieta; Jędrzejewska, Bogumiła Mitochondrial DNA diversity and the population genetic structure of contemporary roe deer (Capreolus capreolus) in Europe Journal Article 102 (5), pp. 1743–1754, 2023, ISSN: 1616-5047, 1618-1476. @article{plis_mitochondrial_2022, title = {Mitochondrial DNA diversity and the population genetic structure of contemporary roe deer (Capreolus capreolus) in Europe}, author = {Kamila Plis and Magdalena Niedziałkowska and Tomasz Borowik and Johannes Lang and Mike Heddergott and Juha Tiainen and Aleksey Bunevich and Nikica Šprem and Ladislav Paule and Aleksey Danilkin and Marina Kholodova and Elena Zvychaynaya and Nadezhda Kashinina and Boštjan Pokorny and Katarina Flajšman and Algimantas Paulauskas and Mihajla Djan and Zoran Ristić and Luboš Novák and Szilvia Kusza and Christine Miller and Dimitris Tsaparis and Stoyan Stoyanov and Maryna Shkvyria and Franz Suchentrunk and Miroslav Kutal and Vukan Lavadinović and Dragana Šnjegota and Ana-Maria Krapal and Gabriel Dănilă and Rauno Veeroja and Elżbieta Dulko and Bogumiła Jędrzejewska}, url = {https://link.springer.com/10.1007/s42991-022-00274-y https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2022-Plis-MAMBIO-pre-print-83.pdf}, doi = {10.1007/s42991-022-00274-y}, issn = {1616-5047, 1618-1476}, year = {2023}, date = {2023-05-23}, urldate = {2023-05-24}, volume = {102}, number = {5}, pages = {1743--1754}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Teixeira, Marcos A L; Langeneck, Joachim; Vieira, Pedro E; Hernández, José Carlos; Sampieri, Bruno R; Kasapidis, Panagiotis; Mucciolo, Serena; Bakken, Torkild; Ravara, Ascensão; Nygren, Arne; Costa, Filipe O Reappraisal of the hyperdiverse Journal Article Invertebrate Systematics, 36 (11), pp. 1017–1061, 2023, ISSN: 1445-5226, 1447-2600. @article{teixeira_reappraisal_2022b, title = {Reappraisal of the hyperdiverse}, author = {Marcos A L Teixeira and Joachim Langeneck and Pedro E Vieira and José Carlos Hernández and Bruno R Sampieri and Panagiotis Kasapidis and Serena Mucciolo and Torkild Bakken and Ascensão Ravara and Arne Nygren and Filipe O Costa}, editor = {Greg Rouse}, url = {https://www.publish.csiro.au/IS/IS21084}, doi = {10.1071/IS21084}, issn = {1445-5226, 1447-2600}, year = {2023}, date = {2023-05-23}, urldate = {2023-05-25}, journal = {Invertebrate Systematics}, volume = {36}, number = {11}, pages = {1017--1061}, abstract = {Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D}, keywords = {}, pubstate = {published}, tppubtype = {article} } Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D |
Teixeira, Marcos A L; Bakken, Torkild; Vieira, Pedro E; Langeneck, Joachim; Sampieri, Bruno R; Kasapidis, Panagiotis; Ravara, AscensÃO; Nygren, Arne; Costa, Filipe O Systematics and Biodiversity, 20 (1), pp. 1–39, 2023, ISSN: 1477-2000, 1478-0933. @article{teixeira_curious_2022, title = {The curious and intricate case of the European textitHediste diversicolor (Annelida, Nereididae) species complex, with description of two new species}, author = {Marcos A L Teixeira and Torkild Bakken and Pedro E Vieira and Joachim Langeneck and Bruno R Sampieri and Panagiotis Kasapidis and AscensÃO Ravara and Arne Nygren and Filipe O Costa}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2022-Teixeira-Syst-Biodiv-85.pdf https://www.tandfonline.com/doi/full/10.1080/14772000.2022.2116124}, doi = {10.1080/14772000.2022.2116124}, issn = {1477-2000, 1478-0933}, year = {2023}, date = {2023-05-23}, urldate = {2023-05-30}, journal = {Systematics and Biodiversity}, volume = {20}, number = {1}, pages = {1--39}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Triga, Adriana; Smyrli, Maria; Katharios, Pantelis Microorganisms, 11 (5), pp. 1197, 2023, ISSN: 2076-2607. @article{triga_pathogenic_2023, title = {Pathogenic and Opportunistic Vibrio spp. Associated with Vibriosis Incidences in the Greek Aquaculture: The Role of Vibrio harveyi as the Principal Cause of Vibriosis}, author = {Adriana Triga and Maria Smyrli and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2023-Triga-microorganisms-19.pdf https://www.mdpi.com/2076-2607/11/5/1197}, doi = {10.3390/microorganisms11051197}, issn = {2076-2607}, year = {2023}, date = {2023-05-17}, urldate = {2023-05-17}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {1197}, abstract = {A monitoring program to follow vibriosis incidents in the Greek marine aquaculture was implemented over the past 13 years. 273 isolates, from various cases originating from eight regions and nine hosts, were collected and characterized. The main aquaculture species of the survey were the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata). Various species of Vibrionaceae were associated with vibriosis. Vibrio harveyi had the highest prevalence and was isolated throughout the year from all hosts. During the warm months, Vibrio harveyi prevailed with frequent co-isolations of Photobacterium damselae subsp. damselae and Vibrio alginolyticus, while during spring, other Vibrio species were more abundant, such as Vibrio lentus, Vibrio cyclitrophicus, and Vibrio gigantis. Phylogenetic analysis using the mreB gene and the metabolic fingerprint of the isolates showed great variability within the species of the collection. The severity of the disease and the frequency of outbreaks make vibriosis (that is, mainly attributed to V. harveyi) an important concern for the regional aquaculture sector.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A monitoring program to follow vibriosis incidents in the Greek marine aquaculture was implemented over the past 13 years. 273 isolates, from various cases originating from eight regions and nine hosts, were collected and characterized. The main aquaculture species of the survey were the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata). Various species of Vibrionaceae were associated with vibriosis. Vibrio harveyi had the highest prevalence and was isolated throughout the year from all hosts. During the warm months, Vibrio harveyi prevailed with frequent co-isolations of Photobacterium damselae subsp. damselae and Vibrio alginolyticus, while during spring, other Vibrio species were more abundant, such as Vibrio lentus, Vibrio cyclitrophicus, and Vibrio gigantis. Phylogenetic analysis using the mreB gene and the metabolic fingerprint of the isolates showed great variability within the species of the collection. The severity of the disease and the frequency of outbreaks make vibriosis (that is, mainly attributed to V. harveyi) an important concern for the regional aquaculture sector. |
Droubogiannis, Stavros; Pavlidi, Lydia; Skliros, Dimitrios; Flemetakis, Emmanouil; Katharios, Pantelis International Journal of Molecular Sciences, 24 (9), pp. 8200, 2023, ISSN: 1422-0067. @article{droubogiannis_comprehensive_2023, title = {Comprehensive Characterization of a Novel Bacteriophage, vB_VhaS_MAG7 against a Fish Pathogenic Strain of Vibrio harveyi and Its In Vivo Efficacy in Phage Therapy Trials}, author = {Stavros Droubogiannis and Lydia Pavlidi and Dimitrios Skliros and Emmanouil Flemetakis and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2023-Droumbogiannis-IJMarSci-18.pdf https://www.mdpi.com/1422-0067/24/9/8200}, doi = {10.3390/ijms24098200}, issn = {1422-0067}, year = {2023}, date = {2023-05-08}, urldate = {2023-05-08}, journal = {International Journal of Molecular Sciences}, volume = {24}, number = {9}, pages = {8200}, abstract = {Vibrio harveyi, a significant opportunistic marine pathogen, has been a challenge to the aquaculture industry, leading to severe economical and production losses. Phage therapy has been an auspicious approach in controlling such bacterial infections in the era of antimicrobial resistance. In this study, we isolated and fully characterized a novel strain-specific phage, vB_VhaS_MAG7, which infects V. harveyi MM46, and tested its efficacy as a therapeutic agent in challenged gilthead seabream larvae. vB_VhaS_MAG7 is a tailed bacteriophage with a double-stranded DNA of 49,315 bp. No genes linked with virulence or antibiotic resistance were harbored in the genome. The phage had a remarkably large burst size of 1393 PFU cell−1 and showed strong lytic ability in in vitro assays. When applied in phage therapy trials in challenged gilthead seabream larvae, vB_VhaS_MAG7 was capable of improving the survival of the larvae up to 20%. Due to its distinct features and safety, vB_VhaS_MAG7 is considered a suitable candidate for applied phage therapy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Vibrio harveyi, a significant opportunistic marine pathogen, has been a challenge to the aquaculture industry, leading to severe economical and production losses. Phage therapy has been an auspicious approach in controlling such bacterial infections in the era of antimicrobial resistance. In this study, we isolated and fully characterized a novel strain-specific phage, vB_VhaS_MAG7, which infects V. harveyi MM46, and tested its efficacy as a therapeutic agent in challenged gilthead seabream larvae. vB_VhaS_MAG7 is a tailed bacteriophage with a double-stranded DNA of 49,315 bp. No genes linked with virulence or antibiotic resistance were harbored in the genome. The phage had a remarkably large burst size of 1393 PFU cell−1 and showed strong lytic ability in in vitro assays. When applied in phage therapy trials in challenged gilthead seabream larvae, vB_VhaS_MAG7 was capable of improving the survival of the larvae up to 20%. Due to its distinct features and safety, vB_VhaS_MAG7 is considered a suitable candidate for applied phage therapy. |
Vogiatzi, Angeliki; Keklikoglou, Kleoniki; Makris, Konstantinos; Argyrou, Dionysia Stamatia; Zacharopoulos, Athanasios; Sotiropoulou, Varvara; Parthenios, Nikolaos; Gkikas, Angelos; Kokkori, Maria; Richardson, Melodie S W; Fenwick, Aimée L; Archontidi, Sofia; Arvanitidis, Christos; Robertson, Jeremy; Parthenios, John; Zacharakis, Giannis; Twigg, Stephen R F; Wilkie, Andrew O M; Mavrothalassitis, George Development of Erf-Mediated Craniosynostosis and Pharmacological Amelioration Journal Article International Journal of Molecular Sciences, 24 (9), pp. 7961, 2023, ISSN: 1422-0067. @article{vogiatzi_development_2023, title = {Development of Erf-Mediated Craniosynostosis and Pharmacological Amelioration}, author = {Angeliki Vogiatzi and Kleoniki Keklikoglou and Konstantinos Makris and Dionysia Stamatia Argyrou and Athanasios Zacharopoulos and Varvara Sotiropoulou and Nikolaos Parthenios and Angelos Gkikas and Maria Kokkori and Melodie S W Richardson and Aimée L Fenwick and Sofia Archontidi and Christos Arvanitidis and Jeremy Robertson and John Parthenios and Giannis Zacharakis and Stephen R F Twigg and Andrew O M Wilkie and George Mavrothalassitis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2023-Vogiatzi-2023-IJMSci-17.pdf https://www.mdpi.com/1422-0067/24/9/7961}, doi = {10.3390/ijms24097961}, issn = {1422-0067}, year = {2023}, date = {2023-05-02}, urldate = {2023-05-02}, journal = {International Journal of Molecular Sciences}, volume = {24}, number = {9}, pages = {7961}, abstract = {ETS2 repressor factor (ERF) insufficiency causes craniosynostosis (CRS4) in humans and mice. ERF is an ETS domain transcriptional repressor regulated by Erk1/2 phosphorylation via nucleo-cytoplasmic shuttling. Here, we analyze the onset and development of the craniosynostosis phenotype in an Erf-insufficient mouse model and evaluate the potential of the residual Erf activity augmented by pharmacological compounds to ameliorate the disease. Erf insufficiency appears to cause an initially compromised frontal bone formation and subsequent multisuture synostosis, reflecting distinct roles of Erf on the cells that give rise to skull and facial bones. We treated animals with Mek1/2 and nuclear export inhibitors, U0126 and KPT-330, respectively, to increase Erf activity by two independent pathways. We implemented both a low dosage locally over the calvaria and a systemic drug administration scheme to evaluate the possible indirect effects from other systems and minimize toxicity. The treatment of mice with either the inhibitors or the administration scheme alleviated the synostosis phenotype with minimal adverse effects. Our data suggest that the ERF level is an important regulator of cranial bone development and that pharmacological modulation of its activity may represent a valid intervention approach both in CRS4 and in other syndromic forms of craniosynostosis mediated by the FGFR-RAS-ERK-ERF pathway.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ETS2 repressor factor (ERF) insufficiency causes craniosynostosis (CRS4) in humans and mice. ERF is an ETS domain transcriptional repressor regulated by Erk1/2 phosphorylation via nucleo-cytoplasmic shuttling. Here, we analyze the onset and development of the craniosynostosis phenotype in an Erf-insufficient mouse model and evaluate the potential of the residual Erf activity augmented by pharmacological compounds to ameliorate the disease. Erf insufficiency appears to cause an initially compromised frontal bone formation and subsequent multisuture synostosis, reflecting distinct roles of Erf on the cells that give rise to skull and facial bones. We treated animals with Mek1/2 and nuclear export inhibitors, U0126 and KPT-330, respectively, to increase Erf activity by two independent pathways. We implemented both a low dosage locally over the calvaria and a systemic drug administration scheme to evaluate the possible indirect effects from other systems and minimize toxicity. The treatment of mice with either the inhibitors or the administration scheme alleviated the synostosis phenotype with minimal adverse effects. Our data suggest that the ERF level is an important regulator of cranial bone development and that pharmacological modulation of its activity may represent a valid intervention approach both in CRS4 and in other syndromic forms of craniosynostosis mediated by the FGFR-RAS-ERK-ERF pathway. |
Skliros, Dimitrios; Papazoglou, Polyxeni; Gkizi, Danai; Paraskevopoulou, Eleni; Katharios, Pantelis; Goumas, Dimitrios E; Tjamos, Sotirios; Flemetakis, Emmanouil In planta interactions of a novel bacteriophage against Pseudomonas syringae pv. tomato Journal Article Applied Microbiology and Biotechnology, 2023, ISSN: 0175-7598, 1432-0614. @article{skliros_planta_2023, title = {In planta interactions of a novel bacteriophage against Pseudomonas syringae pv. tomato}, author = {Dimitrios Skliros and Polyxeni Papazoglou and Danai Gkizi and Eleni Paraskevopoulou and Pantelis Katharios and Dimitrios E Goumas and Sotirios Tjamos and Emmanouil Flemetakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/04/2023-Skliros-AMB-16.pdf https://link.springer.com/10.1007/s00253-023-12493-5}, doi = {10.1007/s00253-023-12493-5}, issn = {0175-7598, 1432-0614}, year = {2023}, date = {2023-04-27}, urldate = {2023-04-27}, journal = {Applied Microbiology and Biotechnology}, abstract = {Abstract The biology and biotechnology of bacteriophages have been extensively studied in recent years to explore new and environmentally friendly methods of controlling phytopathogenic bacteria. Pseudomonas syringae pv. tomato (Pst) is responsible for bacterial speck disease in tomato plants, leading to decreased yield. Disease management strategies rely on the use of copper-based pesticides. The biological control of Pst with the use of bacteriophages could be an alternative environmentally friendly approach to diminish the detrimental effects of Pst in tomato cultivations. The lytic efficacy of bacteriophages can be used in biocontrol-based disease management strategies. Here, we report the isolation and complete characterization of a bacteriophage, named Medea1, which was also tested in planta against Pst, under greenhouse conditions. The application of Medea1 as a root drenching inoculum or foliar spraying reduced 2.5- and fourfold on average, respectively, Pst symptoms in tomato plants, compared to a control group. In addition, it was observed that defense-related genes PR1b and Pin2 were upregulated in the phage-treated plants. Our research explores a new genus of Pseudomonas phages and explores its biocontrol potential against Pst, by utilizing its lytic nature and ability to trigger the immune response of plants. Key points • Medea1 is a newly reported bacteriophage against Pseudomonas syringae pv. tomato having genomic similarities with the phiPSA1 bacteriophage • Two application strategies were reported, one by root drenching the plants with a phage-based solution and one by foliar spraying, showing up to 60- and 6-fold reduction of Pst population and disease severity in some cases, respectively, compared to control • Bacteriophage Medea1 induced the expression of the plant defense-related genes Pin2 and PR1b}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract The biology and biotechnology of bacteriophages have been extensively studied in recent years to explore new and environmentally friendly methods of controlling phytopathogenic bacteria. Pseudomonas syringae pv. tomato (Pst) is responsible for bacterial speck disease in tomato plants, leading to decreased yield. Disease management strategies rely on the use of copper-based pesticides. The biological control of Pst with the use of bacteriophages could be an alternative environmentally friendly approach to diminish the detrimental effects of Pst in tomato cultivations. The lytic efficacy of bacteriophages can be used in biocontrol-based disease management strategies. Here, we report the isolation and complete characterization of a bacteriophage, named Medea1, which was also tested in planta against Pst, under greenhouse conditions. The application of Medea1 as a root drenching inoculum or foliar spraying reduced 2.5- and fourfold on average, respectively, Pst symptoms in tomato plants, compared to a control group. In addition, it was observed that defense-related genes PR1b and Pin2 were upregulated in the phage-treated plants. Our research explores a new genus of Pseudomonas phages and explores its biocontrol potential against Pst, by utilizing its lytic nature and ability to trigger the immune response of plants. Key points • Medea1 is a newly reported bacteriophage against Pseudomonas syringae pv. tomato having genomic similarities with the phiPSA1 bacteriophage • Two application strategies were reported, one by root drenching the plants with a phage-based solution and one by foliar spraying, showing up to 60- and 6-fold reduction of Pst population and disease severity in some cases, respectively, compared to control • Bacteriophage Medea1 induced the expression of the plant defense-related genes Pin2 and PR1b |
Vardali, Sofia; Papadouli, Christina; Rigos, George; Nengas, Ioannis; Panagiotaki, Panagiota; Golomazou, Eleni Recent Advances in Mycotoxin Determination in Fish Feed Ingredients Journal Article Molecules, 28 (6), pp. 2519, 2023, ISSN: 1420-3049. @article{vardali_recent_2023, title = {Recent Advances in Mycotoxin Determination in Fish Feed Ingredients}, author = {Sofia Vardali and Christina Papadouli and George Rigos and Ioannis Nengas and Panagiota Panagiotaki and Eleni Golomazou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/03/2023-Vardali-Mol-15-1.pdf https://www.mdpi.com/1420-3049/28/6/2519}, doi = {10.3390/molecules28062519}, issn = {1420-3049}, year = {2023}, date = {2023-03-13}, urldate = {2023-03-13}, journal = {Molecules}, volume = {28}, number = {6}, pages = {2519}, abstract = {Low-cost plant-based sources used in aquaculture diets are prone to the occurrence of animal feed contaminants, which may in certain conditions affect the quality and safety of aquafeeds. Mycotoxins, a toxic group of small organic molecules produced by fungi, comprise a frequently occurring plant-based feed contaminant in aquafeeds. Mycotoxin contamination can potentially cause significant mortality, reduced productivity, and higher disease susceptibility; thus, its timely detection is crucial to the aquaculture industry. The present review summarizes the methodological advances, developed mainly during the past decade, related to mycotoxin detection in aquafeed ingredients, namely analytical, chromatographic, and immunological methodologies, as well as the use of biosensors and spectroscopic methods which are becoming more prevalent. Rapid and accurate mycotoxin detection is and will continue to be crucial to the food industry, animal production, and the environment, resulting in further improvements and developments in mycotoxin detection techniques.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Low-cost plant-based sources used in aquaculture diets are prone to the occurrence of animal feed contaminants, which may in certain conditions affect the quality and safety of aquafeeds. Mycotoxins, a toxic group of small organic molecules produced by fungi, comprise a frequently occurring plant-based feed contaminant in aquafeeds. Mycotoxin contamination can potentially cause significant mortality, reduced productivity, and higher disease susceptibility; thus, its timely detection is crucial to the aquaculture industry. The present review summarizes the methodological advances, developed mainly during the past decade, related to mycotoxin detection in aquafeed ingredients, namely analytical, chromatographic, and immunological methodologies, as well as the use of biosensors and spectroscopic methods which are becoming more prevalent. Rapid and accurate mycotoxin detection is and will continue to be crucial to the food industry, animal production, and the environment, resulting in further improvements and developments in mycotoxin detection techniques. |
Baltoumas, Fotis A; Karatzas, Evangelos; Paez-Espino, David; Venetsianou, Nefeli K; Aplakidou, Eleni; Oulas, Anastasis; Finn, Robert D; Ovchinnikov, Sergey; Pafilis, Evangelos; Kyrpides, Nikos C; Pavlopoulos, Georgios A Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters Journal Article Frontiers in Bioinformatics, 3 , pp. 1157956, 2023, ISSN: 2673-7647. @article{baltoumas_exploring_2023, title = {Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters}, author = {Fotis A Baltoumas and Evangelos Karatzas and David Paez-Espino and Nefeli K Venetsianou and Eleni Aplakidou and Anastasis Oulas and Robert D Finn and Sergey Ovchinnikov and Evangelos Pafilis and Nikos C Kyrpides and Georgios A Pavlopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/03/2023-Baltoumas-FroΒionform-14.pdf https://www.frontiersin.org/articles/10.3389/fbinf.2023.1157956/full}, doi = {10.3389/fbinf.2023.1157956}, issn = {2673-7647}, year = {2023}, date = {2023-03-08}, urldate = {2023-03-08}, journal = {Frontiers in Bioinformatics}, volume = {3}, pages = {1157956}, abstract = {Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment. |
Tsertou, Maria Ioanna; Triga, Adriana; Droubogiannis, Stavros; Kokkari, Constantina; Anasi, Grammatiki; Katharios, Pantelis Frontiers in Microbiology, 14 , pp. 1078669, 2023, ISSN: 1664-302X. @article{tsertou_isolation_2023, title = {Isolation and characterization of a novel Tenacibaculum species and a corresponding bacteriophage from a Mediterranean fish hatchery: Description of Tenacibaculum larymnensis sp. nov. and Tenacibaculum phage Larrie}, author = {Maria Ioanna Tsertou and Adriana Triga and Stavros Droubogiannis and Constantina Kokkari and Grammatiki Anasi and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/03/2023-Tsertou-FroMicro-13.pdf https://www.frontiersin.org/articles/10.3389/fmicb.2023.1078669/full}, doi = {10.3389/fmicb.2023.1078669}, issn = {1664-302X}, year = {2023}, date = {2023-03-07}, urldate = {2023-03-07}, journal = {Frontiers in Microbiology}, volume = {14}, pages = {1078669}, abstract = {Tenacibaculum larymnensis sp. nov., a novel species of the Tenacibaculum genus was isolated from a commercial fish hatchery in Greece. The novel species is phylogenetically close to T. discolor and was biochemically and genetically characterized. The genome of T . larymnensis has 3.66 Mbps length, 31.83% GC content and the genomic analysis demonstrated that it harbors a wide enzymatic repertoire suggestive of increased degrading capacity but also several virulence factors including hemolysins, secretion systems, transporters, siderophores, pili and extracellular proteins. Using the novel strain, a virulent bacteriophage designated as Tenacibaculum phage Larrie was isolated and characterized. Larrie is a novel Siphovirus with relatively large genome, 77.5 kbps with 111 ORFs, a GC content of 33.7% and an exclusively lytic lifestyle. The new phage-host system can serve as an efficient model to study microbial interactions in the aquatic environment which contribute to the nutrient cycling.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Tenacibaculum larymnensis sp. nov., a novel species of the Tenacibaculum genus was isolated from a commercial fish hatchery in Greece. The novel species is phylogenetically close to T. discolor and was biochemically and genetically characterized. The genome of T . larymnensis has 3.66 Mbps length, 31.83% GC content and the genomic analysis demonstrated that it harbors a wide enzymatic repertoire suggestive of increased degrading capacity but also several virulence factors including hemolysins, secretion systems, transporters, siderophores, pili and extracellular proteins. Using the novel strain, a virulent bacteriophage designated as Tenacibaculum phage Larrie was isolated and characterized. Larrie is a novel Siphovirus with relatively large genome, 77.5 kbps with 111 ORFs, a GC content of 33.7% and an exclusively lytic lifestyle. The new phage-host system can serve as an efficient model to study microbial interactions in the aquatic environment which contribute to the nutrient cycling. |
Garza, Daniel Rios; Gonze, Didier; Zafeiropoulos, Haris; Liu, Bin; Faust, Karoline Metabolic models of human gut microbiota: Advances and challenges Journal Article Cell Systems, 14 (2), pp. 109–121, 2023, ISSN: 24054712. @article{rios_garza_metabolic_2023, title = {Metabolic models of human gut microbiota: Advances and challenges}, author = {Daniel Rios Garza and Didier Gonze and Haris Zafeiropoulos and Bin Liu and Karoline Faust}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/02/2023-Rios-Garza-Cell-Systems-reprint12.pdf https://linkinghub.elsevier.com/retrieve/pii/S2405471222004379}, doi = {10.1016/j.cels.2022.11.002}, issn = {24054712}, year = {2023}, date = {2023-02-28}, urldate = {2023-02-28}, journal = {Cell Systems}, volume = {14}, number = {2}, pages = {109--121}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kalatzis, Panos G; Mauritzen, Jesper Juel; Winther-Have, Caroline Sophie; Michniewski, Slawomir; Millard, Andrew; Tsertou, Maria Ioanna; Katharios, Pantelis; Middelboe, Mathias International Journal of Molecular Sciences, 24 (4), pp. 3937, 2023, ISSN: 1422-0067. @article{kalatzis_staying_2023, title = {Staying below the Radar: Unraveling a New Family of Ubiquitous “Cryptic” Non-Tailed Temperate Vibriophages and Implications for Their Bacterial Hosts}, author = {Panos G Kalatzis and Jesper Juel Mauritzen and Caroline Sophie Winther-Have and Slawomir Michniewski and Andrew Millard and Maria Ioanna Tsertou and Pantelis Katharios and Mathias Middelboe}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/02/2023-Kalatzis-IJMolSci-11.pdf https://www.mdpi.com/1422-0067/24/4/3937}, doi = {10.3390/ijms24043937}, issn = {1422-0067}, year = {2023}, date = {2023-02-17}, urldate = {2023-02-20}, journal = {International Journal of Molecular Sciences}, volume = {24}, number = {4}, pages = {3937}, abstract = {Bacteriophages are the most abundant biological entities in the oceans and play key roles in bacterial activity, diversity and evolution. While extensive research has been conducted on the role of tailed viruses (Class: Caudoviricetes), very little is known about the distribution and functions of the non-tailed viruses (Class: Tectiliviricetes). The recent discovery of the lytic Autolykiviridae family demonstrated the potential importance of this structural lineage, emphasizing the need for further exploration of the role of this group of marine viruses. Here, we report the novel family of temperate phages under the class of Tectiliviricetes, which we propose to name “Asemoviridae” with phage NO16 as a main representative. These phages are widely distributed across geographical regions and isolation sources and found inside the genomes of at least 30 species of Vibrio, in addition to the original V. anguillarum isolation host. Genomic analysis identified dif-like sites, suggesting that NO16 prophages recombine with the bacterial genome based on the XerCD site-specific recombination mechanism. The interactions between the NO16 phage and its V. anguillarum host were linked to cell density and phage–host ratio. High cell density and low phage predation levels were shown to favor the temperate over the lytic lifestyle for NO16 viruses, and their spontaneous induction rate was highly variable between different V. anguillarum lysogenic strains. NO16 prophages coexist with the V. anguillarum host in a mutualistic interaction by rendering fitness properties to the host, such as increased virulence and biofilm formation through lysogenic conversion, likely contributing to their global distribution.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Bacteriophages are the most abundant biological entities in the oceans and play key roles in bacterial activity, diversity and evolution. While extensive research has been conducted on the role of tailed viruses (Class: Caudoviricetes), very little is known about the distribution and functions of the non-tailed viruses (Class: Tectiliviricetes). The recent discovery of the lytic Autolykiviridae family demonstrated the potential importance of this structural lineage, emphasizing the need for further exploration of the role of this group of marine viruses. Here, we report the novel family of temperate phages under the class of Tectiliviricetes, which we propose to name “Asemoviridae” with phage NO16 as a main representative. These phages are widely distributed across geographical regions and isolation sources and found inside the genomes of at least 30 species of Vibrio, in addition to the original V. anguillarum isolation host. Genomic analysis identified dif-like sites, suggesting that NO16 prophages recombine with the bacterial genome based on the XerCD site-specific recombination mechanism. The interactions between the NO16 phage and its V. anguillarum host were linked to cell density and phage–host ratio. High cell density and low phage predation levels were shown to favor the temperate over the lytic lifestyle for NO16 viruses, and their spontaneous induction rate was highly variable between different V. anguillarum lysogenic strains. NO16 prophages coexist with the V. anguillarum host in a mutualistic interaction by rendering fitness properties to the host, such as increased virulence and biofilm formation through lysogenic conversion, likely contributing to their global distribution. |
Nanou, Evangelia; Kotsiri, Mado; Kogiannou, Dimitra; Katsouli, Maria; Grigorakis, Kriton Foods, 12 (3), pp. 505, 2023, ISSN: 2304-8158. @article{nanou_consumer_2023, title = {Consumer Perception of Freshness and Volatile Composition of Fresh Gilthead Seabream and Seabass in Active Packaging with and without CO2-Emitting Pads}, author = {Evangelia Nanou and Mado Kotsiri and Dimitra Kogiannou and Maria Katsouli and Kriton Grigorakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/02/2023-Nanou-foods-10.pdf https://www.mdpi.com/2304-8158/12/3/505}, doi = {10.3390/foods12030505}, issn = {2304-8158}, year = {2023}, date = {2023-02-14}, urldate = {2023-02-15}, journal = {Foods}, volume = {12}, number = {3}, pages = {505}, abstract = {Active packaging with CO2-emitters (pads) has recently been used for shelf-life extension of fresh fish. The aim of this study was to identify consumer attitudes towards fresh fish packaging, to examine whether Greek consumers prefer active packaging with pad over active packaging without pad, to investigate any perceived differences in the sensory freshness of the fish, and to relate consumer perception to volatile composition of fish fillets. In total, 274 consumers participated in the study which included freshness sensory evaluation of gilthead seabream (Sparus aurata) and seabass (Dicentrarchuslabrax), whole-gutted and filleted, raw and cooked, at high quality and at the end of high-quality shelf-life. Samples were packed under modified atmosphere either with a pad or without. Results showed that consumers preferred packages with pads, especially at the end of high quality shelf-life. They perceived raw samples packed with a pad to be fresher and closer to the ideal product, and also had a higher purchase intention towards them. Cooked samples were not perceived differently. Consumers’ perception was in accordance with the GC-MS findings in the volatile compounds that function as freshness or spoilage indicators. Most participants were positive towards fresh fish packaging although they usually buy unpacked fresh fish. Our results suggest that active packaging with CO2 emitters contribute to freshness preservation and that it has a positive potential in the Greek market.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Active packaging with CO2-emitters (pads) has recently been used for shelf-life extension of fresh fish. The aim of this study was to identify consumer attitudes towards fresh fish packaging, to examine whether Greek consumers prefer active packaging with pad over active packaging without pad, to investigate any perceived differences in the sensory freshness of the fish, and to relate consumer perception to volatile composition of fish fillets. In total, 274 consumers participated in the study which included freshness sensory evaluation of gilthead seabream (Sparus aurata) and seabass (Dicentrarchuslabrax), whole-gutted and filleted, raw and cooked, at high quality and at the end of high-quality shelf-life. Samples were packed under modified atmosphere either with a pad or without. Results showed that consumers preferred packages with pads, especially at the end of high quality shelf-life. They perceived raw samples packed with a pad to be fresher and closer to the ideal product, and also had a higher purchase intention towards them. Cooked samples were not perceived differently. Consumers’ perception was in accordance with the GC-MS findings in the volatile compounds that function as freshness or spoilage indicators. Most participants were positive towards fresh fish packaging although they usually buy unpacked fresh fish. Our results suggest that active packaging with CO2 emitters contribute to freshness preservation and that it has a positive potential in the Greek market. |
Antoniou, Aglaia; Manousaki, Tereza; Ramírez, Francisco; Cariani, Alessia; Cannas, Rita; Kasapidis, Panagiotis; Magoulas, Antonios; Albo‐Puigserver, Marta; Lloret‐Lloret, Elena; Bellido, Jose Maria; Pennino, Maria Grazia; Follesa, Maria Cristina; Esteban, Antonio; Saraux, Claire; Sbrana, Mario; Spedicato, Maria Teresa; Coll, Marta; Tsigenopoulos, Costas S Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the textlessspan style= Journal Article Molecular Ecology, pp. mec.16840, 2023, ISSN: 0962-1083, 1365-294X. @article{antoniou_sardines_2023, title = {Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the textlessspan style=}, author = {Aglaia Antoniou and Tereza Manousaki and Francisco Ramírez and Alessia Cariani and Rita Cannas and Panagiotis Kasapidis and Antonios Magoulas and Marta Albo‐Puigserver and Elena Lloret‐Lloret and Jose Maria Bellido and Maria Grazia Pennino and Maria Cristina Follesa and Antonio Esteban and Claire Saraux and Mario Sbrana and Maria Teresa Spedicato and Marta Coll and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/02/2023-Antoniou-Mol-Eco-9-1.pdf https://onlinelibrary.wiley.com/doi/10.1111/mec.16840}, doi = {10.1111/mec.16840}, issn = {0962-1083, 1365-294X}, year = {2023}, date = {2023-02-06}, urldate = {2023-02-06}, journal = {Molecular Ecology}, pages = {mec.16840}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dimogianopoulos, D; Grigorakis, K Effective algorithmic operational framework for fish texture evaluation in industry: Achieving maturity Journal Article Aquaculture and Fisheries, 8 (4), pp. 422–430, 2023, ISSN: 2468550X. @article{dimogianopoulos_effective_2023, title = {Effective algorithmic operational framework for fish texture evaluation in industry: Achieving maturity}, author = {D Dimogianopoulos and K Grigorakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Dimogiannopoulos-AandF-7.pdf https://linkinghub.elsevier.com/retrieve/pii/S2468550X20301386}, doi = {10.1016/j.aaf.2020.10.001}, issn = {2468550X}, year = {2023}, date = {2023-01-31}, urldate = {2023-01-31}, journal = {Aquaculture and Fisheries}, volume = {8}, number = {4}, pages = {422--430}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pavloudi, Christina; Tsertou, Maria Ioanna; Antonopoulou, Efthimia; Katharios, Pantelis Investigation of systemic granulomatosis in cultured meagre, Argyrosomus regius, using clinical metagenomics Journal Article Aquaculture, 567 , pp. 739249, 2023, ISSN: 00448486. @article{pavloudi_investigation_2023, title = {Investigation of systemic granulomatosis in cultured meagre, Argyrosomus regius, using clinical metagenomics}, author = {Christina Pavloudi and Maria Ioanna Tsertou and Efthimia Antonopoulou and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Pavloudi-AQUA-pre-print-8.pdf https://linkinghub.elsevier.com/retrieve/pii/S0044848623000224}, doi = {10.1016/j.aquaculture.2023.739249}, issn = {00448486}, year = {2023}, date = {2023-01-25}, urldate = {2023-01-25}, journal = {Aquaculture}, volume = {567}, pages = {739249}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rees, Andrew P; Faraggiana, Eleonora; Tait, Karen; Celussi, Mauro; Dafnomilli, Eleni; Manna, Vincenzo; Manning, Andrew; Pitta, Paraskevi; Tsiola, Anastasia; Živanović, Snežana Frontiers in Marine Science, 9 , pp. 907269, 2023, ISSN: 2296-7745. @article{rees_presence_2022, title = {The presence of silver nanoparticles reduces demand for dissolved phosphorus to the benefit of biological nitrogen fixation in the coastal eastern Mediterranean Sea}, author = {Andrew P Rees and Eleonora Faraggiana and Karen Tait and Mauro Celussi and Eleni Dafnomilli and Vincenzo Manna and Andrew Manning and Paraskevi Pitta and Anastasia Tsiola and Snežana Živanović}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Rees-fmars-6.pdf https://www.frontiersin.org/articles/10.3389/fmars.2022.907269/full}, doi = {10.3389/fmars.2022.907269}, issn = {2296-7745}, year = {2023}, date = {2023-01-23}, urldate = {2023-01-23}, journal = {Frontiers in Marine Science}, volume = {9}, pages = {907269}, abstract = {The release of silver into the marine environment is of growing concern as its impact on marine life is not fully understood. Despite previous experiments that have shown toxic effects of silver as nanoparticles (AgNPs) and as free ions (Ag + ) on microbial organisms, the impact on important biogeochemical processes, such as marine nitrogen fixation, remains relatively unexplored. The present study investigated the impact of AgNPs and Ag + on nitrogen fixation activity in oligotrophic coastal ecosystems. Nine mesocosm enclosures were set-up in Crete, Greece, for twelve days during May 2019. Three mesocosms were left unamended at ambient light and temperature; three were manipulated with 50 ng AgNPs L -1 d -1 and three were amended with 50 ng Ag + L -1 d -1 . Over the duration of the experiment, mean nitrogen fixation rates proved higher in treated waters; 0.28 ± 0.24 nmol N L -1 d -1 and 0.21 ± 0.19 nmol N L -1 d -1 in AgNP and Ag + which were 2.2 (p< 0.001) and 1.6 (not significant) times higher than control rates of 0.13 ± 0.07 nmol N L -1 d -1 respectively. Changes in nitrogen fixation rates were paralleled by significantly higher concentrations of phosphate and silicate in treated versus control mesocosms, suggesting an inhibition of the uptake of these nutrients by non-diazotrophic groups. Sequencing of 16S and 18S rRNA genes showed shifts in community composition over time but only very minor changes could be linked to the Ag treatments. Decreases to the relative abundance of three diatom species were observed in the Ag treatments but these were considered insufficient to support the relative differences in nutrient concentration. It is therefore speculated that there was physiological disruption of nutrient uptake mechanisms of the non-diazotrophic community. A number of potential diazotrophs were detected and the relative sequence abundance of a number of known nitrogen fixing taxa, including Burkholderiaceae , Oceanospirillales and Pseudomonadales correlated with measured nitrogen fixation rates. Phosphorus limitation of diazotrophic activity was therefore lowered relative to other microbial groups in silver amended treatments and significant increases in particulate nitrogen for both Ag treatments indicate an enhancement in cellular N for the nitrogen fixing communities.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The release of silver into the marine environment is of growing concern as its impact on marine life is not fully understood. Despite previous experiments that have shown toxic effects of silver as nanoparticles (AgNPs) and as free ions (Ag + ) on microbial organisms, the impact on important biogeochemical processes, such as marine nitrogen fixation, remains relatively unexplored. The present study investigated the impact of AgNPs and Ag + on nitrogen fixation activity in oligotrophic coastal ecosystems. Nine mesocosm enclosures were set-up in Crete, Greece, for twelve days during May 2019. Three mesocosms were left unamended at ambient light and temperature; three were manipulated with 50 ng AgNPs L -1 d -1 and three were amended with 50 ng Ag + L -1 d -1 . Over the duration of the experiment, mean nitrogen fixation rates proved higher in treated waters; 0.28 ± 0.24 nmol N L -1 d -1 and 0.21 ± 0.19 nmol N L -1 d -1 in AgNP and Ag + which were 2.2 (p< 0.001) and 1.6 (not significant) times higher than control rates of 0.13 ± 0.07 nmol N L -1 d -1 respectively. Changes in nitrogen fixation rates were paralleled by significantly higher concentrations of phosphate and silicate in treated versus control mesocosms, suggesting an inhibition of the uptake of these nutrients by non-diazotrophic groups. Sequencing of 16S and 18S rRNA genes showed shifts in community composition over time but only very minor changes could be linked to the Ag treatments. Decreases to the relative abundance of three diatom species were observed in the Ag treatments but these were considered insufficient to support the relative differences in nutrient concentration. It is therefore speculated that there was physiological disruption of nutrient uptake mechanisms of the non-diazotrophic community. A number of potential diazotrophs were detected and the relative sequence abundance of a number of known nitrogen fixing taxa, including Burkholderiaceae , Oceanospirillales and Pseudomonadales correlated with measured nitrogen fixation rates. Phosphorus limitation of diazotrophic activity was therefore lowered relative to other microbial groups in silver amended treatments and significant increases in particulate nitrogen for both Ag treatments indicate an enhancement in cellular N for the nitrogen fixing communities. |
Bauer, Sven Le Moine; Lu, Guang-Sin; Goulaouic, Steven; Puzenat, Valentine; Schouw, Anders; Barreyre, Thibaut; Pawlowsky-Glahn, Vera; Egozcue, Juan José; Martelat, Jean-Emmanuel; Escartin, Javier; Amend, Jan P; Nomikou, Paraskevi; Vlasopoulos, Othonas; Polymenakou, Paraskevi; Jørgensen, Steffen Leth Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece Journal Article Frontiers in Microbiology, 13 , pp. 1060168, 2023, ISSN: 1664-302X. @article{le_moine_bauer_structure_2023, title = {Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece}, author = {Sven Le Moine Bauer and Guang-Sin Lu and Steven Goulaouic and Valentine Puzenat and Anders Schouw and Thibaut Barreyre and Vera Pawlowsky-Glahn and Juan José Egozcue and Jean-Emmanuel Martelat and Javier Escartin and Jan P Amend and Paraskevi Nomikou and Othonas Vlasopoulos and Paraskevi Polymenakou and Steffen Leth Jørgensen}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Le-Moine-Bauer-FinMicro-5.pdf https://www.frontiersin.org/articles/10.3389/fmicb.2022.1060168/full}, doi = {10.3389/fmicb.2022.1060168}, issn = {1664-302X}, year = {2023}, date = {2023-01-16}, urldate = {2023-01-16}, journal = {Frontiers in Microbiology}, volume = {13}, pages = {1060168}, abstract = {Introduction Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades. However, a thorough description of the microbial communities inhabiting the bay is still missing. Methods We present the first in-depth characterization of the prokaryotic communities of Paleochori Bay by sampling eight different seafloor types that are distributed along the entire gradient of hydrothermal influence. We used deep sequencing of the 16S rRNA marker gene and complemented the analysis with qPCR quantification of the 16S rRNA gene and several functional genes to gain insights into the metabolic potential of the communities. Results We found that the microbiome of the bay is strongly influenced by the hydrothermal venting, with a succession of various groups dominating the sediments from the coldest to the warmest zones. Prokaryotic diversity and abundance decrease with increasing temperature, and thermophilic archaea overtake the community. Discussion Relevant geochemical cycles of the Bay are discussed. This study expands our limited understanding of subsurface microbial communities in acidic shallow-sea hydrothermal systems and the contribution of their microbial activity to biogeochemical cycling.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Introduction Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades. However, a thorough description of the microbial communities inhabiting the bay is still missing. Methods We present the first in-depth characterization of the prokaryotic communities of Paleochori Bay by sampling eight different seafloor types that are distributed along the entire gradient of hydrothermal influence. We used deep sequencing of the 16S rRNA marker gene and complemented the analysis with qPCR quantification of the 16S rRNA gene and several functional genes to gain insights into the metabolic potential of the communities. Results We found that the microbiome of the bay is strongly influenced by the hydrothermal venting, with a succession of various groups dominating the sediments from the coldest to the warmest zones. Prokaryotic diversity and abundance decrease with increasing temperature, and thermophilic archaea overtake the community. Discussion Relevant geochemical cycles of the Bay are discussed. This study expands our limited understanding of subsurface microbial communities in acidic shallow-sea hydrothermal systems and the contribution of their microbial activity to biogeochemical cycling. |
Papadogiannis, Vasileios; Manousaki, Tereza; Nousias, Orestis; Tsakogiannis, Alexandros; Kristoffersen, Jon B; Mylonas, Constantinos C; Batargias, Costas; Chatziplis, Dimitrios; Tsigenopoulos, Costas S Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution Journal Article Frontiers in Genetics, 13 , pp. 1081760, 2023, ISSN: 1664-8021. @article{papadogiannis_chromosome_2023, title = {Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution}, author = {Vasileios Papadogiannis and Tereza Manousaki and Orestis Nousias and Alexandros Tsakogiannis and Jon B Kristoffersen and Constantinos C Mylonas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Papadogiannis-FinGenetics-4.pdf https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full}, doi = {10.3389/fgene.2022.1081760}, issn = {1664-8021}, year = {2023}, date = {2023-01-10}, urldate = {2023-01-11}, journal = {Frontiers in Genetics}, volume = {13}, pages = {1081760}, abstract = {The meagre, Argyrosomus regius , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The meagre, Argyrosomus regius , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species. |
Valdivieso, Alejandro; Sánchez-Baizán, Núria; Mitrizakis, Nikos; Papandroulakis, Nikos; Piferrer, Francesc Aquaculture, 563 , pp. 738918, 2023, ISSN: 00448486. @article{valdivieso_development_2023, title = {Development of epigenetic biomarkers with diagnostic and prognostic value to assess the lasting effects of early temperature changes in farmed fish}, author = {Alejandro Valdivieso and Núria Sánchez-Baizán and Nikos Mitrizakis and Nikos Papandroulakis and Francesc Piferrer}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/11/2023-Valdivieso-3.pdf https://linkinghub.elsevier.com/retrieve/pii/S0044848622010353}, doi = {10.1016/j.aquaculture.2022.738918}, issn = {00448486}, year = {2023}, date = {2023-01-04}, urldate = {2022-11-10}, journal = {Aquaculture}, volume = {563}, pages = {738918}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Publications
2023 |
The founding charter of the Omic Biodiversity Observation Network (Omic BON) Journal Article GigaScience, 12 , pp. giad068, 2023, ISSN: 2047-217X. |
Mediterranean Marine Science, 24 (3), pp. 482–490, 2023, ISSN: 1791-6763, 1108-393X. |
Ion-driven communication and acclimation strategies in microalgae Journal Article Chemical Engineering Journal, 473 , pp. 144985, 2023, ISSN: 13858947. |
Journal of Fish Diseases, pp. jfd.13854, 2023, ISSN: 0140-7775, 1365-2761. |
Pharmacokinetics of praziquantel in gilthead seabream (Sparus aurata) plasma and gills Journal Article Aquaculture, 577 , pp. 739975, 2023, ISSN: 00448486. |
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