2022 |
Mente, Eleni; Bousdras, Thomas; Feidantsis, Konstantinos; Panteli, Nikolas; Mastoraki, Maria; Kormas, Konstantinos Ar.; Chatzifotis, Stavros; Piccolo, Giovanni; Gasco, Laura; Gai, Francesco; Martin, Samuel A M; Antonopoulou, Efthimia Tenebrio molitor larvae meal inclusion affects hepatic proteome and apoptosis and/or autophagy of three farmed fish species Journal Article Scientific Reports, 12 (1), pp. 121, 2022, ISSN: 2045-2322. @article{mente_tenebrio_2022, title = {Tenebrio molitor larvae meal inclusion affects hepatic proteome and apoptosis and/or autophagy of three farmed fish species}, author = {Eleni Mente and Thomas Bousdras and Konstantinos Feidantsis and Nikolas Panteli and Maria Mastoraki and Konstantinos Ar. Kormas and Stavros Chatzifotis and Giovanni Piccolo and Laura Gasco and Francesco Gai and Samuel A M Martin and Efthimia Antonopoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Mente-SciRep-23.pdf https://www.nature.com/articles/s41598-021-03306-8}, doi = {10.1038/s41598-021-03306-8}, issn = {2045-2322}, year = {2022}, date = {2022-12-01}, urldate = {2022-05-09}, journal = {Scientific Reports}, volume = {12}, number = {1}, pages = {121}, abstract = {Abstract Herein, the effect of dietary inclusion of insect ( Tenebrio molitor ) meal on hepatic pathways of apoptosis and autophagy in three farmed fish species, gilthead seabream ( Sparus aurata ), European seabass ( Dicentrarchus labrax ) and rainbow trout ( Oncorhynchus mykiss ), fed diets at 25%, 50% and 60% insect meal inclusion levels respectively, was investigated. Hepatic proteome was examined by liver protein profiles from the three fish species, obtained by two-dimensional gel electrophoresis. Although cellular stress was evident in the three teleost species following insect meal, inclusion by T. molitor , D. labrax and O. mykiss suppressed apoptosis through induction of hepatic autophagy, while in S. aurata both cellular procedures were activated. Protein abundance showed that a total of 30, 81 and 74 spots were altered significantly in seabream, European seabass and rainbow trout, respectively. Insect meal inclusion resulted in individual protein abundance changes, with less number of proteins altered in gilthead seabream compared to European seabass and rainbow trout. This is the first study demonstrating that insect meal in fish diets is causing changes in liver protein abundances. However, a species-specific response both in the above mentioned bioindicators, indicates the need to strategically manage fish meal replacement in fish diets per species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Herein, the effect of dietary inclusion of insect ( Tenebrio molitor ) meal on hepatic pathways of apoptosis and autophagy in three farmed fish species, gilthead seabream ( Sparus aurata ), European seabass ( Dicentrarchus labrax ) and rainbow trout ( Oncorhynchus mykiss ), fed diets at 25%, 50% and 60% insect meal inclusion levels respectively, was investigated. Hepatic proteome was examined by liver protein profiles from the three fish species, obtained by two-dimensional gel electrophoresis. Although cellular stress was evident in the three teleost species following insect meal, inclusion by T. molitor , D. labrax and O. mykiss suppressed apoptosis through induction of hepatic autophagy, while in S. aurata both cellular procedures were activated. Protein abundance showed that a total of 30, 81 and 74 spots were altered significantly in seabream, European seabass and rainbow trout, respectively. Insect meal inclusion resulted in individual protein abundance changes, with less number of proteins altered in gilthead seabream compared to European seabass and rainbow trout. This is the first study demonstrating that insect meal in fish diets is causing changes in liver protein abundances. However, a species-specific response both in the above mentioned bioindicators, indicates the need to strategically manage fish meal replacement in fish diets per species. |
Foundation, Tara Ocean; Abreu, Andre; Bourgois, Etienne; Gristwood, Adam; Troublé, Romain; Oceans, Tara; Acinas, Silvia G; Bork, Peer; Boss, Emmanuel; Bowler, Chris; Budinich, Marko; Chaffron, Samuel; de Vargas, Colomban; Delmont, Tom O; Eveillard, Damien; Guidi, Lionel; Iudicone, Daniele; Kandels, Stephanie; Morlon, Hélène; Lombard, Fabien; Pepperkok, Rainer; Karlusich, Juan José Pierella; Piganeau, Gwenael; Régimbeau, Antoine; Sommeria-Klein, Guilhem; Stemmann, Lars; Sullivan, Matthew B; Sunagawa, Shinichi; Wincker, Patrick; Zablocki, Olivier; (EMBL), European Molecular Biology Laboratory; Arendt, Detlev; Bilic, Josipa; Finn, Robert; Heard, Edith; Rouse, Brendan; Vamathevan, Jessica; (EMBRC-ERIC), European Marine Biological Resource Centre European Research Infrastructure Consortium -; Casotti, Raffaella; Cancio, Ibon; Cunliffe, Michael; Kervella, Anne Emmanuelle; Kooistra, Wiebe H C F; Obst, Matthias; Pade, Nicolas; Power, Deborah M; Santi, Ioulia; Tsagaraki, Tatiana Margo; Vanaverbeke, Jan Priorities for ocean microbiome research Journal Article Nature Microbiology, 7 (7), pp. 937–947, 2022, ISSN: 2058-5276. @article{tara_ocean_foundation_priorities_2022, title = {Priorities for ocean microbiome research}, author = {Tara Ocean Foundation and Andre Abreu and Etienne Bourgois and Adam Gristwood and Romain Troublé and Tara Oceans and Silvia G Acinas and Peer Bork and Emmanuel Boss and Chris Bowler and Marko Budinich and Samuel Chaffron and Colomban de Vargas and Tom O Delmont and Damien Eveillard and Lionel Guidi and Daniele Iudicone and Stephanie Kandels and Hélène Morlon and Fabien Lombard and Rainer Pepperkok and Juan José Pierella Karlusich and Gwenael Piganeau and Antoine Régimbeau and Guilhem Sommeria-Klein and Lars Stemmann and Matthew B Sullivan and Shinichi Sunagawa and Patrick Wincker and Olivier Zablocki and European Molecular Biology Laboratory (EMBL) and Detlev Arendt and Josipa Bilic and Robert Finn and Edith Heard and Brendan Rouse and Jessica Vamathevan and European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC) and Raffaella Casotti and Ibon Cancio and Michael Cunliffe and Anne Emmanuelle Kervella and Wiebe H C F Kooistra and Matthias Obst and Nicolas Pade and Deborah M Power and Ioulia Santi and Tatiana Margo Tsagaraki and Jan Vanaverbeke}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Sandi-et-al.-Priorities_for_ocean_microbiome_research-51.pdf https://www.nature.com/articles/s41564-022-01145-5}, doi = {10.1038/s41564-022-01145-5}, issn = {2058-5276}, year = {2022}, date = {2022-07-01}, urldate = {2022-07-29}, journal = {Nature Microbiology}, volume = {7}, number = {7}, pages = {937--947}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sarropoulou, Xenia; Tsaparis, Dimitris; Tsagarakis, Konstantinos; Badouvas, Nicholas; Tsigenopoulos, Costas S Different patterns of population structure and genetic diversity of three mesopelagic fishes in the Greek Seas Journal Article Mediterranean Marine Science, 23 (3), pp. 536–545, 2022, ISSN: 1791-6763. @article{sarropoulou_different_2022, title = {Different patterns of population structure and genetic diversity of three mesopelagic fishes in the Greek Seas}, author = {Xenia Sarropoulou and Dimitris Tsaparis and Konstantinos Tsagarakis and Nicholas Badouvas and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Sarropoulou-MMS-49.pdf https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/28567}, doi = {10.12681/mms.28567}, issn = {1791-6763}, year = {2022}, date = {2022-06-01}, urldate = {2022-07-29}, journal = {Mediterranean Marine Science}, volume = {23}, number = {3}, pages = {536--545}, abstract = {Mesopelagic fishes are among the most abundant groups of vertebrates on Earth. Despite their unique biological and ecological traits, research in this group has been particularly scarce. The present study investigates the intraspecific genetic diversity of three mesopelagic fishes (Hygophum benoiti, Maurolicus muelleri, and Benthosema glaciale) in the Greek Seas. Analyses of three mitochondrial DNA genes (COI, 12S, and 16S) from a total of 168 samples revealed a lack of genetic structure for M. muelleri and B. glaciale across the studied area. However, H. benoiti specimens from the Corinthian Gulf were differentiated from the rest of the populations, suggesting that the limited connection between the Corinthian and neighboring seas may act as a barrier to gene flow. Furthermore, the COI data of this study were co-analyzed with publicly available sequences, demonstrating lack of phylogeographic structure for all three species through their distribution range. Therefore, even though indications of genetic differentiation were observed, the three mesopelagic fishes are generally characterized by genetic homogeneity, which may be the result of their recent evolutionary history.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mesopelagic fishes are among the most abundant groups of vertebrates on Earth. Despite their unique biological and ecological traits, research in this group has been particularly scarce. The present study investigates the intraspecific genetic diversity of three mesopelagic fishes (Hygophum benoiti, Maurolicus muelleri, and Benthosema glaciale) in the Greek Seas. Analyses of three mitochondrial DNA genes (COI, 12S, and 16S) from a total of 168 samples revealed a lack of genetic structure for M. muelleri and B. glaciale across the studied area. However, H. benoiti specimens from the Corinthian Gulf were differentiated from the rest of the populations, suggesting that the limited connection between the Corinthian and neighboring seas may act as a barrier to gene flow. Furthermore, the COI data of this study were co-analyzed with publicly available sequences, demonstrating lack of phylogeographic structure for all three species through their distribution range. Therefore, even though indications of genetic differentiation were observed, the three mesopelagic fishes are generally characterized by genetic homogeneity, which may be the result of their recent evolutionary history. |
Villanueva, Beatriz; Fernández, Almudena; Peiró-Pastor, Ramón; Peñaloza, Carolina; Houston, Ross D; Sonesson, Anna K; Tsigenopoulos, Costas S; Bargelloni, Luca; Gamsız, Kutsal; Karahan, Bilge; Gökçek, Emel Ö; Fernández, Jesús; Saura, María Aquaculture Reports, 24 , pp. 101145, 2022, ISSN: 23525134. @article{villanueva_population_2022, title = {Population structure and genetic variability in wild and farmed Mediterranean populations of gilthead seabream and European seabass inferred from a 60K combined species SNP array}, author = {Beatriz Villanueva and Almudena Fernández and Ramón Peiró-Pastor and Carolina Peñaloza and Ross D Houston and Anna K Sonesson and Costas S Tsigenopoulos and Luca Bargelloni and Kutsal Gamsız and Bilge Karahan and Emel Ö Gökçek and Jesús Fernández and María Saura}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Villanueva-37.pdf https://linkinghub.elsevier.com/retrieve/pii/S2352513422001417}, doi = {10.1016/j.aqrep.2022.101145}, issn = {23525134}, year = {2022}, date = {2022-06-01}, urldate = {2022-07-29}, journal = {Aquaculture Reports}, volume = {24}, pages = {101145}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
de Mello, Paulo H; Divanach, Pascal; Papadakis, Ioannis E Aquaculture Research, 53 (9), pp. 3416–3429, 2022, ISSN: 1355-557X, 1365-2109. @article{de_mello_temperature_2022, title = {Temperature influences growth, digestive system ontogeny and lipids deposition in the liver in gilthead seabream ( textitSparus aurata ) larvae and juveniles}, author = {Paulo H de Mello and Pascal Divanach and Ioannis E Papadakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-de-Mello-ARE-pre-print-44.pdf https://onlinelibrary.wiley.com/doi/10.1111/are.15849}, doi = {10.1111/are.15849}, issn = {1355-557X, 1365-2109}, year = {2022}, date = {2022-06-01}, urldate = {2022-07-29}, journal = {Aquaculture Research}, volume = {53}, number = {9}, pages = {3416--3429}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Skouradakis, Grigorios; Dounas, Costas; Androulakis, Dimitrios N; Papadaki, Maria; Koulouri, Panayota; Pavlidis, Michail A Study of Arca noae (Linnaeus, 1758) in Elounda Bay, Crete, Eastern Mediterranean Journal Article Journal of Marine Science and Engineering, 10 (5), pp. 673, 2022, ISSN: 2077-1312. @article{skouradakis_study_2022, title = {A Study of Arca noae (Linnaeus, 1758) in Elounda Bay, Crete, Eastern Mediterranean}, author = {Grigorios Skouradakis and Costas Dounas and Dimitrios N Androulakis and Maria Papadaki and Panayota Koulouri and Michail Pavlidis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Skouradakis-jmse-38.pdf https://www.mdpi.com/2077-1312/10/5/673}, doi = {10.3390/jmse10050673}, issn = {2077-1312}, year = {2022}, date = {2022-05-01}, urldate = {2022-07-29}, journal = {Journal of Marine Science and Engineering}, volume = {10}, number = {5}, pages = {673}, abstract = {There is growing interest about marine bivalve aquaculture globally, not only for the market value of the goods produced, but also for the socio-economic and environmental services that this activity can provide. Arca noae is an endemic Mediterranean bivalve of commercial value, whose previously undescribed population in Elounda Bay we studied in terms of its structure and reproduction, while constructing a timeseries of the basic environmental parameters of the bay, thus, gaining fundamental knowledge for the potential future exploitation of the species in the area. We found a variable spatial distribution of arks in the study area, with local high peaks in the population density, consisting of smaller size individuals, in comparison to other areas. Because of protandry of the species, human pressure on this population could have a strong negative effect, by targeting the limited numbers of large females in the study area. The reproduction pattern was similar to the reports from other Mediterranean locations. The abiotic conditions in Elounda Bay differed from those in the adjacent coastal zone, confirming that the Bay is a unique semi-enclosed marine area in the island of Crete.}, keywords = {}, pubstate = {published}, tppubtype = {article} } There is growing interest about marine bivalve aquaculture globally, not only for the market value of the goods produced, but also for the socio-economic and environmental services that this activity can provide. Arca noae is an endemic Mediterranean bivalve of commercial value, whose previously undescribed population in Elounda Bay we studied in terms of its structure and reproduction, while constructing a timeseries of the basic environmental parameters of the bay, thus, gaining fundamental knowledge for the potential future exploitation of the species in the area. We found a variable spatial distribution of arks in the study area, with local high peaks in the population density, consisting of smaller size individuals, in comparison to other areas. Because of protandry of the species, human pressure on this population could have a strong negative effect, by targeting the limited numbers of large females in the study area. The reproduction pattern was similar to the reports from other Mediterranean locations. The abiotic conditions in Elounda Bay differed from those in the adjacent coastal zone, confirming that the Bay is a unique semi-enclosed marine area in the island of Crete. |
Digenis, Markos; Arvanitidis, Christos; Dailianis, Thanos; Gerovasileiou, Vasilis Comparative Study of Marine Cave Communities in a Protected Area of the South-Eastern Aegean Sea, Greece Journal Article Journal of Marine Science and Engineering, 10 (5), pp. 660, 2022, ISSN: 2077-1312. @article{digenis_comparative_2022, title = {Comparative Study of Marine Cave Communities in a Protected Area of the South-Eastern Aegean Sea, Greece}, author = {Markos Digenis and Christos Arvanitidis and Thanos Dailianis and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Digenis-jmse-40.pdf https://www.mdpi.com/2077-1312/10/5/660}, doi = {10.3390/jmse10050660}, issn = {2077-1312}, year = {2022}, date = {2022-05-01}, urldate = {2022-07-29}, journal = {Journal of Marine Science and Engineering}, volume = {10}, number = {5}, pages = {660}, abstract = {Although more than 600 marine caves have been recorded so far along the Greek coasts of the Aegean Sea (Eastern Mediterranean), only a few have been systematically studied for their biodiversity. In this study, the benthic communities of six marine caves within a Protected Area of South-Eastern Aegean were studied for the first time, both qualitatively and quantitatively. The association of different geomorphological and topographical factors of the caves with the benthic community structure was investigated. A total of 120 photographic quadrats covering the entrance and semi-dark cave zones were analysed, with regard to coverage and taxon abundance, while motile taxa were qualitatively recorded by visual census. The ecological quality status of the caves was also assessed under an ecosystem-based approach. In total, 81 sessile and 45 motile taxa were recorded, including 12 protected and 10 non-indigenous species. Multivariate community analysis demonstrated that the geomorphological and topographical variables of the caves are significantly associated with the observed biotic patterns. The ecological quality of the caves was assessed as poor or moderate according to the CavEBQI index, highlighting the necessity for systematic monitoring. This study paves the way for similar studies in marine cave habitats aiming at the development of management and conservation actions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although more than 600 marine caves have been recorded so far along the Greek coasts of the Aegean Sea (Eastern Mediterranean), only a few have been systematically studied for their biodiversity. In this study, the benthic communities of six marine caves within a Protected Area of South-Eastern Aegean were studied for the first time, both qualitatively and quantitatively. The association of different geomorphological and topographical factors of the caves with the benthic community structure was investigated. A total of 120 photographic quadrats covering the entrance and semi-dark cave zones were analysed, with regard to coverage and taxon abundance, while motile taxa were qualitatively recorded by visual census. The ecological quality status of the caves was also assessed under an ecosystem-based approach. In total, 81 sessile and 45 motile taxa were recorded, including 12 protected and 10 non-indigenous species. Multivariate community analysis demonstrated that the geomorphological and topographical variables of the caves are significantly associated with the observed biotic patterns. The ecological quality of the caves was assessed as poor or moderate according to the CavEBQI index, highlighting the necessity for systematic monitoring. This study paves the way for similar studies in marine cave habitats aiming at the development of management and conservation actions. |
Intze, Evangelia; Lagkouvardos, Ilias DivCom: A Tool for Systematic Partition of Groups of Microbial Profiles Into Intrinsic Subclusters and Distance-Based Subgroup Comparisons Journal Article Frontiers in Bioinformatics, 2 , pp. 864382, 2022, ISSN: 2673-7647. @article{intze_divcom_2022, title = {DivCom: A Tool for Systematic Partition of Groups of Microbial Profiles Into Intrinsic Subclusters and Distance-Based Subgroup Comparisons}, author = {Evangelia Intze and Ilias Lagkouvardos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Intze-DivCom-42.pdf https://www.frontiersin.org/articles/10.3389/fbinf.2022.864382/full}, doi = {10.3389/fbinf.2022.864382}, issn = {2673-7647}, year = {2022}, date = {2022-05-01}, urldate = {2022-07-29}, journal = {Frontiers in Bioinformatics}, volume = {2}, pages = {864382}, abstract = {When analyzing microbiome data, one of the main objectives is to effectively compare the microbial profiles of samples belonging to different groups. Beta diversity measures the level of similarity among samples, usually in the form of dissimilarity matrices. The use of suitable statistical tests in conjunction with those matrices typically provides us with all the necessary information to evaluate the overall similarity of groups of microbial communities. However, in some cases, this approach can lead us to deceptive conclusions, mainly due to the uneven dispersions of the groups and the existence of unique or unexpected substructures in the dataset. To address these issues, we developed divide and compare (DivCom), an automated tool for advanced beta diversity analysis. DivCom reveals the inner structure of groups by dividing their samples into the appropriate number of clusters and then compares the distances of every profile to the centers of these clusters. This information can be used for determining the existing interrelation of the groups. The proposed methodology and the developed tool were assessed by comparing the response of anemic patients with or without inflammatory bowel disease to different iron replacement therapies. DivCom generated results that revealed the inner structure of the dataset, evaluated the relationship among the clusters, and assessed the effect of the treatments. The DivCom tool is freely available at: https://github.com/Lagkouvardos/DivCom .}, keywords = {}, pubstate = {published}, tppubtype = {article} } When analyzing microbiome data, one of the main objectives is to effectively compare the microbial profiles of samples belonging to different groups. Beta diversity measures the level of similarity among samples, usually in the form of dissimilarity matrices. The use of suitable statistical tests in conjunction with those matrices typically provides us with all the necessary information to evaluate the overall similarity of groups of microbial communities. However, in some cases, this approach can lead us to deceptive conclusions, mainly due to the uneven dispersions of the groups and the existence of unique or unexpected substructures in the dataset. To address these issues, we developed divide and compare (DivCom), an automated tool for advanced beta diversity analysis. DivCom reveals the inner structure of groups by dividing their samples into the appropriate number of clusters and then compares the distances of every profile to the centers of these clusters. This information can be used for determining the existing interrelation of the groups. The proposed methodology and the developed tool were assessed by comparing the response of anemic patients with or without inflammatory bowel disease to different iron replacement therapies. DivCom generated results that revealed the inner structure of the dataset, evaluated the relationship among the clusters, and assessed the effect of the treatments. The DivCom tool is freely available at: https://github.com/Lagkouvardos/DivCom . |
Rallis, Ioannis; Chatzigeorgiou, Giorgos; Florido, Marta; Sedano, Francisco; Procopiou, Avgi; Chertz-Bynichaki, Melina; Vernadou, Emmanouela; Plaiti, Wanda; Koulouri, Panayota; Dounas, Costas; Gerovasileiou, Vasilis; Dailianis, Thanos Early Succession Patterns of Benthic Assemblages on Artificial Reefs in the Oligotrophic Eastern Mediterranean Basin Journal Article Journal of Marine Science and Engineering, 10 (5), pp. 620, 2022, ISSN: 2077-1312. @article{rallis_early_2022, title = {Early Succession Patterns of Benthic Assemblages on Artificial Reefs in the Oligotrophic Eastern Mediterranean Basin}, author = {Ioannis Rallis and Giorgos Chatzigeorgiou and Marta Florido and Francisco Sedano and Avgi Procopiou and Melina Chertz-Bynichaki and Emmanouela Vernadou and Wanda Plaiti and Panayota Koulouri and Costas Dounas and Vasilis Gerovasileiou and Thanos Dailianis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Rallis-jmse-35.pdf https://www.mdpi.com/2077-1312/10/5/620}, doi = {10.3390/jmse10050620}, issn = {2077-1312}, year = {2022}, date = {2022-05-01}, urldate = {2022-05-09}, journal = {Journal of Marine Science and Engineering}, volume = {10}, number = {5}, pages = {620}, abstract = {The colonization of artificial structures by benthic organisms in the marine realm is known to be affected by the general trophic patterns of the biogeographical zone and the prevailing environmental traits at the local scale. The present work aims to present quantitative data on the early settlement progress of macrofaunal benthic assemblages developing on artificial reefs (ARs) deployed at the Underwater Biotechnological Park of Crete (UBPC) in the oligotrophic Eastern Mediterranean. Visual census and subsequent image analysis combined with scraped quadrats were used to describe the establishment of the communities and their development over three consecutive campaigns, spanning 5 years post-deployment. Macroalgae consistently dominated in terms of coverage, while sessile invertebrates displayed different patterns over the years. Polychaeta and Bryozoa were gradually replaced by Cnidaria, while Porifera and Mollusca displayed an increasing trend over the years. Motile benthos was mainly represented by Mollusca, while the abundance of Polychaeta increased in contrast to that of Crustacea. For both sessile and motile assemblages, significant differences were observed among the years. The results of this study indicate that ecological succession is still ongoing, and further improvement in the monitoring methodology can assist towards a more accurate assessment of the community composition in complex AR structures.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The colonization of artificial structures by benthic organisms in the marine realm is known to be affected by the general trophic patterns of the biogeographical zone and the prevailing environmental traits at the local scale. The present work aims to present quantitative data on the early settlement progress of macrofaunal benthic assemblages developing on artificial reefs (ARs) deployed at the Underwater Biotechnological Park of Crete (UBPC) in the oligotrophic Eastern Mediterranean. Visual census and subsequent image analysis combined with scraped quadrats were used to describe the establishment of the communities and their development over three consecutive campaigns, spanning 5 years post-deployment. Macroalgae consistently dominated in terms of coverage, while sessile invertebrates displayed different patterns over the years. Polychaeta and Bryozoa were gradually replaced by Cnidaria, while Porifera and Mollusca displayed an increasing trend over the years. Motile benthos was mainly represented by Mollusca, while the abundance of Polychaeta increased in contrast to that of Crustacea. For both sessile and motile assemblages, significant differences were observed among the years. The results of this study indicate that ecological succession is still ongoing, and further improvement in the monitoring methodology can assist towards a more accurate assessment of the community composition in complex AR structures. |
Droubogiannis, Stavros; Katharios, Pantelis Pathogens, 11 (6), pp. 630, 2022, ISSN: 2076-0817. @article{droubogiannis_genomic_2022, title = {Genomic and Biological Profile of a Novel Bacteriophage, Vibrio phage Virtus, Which Improves Survival of Sparus aurata Larvae Challenged with Vibrio harveyi}, author = {Stavros Droubogiannis and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Droubogiannis-Pathogens-46.pdf https://www.mdpi.com/2076-0817/11/6/630}, doi = {10.3390/pathogens11060630}, issn = {2076-0817}, year = {2022}, date = {2022-05-01}, urldate = {2022-07-29}, journal = {Pathogens}, volume = {11}, number = {6}, pages = {630}, abstract = {Due to the emergence of multidrug-resistant bacteria, commonly known as “superbugs”, phage therapy for the control of bacterial diseases rose in popularity. In this context, the use of phages for the management of many important bacterial diseases in the aquaculture environment is auspicious. Vibrio harveyi, a well-known and serious bacterial pathogen, is responsible for many disease outbreaks in aquaculture, resulting in huge economic and production losses. We isolated and fully characterized a novel bacteriophage, Vibrio phage Virtus, infecting V. harveyi strain VH2. Vibrio phage Virtus can infect a wide spectrum of Vibrio spp., including strains of V. harveyi, V. owensii, V. campbellii, V. parahaemolyticus, and V. mediterranei. It has a latent period of 40 min with an unusually high burst size of 3200 PFU/cell. Vibrio phage Virtus has a double-stranded DNA of 82,960 base pairs with 127 predicted open reading frames (ORFs). No virulence, antibiotic resistance, or integrase-encoding genes were detected. In vivo phage therapy trials in gilthead seabream, Sparus aurata, larvae demonstrated that Vibrio phage Virtus was able to significantly improve the survival of larvae for five days at a multiplicity of infection (MOI) of 10, which suggests that it can be an excellent candidate for phage therapy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Due to the emergence of multidrug-resistant bacteria, commonly known as “superbugs”, phage therapy for the control of bacterial diseases rose in popularity. In this context, the use of phages for the management of many important bacterial diseases in the aquaculture environment is auspicious. Vibrio harveyi, a well-known and serious bacterial pathogen, is responsible for many disease outbreaks in aquaculture, resulting in huge economic and production losses. We isolated and fully characterized a novel bacteriophage, Vibrio phage Virtus, infecting V. harveyi strain VH2. Vibrio phage Virtus can infect a wide spectrum of Vibrio spp., including strains of V. harveyi, V. owensii, V. campbellii, V. parahaemolyticus, and V. mediterranei. It has a latent period of 40 min with an unusually high burst size of 3200 PFU/cell. Vibrio phage Virtus has a double-stranded DNA of 82,960 base pairs with 127 predicted open reading frames (ORFs). No virulence, antibiotic resistance, or integrase-encoding genes were detected. In vivo phage therapy trials in gilthead seabream, Sparus aurata, larvae demonstrated that Vibrio phage Virtus was able to significantly improve the survival of larvae for five days at a multiplicity of infection (MOI) of 10, which suggests that it can be an excellent candidate for phage therapy. |
Papadogiannis, Vasileios; Pennati, Alessandro; Parker, Hugo J; Rothbächer, Ute; Patthey, Cedric; Bronner, Marianne E; Shimeld, Sebastian M Hmx gene conservation identifies the origin of vertebrate cranial ganglia Journal Article Nature, 605 (7911), pp. 701–705, 2022, ISSN: 0028-0836, 1476-4687. @article{papadogiannis_hmx_2022, title = {Hmx gene conservation identifies the origin of vertebrate cranial ganglia}, author = {Vasileios Papadogiannis and Alessandro Pennati and Hugo J Parker and Ute Rothbächer and Cedric Patthey and Marianne E Bronner and Sebastian M Shimeld}, url = {https://www.nature.com/articles/s41586-022-04742-w.epdf?sharing_token=0xZJF5h0PJfpVUdefAf4R9RgN0jAjWel9jnR3ZoTv0PSCAbGc3qtbGpsTuLrcmb7ttAtuhgvjAvX1_k8Ag7g7vn007aa4q9FN_-aaVkwteXRU-W2Z6yGfxXTk4K9POn9sdB02QtTVBOCYrkTIU4SKKE5Vu5NqJLHbbWXMbZGPEI%3D https://www.nature.com/articles/s41586-022-04742-w}, doi = {10.1038/s41586-022-04742-w}, issn = {0028-0836, 1476-4687}, year = {2022}, date = {2022-05-01}, urldate = {2022-07-29}, journal = {Nature}, volume = {605}, number = {7911}, pages = {701--705}, 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 Pan‐European phylogeography of the European roe deer ( textitCapreolus capreolus ) Journal Article Ecology and Evolution, 12 (5), 2022, ISSN: 2045-7758, 2045-7758. @article{plis_paneuropean_2022, title = {Pan‐European phylogeography of the European roe deer ( textitCapreolus capreolus )}, 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://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Pils-Ecology-and-Evolution-43.pdf https://onlinelibrary.wiley.com/doi/10.1002/ece3.8931}, doi = {10.1002/ece3.8931}, issn = {2045-7758, 2045-7758}, year = {2022}, date = {2022-05-01}, urldate = {2022-07-29}, journal = {Ecology and Evolution}, volume = {12}, number = {5}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Smyrli, Maria; Anka, Ishrat Zahan; Koutsoni, Olga; Dotsika, Eleni; Kyriazis, Ioannis D; Pavlidis, Michail; Katharios, Pantelis Development of autogenous vaccines for farmed European seabass against Aeromonas veronii using zebrafish as a model for efficacy assessment Journal Article Fish & Shellfish Immunology, 123 , pp. 381–387, 2022, ISSN: 10504648. @article{smyrli_development_2022, title = {Development of autogenous vaccines for farmed European seabass against Aeromonas veronii using zebrafish as a model for efficacy assessment}, author = {Maria Smyrli and Ishrat Zahan Anka and Olga Koutsoni and Eleni Dotsika and Ioannis D Kyriazis and Michail Pavlidis and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Smyrli-FSImmune-24-pre-print.pdf https://linkinghub.elsevier.com/retrieve/pii/S1050464822001450}, doi = {10.1016/j.fsi.2022.03.019}, issn = {10504648}, year = {2022}, date = {2022-04-01}, urldate = {2022-05-09}, journal = {Fish & Shellfish Immunology}, volume = {123}, pages = {381--387}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Formenti Giulio; Secomandi, Simona; Studer Bruno; Theodoridis Spyros; Thines Marco; Urban Lara;Theissinger Kathrin; Manousaki Tereza; Wörheide Gert; Wurm Yannick; Zammit Gabrielle... The era of reference genomes in conservation genomics Journal Article Trends in Ecology & Evolution, 37 , pp. 197-202, 2022, ISSN: 01695347. @article{FormentiGiulio2022, title = {The era of reference genomes in conservation genomics}, author = {Formenti, Giulio; Secomandi, Simona; Studer, Bruno; Theodoridis, Spyros; Thines, Marco; Urban, Lara;Theissinger, Kathrin; Manousaki, Tereza; Wörheide, Gert; Wurm, Yannick; Zammit, Gabrielle...}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Formenti-Trends-in-EE-10-1.pdf}, doi = {10.1016/j.tree.2021.11.008}, issn = {01695347}, year = {2022}, date = {2022-03-05}, journal = {Trends in Ecology & Evolution}, volume = {37}, pages = {197-202}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bouranta, Andrianna; Tudose, Ioan Valentin; Georgescu, Luciana; Karaiskou, Anna; Vrithias, Nikolaos Rafail; Viskadourakis, Zacharias; Kenanakis, George; Sfakaki, Efsevia; Mitrizakis, Nikolaos; Strakantounas, George; Papandroulakis, Nikolaos; Romanitan, Cosmin; Pachiu, Cristina; Tutunaru, Oana; Barbu-Tudoran, Lucian; Suchea, Mirela Petruta; Koudoumas, Emmanouel 3D Printed Metal Oxide-Polymer Composite Materials for Antifouling Applications Journal Article Nanomaterials, 12 (6), pp. 917, 2022, ISSN: 2079-4991. @article{bouranta_3d_2022, title = {3D Printed Metal Oxide-Polymer Composite Materials for Antifouling Applications}, author = {Andrianna Bouranta and Ioan Valentin Tudose and Luciana Georgescu and Anna Karaiskou and Nikolaos Rafail Vrithias and Zacharias Viskadourakis and George Kenanakis and Efsevia Sfakaki and Nikolaos Mitrizakis and George Strakantounas and Nikolaos Papandroulakis and Cosmin Romanitan and Cristina Pachiu and Oana Tutunaru and Lucian Barbu-Tudoran and Mirela Petruta Suchea and Emmanouel Koudoumas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Bouranta-nanomaterials-19.pdf https://www.mdpi.com/2079-4991/12/6/917}, doi = {10.3390/nano12060917}, issn = {2079-4991}, year = {2022}, date = {2022-03-01}, urldate = {2022-05-09}, journal = {Nanomaterials}, volume = {12}, number = {6}, pages = {917}, abstract = {Current technology to prevent biofouling usually relies on the use of toxic, biocide-containing materials, which can become a serious threat to marine ecosystems, affecting both targeted and nontargeted organisms. Therefore, the development of broad-spectrum, less toxic antifouling materials is a challenge for researchers; such materials would be quite important in applications like aquaculture. In this respect, surface chemistry, physical properties, durability and attachment scheme can play a vital role in the performance of the materials. In this work, acrylonitrile butadiene styrene (ABS)/micro ZnO or nano ZnO composite lattices with different metal oxide contents were developed using 3D printing. Their antifouling behavior was examined with respect to aquaculture applications by monitoring growth on them of the diatoms Navicula sp. and the monocellular algae Chlorella sp. with image analysis techniques. As shown, the presence of metal oxides in the composite materials can bring about antifouling ability at particular concentrations. The present study showed promising results, but further improvements are needed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Current technology to prevent biofouling usually relies on the use of toxic, biocide-containing materials, which can become a serious threat to marine ecosystems, affecting both targeted and nontargeted organisms. Therefore, the development of broad-spectrum, less toxic antifouling materials is a challenge for researchers; such materials would be quite important in applications like aquaculture. In this respect, surface chemistry, physical properties, durability and attachment scheme can play a vital role in the performance of the materials. In this work, acrylonitrile butadiene styrene (ABS)/micro ZnO or nano ZnO composite lattices with different metal oxide contents were developed using 3D printing. Their antifouling behavior was examined with respect to aquaculture applications by monitoring growth on them of the diatoms Navicula sp. and the monocellular algae Chlorella sp. with image analysis techniques. As shown, the presence of metal oxides in the composite materials can bring about antifouling ability at particular concentrations. The present study showed promising results, but further improvements are needed. |
Cascarano, Maria Chiara; Ruetten, Maja; Vaughan, Lloyd; Tsertou, Maria Ioanna; Georgopoulou, Dimitra; Keklikoglou, Kleoniki; Papandroulakis, Nikos; Katharios, Pantelis Epitheliocystis in Greater Amberjack: Evidence of a Novel Causative Agent, Pathology, Immune Response and Epidemiological Findings Journal Article Microorganisms, 10 (3), pp. 627, 2022, ISSN: 2076-2607. @article{cascarano_epitheliocystis_2022, title = {Epitheliocystis in Greater Amberjack: Evidence of a Novel Causative Agent, Pathology, Immune Response and Epidemiological Findings}, author = {Maria Chiara Cascarano and Maja Ruetten and Lloyd Vaughan and Maria Ioanna Tsertou and Dimitra Georgopoulou and Kleoniki Keklikoglou and Nikos Papandroulakis and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Cascarano-Microorganisms-20.pdf https://www.mdpi.com/2076-2607/10/3/627}, doi = {10.3390/microorganisms10030627}, issn = {2076-2607}, year = {2022}, date = {2022-03-01}, urldate = {2022-05-09}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {627}, abstract = {Epitheliocystis is a fish gill disease caused by a broad range of intracellular bacteria infecting freshwater and marine fish worldwide. Here we report the occurrence and progression of epitheliocystis in greater amberjack reared in Crete (Greece). The disease appears to be caused mainly by a novel Betaproteobacteria belonging to the Candidatus Ichthyocystis genus with a second agent genetically similar to Ca. Parilichlamydia carangidicola coinfecting the gills in some cases. After a first detection of the disease in 2017, we investigated epitheliocystis in the following year’s cohort of greater amberjack juveniles (cohort 2018) transferred from inland tanks to the same cage farm in the open sea where the first outbreak was detected. This cohort was monitored for over a year together with stocks of gilthead seabream and meagre co-farmed in the same area. Our observations showed that epitheliocystis could be detected in greater amberjack gills as early as a month following the transfer to sea cages, with ionocytes at the base of the gill lamellae being initially infected. Cyst formation appears to trigger a proliferative response, leading to the fusion of lamellae, impairment of gill functions and subsequently to mortality. Lesions are characterized by infiltration of immune cells, indicating activation of the innate immune response. At later stages of the outbreak, cysts were no longer found in ionocytes but were observed in mucocytes at the trailing edge of the filament. Whole cysts appeared finally to be expelled from infected mucocytes directly into the water, which might constitute a novel means of dispersion of the infectious agents. Molecular screening indicates that meagre is not affected by this disease and confirms the presence of previously described epitheliocystis agents, Ca. Ichthyocystis sparus, Ca. Ichthyocystis hellenicum and Ca. Similichlamydia spp., in gilthead seabream. Prevalence data show that the bacteria persist in both gilthead seabream and greater amberjack cohorts after first infection.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Epitheliocystis is a fish gill disease caused by a broad range of intracellular bacteria infecting freshwater and marine fish worldwide. Here we report the occurrence and progression of epitheliocystis in greater amberjack reared in Crete (Greece). The disease appears to be caused mainly by a novel Betaproteobacteria belonging to the Candidatus Ichthyocystis genus with a second agent genetically similar to Ca. Parilichlamydia carangidicola coinfecting the gills in some cases. After a first detection of the disease in 2017, we investigated epitheliocystis in the following year’s cohort of greater amberjack juveniles (cohort 2018) transferred from inland tanks to the same cage farm in the open sea where the first outbreak was detected. This cohort was monitored for over a year together with stocks of gilthead seabream and meagre co-farmed in the same area. Our observations showed that epitheliocystis could be detected in greater amberjack gills as early as a month following the transfer to sea cages, with ionocytes at the base of the gill lamellae being initially infected. Cyst formation appears to trigger a proliferative response, leading to the fusion of lamellae, impairment of gill functions and subsequently to mortality. Lesions are characterized by infiltration of immune cells, indicating activation of the innate immune response. At later stages of the outbreak, cysts were no longer found in ionocytes but were observed in mucocytes at the trailing edge of the filament. Whole cysts appeared finally to be expelled from infected mucocytes directly into the water, which might constitute a novel means of dispersion of the infectious agents. Molecular screening indicates that meagre is not affected by this disease and confirms the presence of previously described epitheliocystis agents, Ca. Ichthyocystis sparus, Ca. Ichthyocystis hellenicum and Ca. Similichlamydia spp., in gilthead seabream. Prevalence data show that the bacteria persist in both gilthead seabream and greater amberjack cohorts after first infection. |
Cascarano, Maria Chiara; Katharios, Pantelis Expansion of the Beta-Proteobacterial Genus Ca. Ichthyocystis: A Case Report of Epitheliocystis in the Pompano Trachinotus ovatus Journal Article Pathogens, 11 (4), pp. 421, 2022, ISSN: 2076-0817. @article{cascarano_expansion_2022, title = {Expansion of the Beta-Proteobacterial Genus Ca. Ichthyocystis: A Case Report of Epitheliocystis in the Pompano Trachinotus ovatus}, author = {Maria Chiara Cascarano and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Cascarano-Pathogens-28.pdf https://www.mdpi.com/2076-0817/11/4/421}, doi = {10.3390/pathogens11040421}, issn = {2076-0817}, year = {2022}, date = {2022-03-01}, urldate = {2022-05-09}, journal = {Pathogens}, volume = {11}, number = {4}, pages = {421}, abstract = {Epitheliocystis is a disease caused by a wide variety of host-specific intracellular bacteria infecting fish gills. In the Mediterranean Sea, epitheliocystis has been recently associated with a novel genus of beta-proteobacteria, the Ca. Ichthyocystis genus. In the present study, we report a case of epitheliocystis in a wild-caught specimen of pompano Trachinotus ovatus in Crete, Greece. Molecular analysis of partial 16s rRNA sequence led to the discovery of a putative novel species of the Ca. Ichthyocystis genus. Investigation of the phylogenetic relationship between closely related sequences deposited in NCBI suggests that bacterial ancestors in gilthead seabream might have a pivotal role in the differentiation of genus.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Epitheliocystis is a disease caused by a wide variety of host-specific intracellular bacteria infecting fish gills. In the Mediterranean Sea, epitheliocystis has been recently associated with a novel genus of beta-proteobacteria, the Ca. Ichthyocystis genus. In the present study, we report a case of epitheliocystis in a wild-caught specimen of pompano Trachinotus ovatus in Crete, Greece. Molecular analysis of partial 16s rRNA sequence led to the discovery of a putative novel species of the Ca. Ichthyocystis genus. Investigation of the phylogenetic relationship between closely related sequences deposited in NCBI suggests that bacterial ancestors in gilthead seabream might have a pivotal role in the differentiation of genus. |
Vela-Avitúa, Sergio; Thorland, Ingunn; Bakopoulos, Vasileios; Papanna, Kantham; Dimitroglou, Arkadios; Kottaras, Eleftherios; Leonidas, Papaharisis; Guinand, Bruno; Tsigenopoulos, Costas S; Aslam, Muhammad L Frontiers in Genetics, 13 , pp. 804584, 2022, ISSN: 1664-8021. @article{vela-avitua_genetic_2022, title = {Genetic Basis for Resistance Against Viral Nervous Necrosis: GWAS and Potential of Genomic Prediction Explored in Farmed European Sea Bass (Dicentrarchus labrax)}, author = {Sergio Vela-Avitúa and Ingunn Thorland and Vasileios Bakopoulos and Kantham Papanna and Arkadios Dimitroglou and Eleftherios Kottaras and Papaharisis Leonidas and Bruno Guinand and Costas S Tsigenopoulos and Muhammad L Aslam}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Vela-Avitua-Frontiers-in-Gen-26.pdf}, doi = {10.3389/fgene.2022.804584}, issn = {1664-8021}, year = {2022}, date = {2022-03-01}, urldate = {2022-05-09}, journal = {Frontiers in Genetics}, volume = {13}, pages = {804584}, abstract = {Viral nervous necrosis (VNN) is an infectious disease caused by the red-spotted grouper nervous necrosis virus (RGNNV) in European sea bass and is considered a serious concern for the aquaculture industry with fry and juveniles being highly susceptible. To understand the genetic basis for resistance against VNN, a survival phenotype through the challenge test against the RGNNV was recorded in populations from multiple year classes (YC2016 and YC2017). A total of 4,851 individuals from 181 families were tested, and a subset (n∼1,535) belonging to 122 families was genotyped using a ∼57K Affymetrix Axiom array. The survival against the RGNNV showed low to moderate heritability with observed scale estimates of 0.18 and 0.25 obtained using pedigree vs. genomic information, respectively. The genome-wide association analysis showed a strong signal of quantitative trait loci (QTL) at LG12 which explained ∼33% of the genetic variance. The QTL region contained multiple genes ( ITPK1 , PLK4 , HSPA4L , REEP1 , CHMP2 , MRPL35 , and SCUBE ) with HSPA4L and/or REEP1 genes being highly relevant with a likely effect on host response in managing disease-associated symptoms. The results on the accuracy of predicting breeding values presented 20–43% advantage in accuracy using genomic over pedigree-based information which varied across model types and applied validation schemes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Viral nervous necrosis (VNN) is an infectious disease caused by the red-spotted grouper nervous necrosis virus (RGNNV) in European sea bass and is considered a serious concern for the aquaculture industry with fry and juveniles being highly susceptible. To understand the genetic basis for resistance against VNN, a survival phenotype through the challenge test against the RGNNV was recorded in populations from multiple year classes (YC2016 and YC2017). A total of 4,851 individuals from 181 families were tested, and a subset (n∼1,535) belonging to 122 families was genotyped using a ∼57K Affymetrix Axiom array. The survival against the RGNNV showed low to moderate heritability with observed scale estimates of 0.18 and 0.25 obtained using pedigree vs. genomic information, respectively. The genome-wide association analysis showed a strong signal of quantitative trait loci (QTL) at LG12 which explained ∼33% of the genetic variance. The QTL region contained multiple genes ( ITPK1 , PLK4 , HSPA4L , REEP1 , CHMP2 , MRPL35 , and SCUBE ) with HSPA4L and/or REEP1 genes being highly relevant with a likely effect on host response in managing disease-associated symptoms. The results on the accuracy of predicting breeding values presented 20–43% advantage in accuracy using genomic over pedigree-based information which varied across model types and applied validation schemes. |
Cheimonopoulou, Maria; Koulouri, Panayota; Previati, Monica; Realdon, Giulia; Mokos, Melita; Mogias, Athanasios Implementation of a new research tool for evaluating Mediterranean Sea Literacy (MSL) of high school students: A pilot study Journal Article Mediterranean Marine Science, 23 (2), pp. 302–309, 2022, ISSN: 1791-6763, 1108-393X. @article{cheimonopoulou_implementation_2022, title = {Implementation of a new research tool for evaluating Mediterranean Sea Literacy (MSL) of high school students: A pilot study}, author = {Maria Cheimonopoulou and Panayota Koulouri and Monica Previati and Giulia Realdon and Melita Mokos and Athanasios Mogias}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Cheimonopoulou-MedMarSci-32-1.pdf https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/29712}, doi = {10.12681/mms.29712}, issn = {1791-6763, 1108-393X}, year = {2022}, date = {2022-03-01}, urldate = {2022-05-09}, journal = {Mediterranean Marine Science}, volume = {23}, number = {2}, pages = {302--309}, abstract = {The Mediterranean Sea is recognized as a key component in the development, economy, and culture of European, North African, and Middle East countries. With respect to heterogeneity across the region in different sectors, Ocean Literacy, though still in its infancy, is nevertheless a requisite for a better understanding of the two-way interaction between the Sea and its people. In the present study, marine issues in relation to the content knowledge of 154 high school students from the Mediterranean region were investigated by using a structured questionnaire based on the recently published Mediterranean Sea Literacy guide. Data analysis involved descriptive statistics to portray frequencies and knowledge scores of the participants, and inferential statistics to assess the effects of grade level on students’ knowledge. The study which focused for the first time on the unique features of the Mediterranean marine ecosystems, found the level of content knowledge of the participants to be low to moderate. It is therefore of the utmost importance for the organizations and networks working on marine issues in the Mediterranean Sea to develop synergies and coordinate research programmes to broaden engagement with human societies in the region.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Mediterranean Sea is recognized as a key component in the development, economy, and culture of European, North African, and Middle East countries. With respect to heterogeneity across the region in different sectors, Ocean Literacy, though still in its infancy, is nevertheless a requisite for a better understanding of the two-way interaction between the Sea and its people. In the present study, marine issues in relation to the content knowledge of 154 high school students from the Mediterranean region were investigated by using a structured questionnaire based on the recently published Mediterranean Sea Literacy guide. Data analysis involved descriptive statistics to portray frequencies and knowledge scores of the participants, and inferential statistics to assess the effects of grade level on students’ knowledge. The study which focused for the first time on the unique features of the Mediterranean marine ecosystems, found the level of content knowledge of the participants to be low to moderate. It is therefore of the utmost importance for the organizations and networks working on marine issues in the Mediterranean Sea to develop synergies and coordinate research programmes to broaden engagement with human societies in the region. |
Nomikou, Paraskevi; Polymenakou, Paraskevi N; Rizzo, Andrea Luca; Petersen, Sven; Hannington, Mark; Kilias, Stephanos Pantelis; Papanikolaou, Dimitris; Escartin, Javier; Karantzalos, Konstantinos; Mertzimekis, Theodoros J; Antoniou, Varvara; Krokos, Mel; Grammatikopoulos, Lazaros; Italiano, Francesco; Caruso, Cinzia Giuseppina; Lazzaro, Gianluca; Longo, Manfredi; Scappuzzo, Sergio Sciré; D’Alessandro, Walter; Grassa, Fausto; Bejelou, Konstantina; Lampridou, Danai; Katsigera, Anna; Dura, Anne SANTORY: SANTORini’s Seafloor Volcanic ObservatorY Journal Article Frontiers in Marine Science, 9 , pp. 796376, 2022, ISSN: 2296-7745. @article{nomikou_santory_2022, title = {SANTORY: SANTORini’s Seafloor Volcanic ObservatorY}, author = {Paraskevi Nomikou and Paraskevi N Polymenakou and Andrea Luca Rizzo and Sven Petersen and Mark Hannington and Stephanos Pantelis Kilias and Dimitris Papanikolaou and Javier Escartin and Konstantinos Karantzalos and Theodoros J Mertzimekis and Varvara Antoniou and Mel Krokos and Lazaros Grammatikopoulos and Francesco Italiano and Cinzia Giuseppina Caruso and Gianluca Lazzaro and Manfredi Longo and Sergio Sciré Scappuzzo and Walter D’Alessandro and Fausto Grassa and Konstantina Bejelou and Danai Lampridou and Anna Katsigera and Anne Dura}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Nomikou-FroMarSci-31.pdf https://www.frontiersin.org/articles/10.3389/fmars.2022.796376/full}, doi = {10.3389/fmars.2022.796376}, issn = {2296-7745}, year = {2022}, date = {2022-03-01}, urldate = {2022-05-09}, journal = {Frontiers in Marine Science}, volume = {9}, pages = {796376}, abstract = {Submarine hydrothermal systems along active volcanic ridges and arcs are highly dynamic, responding to both oceanographic (e.g., currents, tides) and deep-seated geological forcing (e.g., magma eruption, seismicity, hydrothermalism, and crustal deformation, etc.). In particular, volcanic and hydrothermal activity may also pose profoundly negative societal impacts (tsunamis, the release of climate-relevant gases and toxic metal(loid)s). These risks are particularly significant in shallow (<1000m) coastal environments, as demonstrated by the January 2022 submarine paroxysmal eruption by the Hunga Tonga-Hunga Ha’apai Volcano that destroyed part of the island, and the October 2011 submarine eruption of El Hierro (Canary Islands) that caused vigorous upwelling, floating lava bombs, and natural seawater acidification. Volcanic hazards may be posed by the Kolumbo submarine volcano, which is part of the subduction-related Hellenic Volcanic Arc at the intersection between the Eurasian and African tectonic plates. There, the Kolumbo submarine volcano, 7 km NE of Santorini and part of Santorini’s volcanic complex, hosts an active hydrothermal vent field (HVF) on its crater floor (textasciitilde500m b.s.l.), which degasses boiling CO 2 –dominated fluids at high temperatures (textasciitilde265°C) with a clear mantle signature. Kolumbo’s HVF hosts actively forming seafloor massive sulfide deposits with high contents of potentially toxic, volatile metal(loid)s (As, Sb, Pb, Ag, Hg, and Tl). The proximity to highly populated/tourist areas at Santorini poses significant risks. However, we have limited knowledge of the potential impacts of this type of magmatic and hydrothermal activity, including those from magmatic gases and seismicity. To better evaluate such risks the activity of the submarine system must be continuously monitored with multidisciplinary and high resolution instrumentation as part of an in-situ observatory supported by discrete sampling and measurements. This paper is a design study that describes a new long-term seafloor observatory that will be installed within the Kolumbo volcano, including cutting-edge and innovative marine-technology that integrates hyperspectral imaging, temperature sensors, a radiation spectrometer, fluid/gas samplers, and pressure gauges. These instruments will be integrated into a hazard monitoring platform aimed at identifying the precursors of potentially disastrous explosive volcanic eruptions, earthquakes, landslides of the hydrothermally weakened volcanic edifice and the release of potentially toxic elements into the water column.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Submarine hydrothermal systems along active volcanic ridges and arcs are highly dynamic, responding to both oceanographic (e.g., currents, tides) and deep-seated geological forcing (e.g., magma eruption, seismicity, hydrothermalism, and crustal deformation, etc.). In particular, volcanic and hydrothermal activity may also pose profoundly negative societal impacts (tsunamis, the release of climate-relevant gases and toxic metal(loid)s). These risks are particularly significant in shallow (<1000m) coastal environments, as demonstrated by the January 2022 submarine paroxysmal eruption by the Hunga Tonga-Hunga Ha’apai Volcano that destroyed part of the island, and the October 2011 submarine eruption of El Hierro (Canary Islands) that caused vigorous upwelling, floating lava bombs, and natural seawater acidification. Volcanic hazards may be posed by the Kolumbo submarine volcano, which is part of the subduction-related Hellenic Volcanic Arc at the intersection between the Eurasian and African tectonic plates. There, the Kolumbo submarine volcano, 7 km NE of Santorini and part of Santorini’s volcanic complex, hosts an active hydrothermal vent field (HVF) on its crater floor (textasciitilde500m b.s.l.), which degasses boiling CO 2 –dominated fluids at high temperatures (textasciitilde265°C) with a clear mantle signature. Kolumbo’s HVF hosts actively forming seafloor massive sulfide deposits with high contents of potentially toxic, volatile metal(loid)s (As, Sb, Pb, Ag, Hg, and Tl). The proximity to highly populated/tourist areas at Santorini poses significant risks. However, we have limited knowledge of the potential impacts of this type of magmatic and hydrothermal activity, including those from magmatic gases and seismicity. To better evaluate such risks the activity of the submarine system must be continuously monitored with multidisciplinary and high resolution instrumentation as part of an in-situ observatory supported by discrete sampling and measurements. This paper is a design study that describes a new long-term seafloor observatory that will be installed within the Kolumbo volcano, including cutting-edge and innovative marine-technology that integrates hyperspectral imaging, temperature sensors, a radiation spectrometer, fluid/gas samplers, and pressure gauges. These instruments will be integrated into a hazard monitoring platform aimed at identifying the precursors of potentially disastrous explosive volcanic eruptions, earthquakes, landslides of the hydrothermally weakened volcanic edifice and the release of potentially toxic elements into the water column. |
Mammola, Stefano; Meierhofer, Melissa B; Borges, Paulo A V; Colado, Raquel; Culver, David C; Deharveng, Louis; Delić, Teo; Lorenzo, Tiziana Di; Dražina, Tvrtko; Ferreira, Rodrigo L; Fiasca, Barbara; Fišer, Cene; Galassi, Diana M P; Garzoli, Laura; Gerovasileiou, Vasilis; Griebler, Christian; Halse, Stuart; Howarth, Francis G; Isaia, Marco; Johnson, Joseph S; Komerički, Ana; Martínez, Alejandro; Milano, Filippo; Moldovan, Oana T; Nanni, Veronica; Nicolosi, Giuseppe; Niemiller, Matthew L; Pallarés, Susana; Pavlek, Martina; Piano, Elena; Pipan, Tanja; Sanchez‐Fernandez, David; Santangeli, Andrea; Schmidt, Susanne I; Wynne, Judson J; Zagmajster, Maja; Zakšek, Valerija; Cardoso, Pedro Towards evidence‐based conservation of subterranean ecosystems Journal Article Biological Reviews, pp. brv.12851, 2022, ISSN: 1464-7931, 1469-185X. @article{mammola_towards_2022, title = {Towards evidence‐based conservation of subterranean ecosystems}, author = {Stefano Mammola and Melissa B Meierhofer and Paulo A V Borges and Raquel Colado and David C Culver and Louis Deharveng and Teo Delić and Tiziana Di Lorenzo and Tvrtko Dražina and Rodrigo L Ferreira and Barbara Fiasca and Cene Fišer and Diana M P Galassi and Laura Garzoli and Vasilis Gerovasileiou and Christian Griebler and Stuart Halse and Francis G Howarth and Marco Isaia and Joseph S Johnson and Ana Komerički and Alejandro Martínez and Filippo Milano and Oana T Moldovan and Veronica Nanni and Giuseppe Nicolosi and Matthew L Niemiller and Susana Pallarés and Martina Pavlek and Elena Piano and Tanja Pipan and David Sanchez‐Fernandez and Andrea Santangeli and Susanne I Schmidt and Judson J Wynne and Maja Zagmajster and Valerija Zakšek and Pedro Cardoso}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Mammola-Biological-Reviews-25.pdf}, doi = {10.1111/brv.12851}, issn = {1464-7931, 1469-185X}, year = {2022}, date = {2022-03-01}, urldate = {2022-05-09}, journal = {Biological Reviews}, pages = {brv.12851}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Grau, Amalia; Villalba, Antonio; Navas, José I; Hansjosten, Beatriz; Valencia, José M; García-March, José R; Prado, Patricia; Follana-Berná, Guillermo; Morage, Titouan; Vázquez-Luis, Maite; Álvarez, Elvira; Katharios, Pantelis; Pavloudi, Christina; Nebot-Colomer, Elisabet; Tena-Medialdea, José; Lopez-Sanmartín, Monserrat; Peyran, Claire; Čižmek, Hrvoje; Sarafidou, Georgia; Issaris, Yiannis; Tüney-Kizilkaya, Inci; Deudero, Salud; Planes, Serge; Catanese, Gaetano Wide-Geographic and Long-Term Analysis of the Role of Pathogens in the Decline of Pinna nobilis to Critically Endangered Species Journal Article Frontiers in Marine Science, 9 , pp. 666640, 2022, ISSN: 2296-7745. @article{grau_wide-geographic_2022, title = {Wide-Geographic and Long-Term Analysis of the Role of Pathogens in the Decline of Pinna nobilis to Critically Endangered Species}, author = {Amalia Grau and Antonio Villalba and José I Navas and Beatriz Hansjosten and José M Valencia and José R García-March and Patricia Prado and Guillermo Follana-Berná and Titouan Morage and Maite Vázquez-Luis and Elvira Álvarez and Pantelis Katharios and Christina Pavloudi and Elisabet Nebot-Colomer and José Tena-Medialdea and Monserrat Lopez-Sanmartín and Claire Peyran and Hrvoje Čižmek and Georgia Sarafidou and Yiannis Issaris and Inci Tüney-Kizilkaya and Salud Deudero and Serge Planes and Gaetano Catanese}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Grau-FMSci-21.pdf https://www.frontiersin.org/articles/10.3389/fmars.2022.666640/full}, doi = {10.3389/fmars.2022.666640}, issn = {2296-7745}, year = {2022}, date = {2022-03-01}, urldate = {2022-05-09}, journal = {Frontiers in Marine Science}, volume = {9}, pages = {666640}, abstract = {A mass mortality event (MME) affecting the fan mussel Pinna nobilis was first detected in Spain in autumn 2016 and spread north- and eastward through the Mediterranean Sea. Various pathogens have been blamed for contributing to the MME, with emphasis in Haplosporidium pinnae , Mycobacterium sp. and Vibrio spp. In this study, samples from 762 fan mussels (necropsies from 263 individuals, mantle biopsies from 499) of various health conditions, with wide geographic and age range, taken before and during the MME spread from various environments along Mediterranean Sea, were used to assess the role of pathogens in the MME. The number of samples processed by both histological and molecular methods was 83. The most important factor playing a main role on the onset of the mass mortality of P. nobilis throughout the Mediterranean Sea was the infection by H. pinnae . It was the only non-detected pathogen before the MME while, during MME spreading, its prevalence was higher in sick and dead individuals than in asymptomatic ones, in MME-affected areas than in non-affected sites, and it was not associated with host size, infecting both juveniles and adults. Conversely, infection with mycobacteria was independent from the period (before or during MME), from the affection of the area by MME and from the host health condition, and it was associated with host size. Gram (-) bacteria neither appeared associated with MME.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A mass mortality event (MME) affecting the fan mussel Pinna nobilis was first detected in Spain in autumn 2016 and spread north- and eastward through the Mediterranean Sea. Various pathogens have been blamed for contributing to the MME, with emphasis in Haplosporidium pinnae , Mycobacterium sp. and Vibrio spp. In this study, samples from 762 fan mussels (necropsies from 263 individuals, mantle biopsies from 499) of various health conditions, with wide geographic and age range, taken before and during the MME spread from various environments along Mediterranean Sea, were used to assess the role of pathogens in the MME. The number of samples processed by both histological and molecular methods was 83. The most important factor playing a main role on the onset of the mass mortality of P. nobilis throughout the Mediterranean Sea was the infection by H. pinnae . It was the only non-detected pathogen before the MME while, during MME spreading, its prevalence was higher in sick and dead individuals than in asymptomatic ones, in MME-affected areas than in non-affected sites, and it was not associated with host size, infecting both juveniles and adults. Conversely, infection with mycobacteria was independent from the period (before or during MME), from the affection of the area by MME and from the host health condition, and it was associated with host size. Gram (-) bacteria neither appeared associated with MME. |
Fountoulaki, E; Vasilaki, A; Nikolopoulou, D; Schrama, J; Kaushik, S J; Prabhu, Antony Jesu P Faecal waste production, characteristics and recovery in European seabass (Dicentrarchus labrax) is affected by dietary ingredient composition Journal Article Aquaculture, 548 , pp. 737582, 2022, ISSN: 00448486. @article{fountoulaki_faecal_2022b, title = {Faecal waste production, characteristics and recovery in European seabass (Dicentrarchus labrax) is affected by dietary ingredient composition}, author = {E Fountoulaki and A Vasilaki and D Nikolopoulou and J Schrama and S J Kaushik and P Antony Jesu Prabhu}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Fountoulaki-AQUA-preprint-1.pdf https://linkinghub.elsevier.com/retrieve/pii/S004484862101245X}, doi = {10.1016/j.aquaculture.2021.737582}, issn = {00448486}, year = {2022}, date = {2022-02-01}, urldate = {2022-03-11}, journal = {Aquaculture}, volume = {548}, pages = {737582}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bolgan, Marta; Iorio, Lucia Di; Dailianis, Thanos; Catalan, Ignacio A; Lejeune, Pierre; Picciulin, Marta; Parmentier, Eric Fish acoustic community structure in Neptune seagrass meadows across the Mediterranean basin Journal Article Aquatic Conservation: Marine and Freshwater Ecosystems, 32 (2), pp. 329–347, 2022, ISSN: 1052-7613, 1099-0755. @article{bolgan_fish_2022, title = {Fish acoustic community structure in Neptune seagrass meadows across the Mediterranean basin}, author = {Marta Bolgan and Lucia Di Iorio and Thanos Dailianis and Ignacio A Catalan and Pierre Lejeune and Marta Picciulin and Eric Parmentier}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Bolgan-AqCon-15-pre-print.pdf https://onlinelibrary.wiley.com/doi/10.1002/aqc.3764}, doi = {10.1002/aqc.3764}, issn = {1052-7613, 1099-0755}, year = {2022}, date = {2022-02-01}, urldate = {2022-03-11}, journal = {Aquatic Conservation: Marine and Freshwater Ecosystems}, volume = {32}, number = {2}, pages = {329--347}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kogiannou, Dimitra; Kotsiri, Mado; Grigorakis, Kriton A method to assess gaping in Sparidae species fillets Journal Article Aquaculture Research, 53 (2), pp. 689–693, 2022, ISSN: 1355-557X, 1365-2109. @article{kogiannou_method_2022, title = {A method to assess gaping in Sparidae species fillets}, author = {Dimitra Kogiannou and Mado Kotsiri and Kriton Grigorakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Kogianou-ARE-preprint-88.pdf https://onlinelibrary.wiley.com/doi/10.1111/are.15590}, doi = {10.1111/are.15590}, issn = {1355-557X, 1365-2109}, year = {2022}, date = {2022-01-01}, urldate = {2022-01-12}, journal = {Aquaculture Research}, volume = {53}, number = {2}, pages = {689--693}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Varamogianni-Mamatsi, Despoina; Anastasiou, Thekla I; Vernadou, Emmanouela; Papandroulakis, Nikos; Kalogerakis, Nicolas; Dailianis, Thanos; Mandalakis, Manolis A Multi-Species Investigation of Sponges’ Filtering Activity towards Marine Microalgae Journal Article Marine Drugs, 20 (1), pp. 24, 2022, ISSN: 1660-3397. @article{varamogianni-mamatsi_multi-species_2022, title = {A Multi-Species Investigation of Sponges’ Filtering Activity towards Marine Microalgae}, author = {Despoina Varamogianni-Mamatsi and Thekla I Anastasiou and Emmanouela Vernadou and Nikos Papandroulakis and Nicolas Kalogerakis and Thanos Dailianis and Manolis Mandalakis}, url = {https://www.mdpi.com/1660-3397/20/1/24}, doi = {10.3390/md20010024}, issn = {1660-3397}, year = {2022}, date = {2022-01-01}, urldate = {2022-02-28}, journal = {Marine Drugs}, volume = {20}, number = {1}, pages = {24}, abstract = {Chronic discharge of surplus organic matter is a typical side effect of fish aquaculture, occasionally leading to coastal eutrophication and excessive phytoplankton growth. Owing to their innate filter-feeding capacity, marine sponges could mitigate environmental impact under integrated multitrophic aquaculture (IMTA) scenarios. Herein, we investigated the clearance capacity of four ubiquitous Mediterranean sponges (Agelas oroides, Axinella cannabina, Chondrosia reniformis and Sarcotragus foetidus) against three microalgal substrates with different size/motility characteristics: the nanophytoplankton Nannochloropsis sp. (textasciitilde3.2 μm, nonmotile) and Isochrysis sp. (textasciitilde3.8 μm, motile), as well as the diatom Phaeodactylum tricornutum (textasciitilde21.7 μm, nonmotile). In vitro cleaning experiments were conducted using sponge explants in 1 L of natural seawater and applying different microalgal cell concentrations under light/dark conditions. The investigated sponges exhibited a wide range of retention efficiencies for the different phytoplankton cells, with the lowest average values found for A. cannabina (37%) and the highest for A. oroides (70%). The latter could filter up to 14.1 mL seawater per hour and gram of sponge wet weight, by retaining 100% of Isochrysis at a density of 105 cells mL−1, under darkness. Our results highlight differences in filtering capacity among sponge species and preferences for microalgal substrates with distinct size and motility traits.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Chronic discharge of surplus organic matter is a typical side effect of fish aquaculture, occasionally leading to coastal eutrophication and excessive phytoplankton growth. Owing to their innate filter-feeding capacity, marine sponges could mitigate environmental impact under integrated multitrophic aquaculture (IMTA) scenarios. Herein, we investigated the clearance capacity of four ubiquitous Mediterranean sponges (Agelas oroides, Axinella cannabina, Chondrosia reniformis and Sarcotragus foetidus) against three microalgal substrates with different size/motility characteristics: the nanophytoplankton Nannochloropsis sp. (textasciitilde3.2 μm, nonmotile) and Isochrysis sp. (textasciitilde3.8 μm, motile), as well as the diatom Phaeodactylum tricornutum (textasciitilde21.7 μm, nonmotile). In vitro cleaning experiments were conducted using sponge explants in 1 L of natural seawater and applying different microalgal cell concentrations under light/dark conditions. The investigated sponges exhibited a wide range of retention efficiencies for the different phytoplankton cells, with the lowest average values found for A. cannabina (37%) and the highest for A. oroides (70%). The latter could filter up to 14.1 mL seawater per hour and gram of sponge wet weight, by retaining 100% of Isochrysis at a density of 105 cells mL−1, under darkness. Our results highlight differences in filtering capacity among sponge species and preferences for microalgal substrates with distinct size and motility traits. |
Tsaparis, Dimitrios; Lecocq, Thomas; Kyriakis, Dimitrios; Oikonomaki, Katerina; Fontaine, Pascal; Tsigenopoulos, Costas S Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming Journal Article Animals, 12 (9), pp. 1178, 2022, ISSN: 2076-2615. @article{tsaparis_assessing_2022, title = {Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming}, author = {Dimitrios Tsaparis and Thomas Lecocq and Dimitrios Kyriakis and Katerina Oikonomaki and Pascal Fontaine and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Tsaparis-Animals-36.pdf https://www.mdpi.com/2076-2615/12/9/1178}, doi = {10.3390/ani12091178}, issn = {2076-2615}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Animals}, volume = {12}, number = {9}, pages = {1178}, abstract = {The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions. |
Paragkamian, Savvas; Sarafidou, Georgia; Mavraki, Dimitra; Pavloudi, Christina; Beja, Joana; Eliezer, Menashè; Lipizer, Marina; Boicenco, Laura; Vandepitte, Leen; Perez-Perez, Ruben; Zafeiropoulos, Haris; Arvanitidis, Christos; Pafilis, Evangelos; Gerovasileiou, Vasilis Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow Journal Article Frontiers in Marine Science, 9 , pp. 940844, 2022, ISSN: 2296-7745. @article{paragkamian_automating_2022, title = {Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow}, author = {Savvas Paragkamian and Georgia Sarafidou and Dimitra Mavraki and Christina Pavloudi and Joana Beja and Menashè Eliezer and Marina Lipizer and Laura Boicenco and Leen Vandepitte and Ruben Perez-Perez and Haris Zafeiropoulos and Christos Arvanitidis and Evangelos Pafilis and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Paragkaminan-fmars-53.pdf }, doi = {10.3389/fmars.2022.940844}, issn = {2296-7745}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Frontiers in Marine Science}, volume = {9}, pages = {940844}, abstract = {Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires a multidisciplinary effort involving four tasks: (a) Document digitisation (b) Transcription, which involves text recognition and correction, and (c) Information Extraction, which is performed using text mining tools and involves the entity identification, their normalisation and their co-mentions in text. Finally, the extracted data go through (d) Publication to a data repository in a standardised format. Each of these tasks requires a dedicated multistep methodology with standards and procedures. During the past 8 years, Information Extraction (IE) tools have undergone remarkable advances, which created a landscape of various tools with distinct capabilities specific to biodiversity data. These tools recognise entities in text such as taxon names, localities, phenotypic traits and thus automate, accelerate and facilitate the curation process. Furthermore, they assist the normalisation and mapping of entities to specific identifiers. This work focuses on the IE step (c) from the marine historical biodiversity data perspective. It orchestrates IE tools and provides the curators with a unified view of the methodology; as a result the documentation of the strengths, limitations and dependencies of several tools was drafted. Additionally, the classification of tools into Graphical User Interface (web and standalone) applications and Command Line Interface ones enables the data curators to select the most suitable tool for their needs, according to their specific features. In addition, the high volume of already digitised marine documents that await curation is amassed and a demonstration of the methodology, with a new scalable, extendable and containerised tool, “DECO” (bioDivErsity data Curation programming wOrkflow) is presented. DECO’s usage will provide a solid basis for future curation initiatives and an augmented degree of reliability towards high value data products that allow for the connection between the past and the present, in marine biodiversity research.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires a multidisciplinary effort involving four tasks: (a) Document digitisation (b) Transcription, which involves text recognition and correction, and (c) Information Extraction, which is performed using text mining tools and involves the entity identification, their normalisation and their co-mentions in text. Finally, the extracted data go through (d) Publication to a data repository in a standardised format. Each of these tasks requires a dedicated multistep methodology with standards and procedures. During the past 8 years, Information Extraction (IE) tools have undergone remarkable advances, which created a landscape of various tools with distinct capabilities specific to biodiversity data. These tools recognise entities in text such as taxon names, localities, phenotypic traits and thus automate, accelerate and facilitate the curation process. Furthermore, they assist the normalisation and mapping of entities to specific identifiers. This work focuses on the IE step (c) from the marine historical biodiversity data perspective. It orchestrates IE tools and provides the curators with a unified view of the methodology; as a result the documentation of the strengths, limitations and dependencies of several tools was drafted. Additionally, the classification of tools into Graphical User Interface (web and standalone) applications and Command Line Interface ones enables the data curators to select the most suitable tool for their needs, according to their specific features. In addition, the high volume of already digitised marine documents that await curation is amassed and a demonstration of the methodology, with a new scalable, extendable and containerised tool, “DECO” (bioDivErsity data Curation programming wOrkflow) is presented. DECO’s usage will provide a solid basis for future curation initiatives and an augmented degree of reliability towards high value data products that allow for the connection between the past and the present, in marine biodiversity research. |
Dimitriou, Panagiotis D; Santi, Ioulia; Moraitis, Manos L; Tsikopoulou, Irini; Pitta, Paraskevi; Karakassis, Ioannis Benthic–Pelagic Coupling in the Oligotrophic Eastern Mediterranean: A Synthesis of the HYPOXIA Project Results Journal Article Frontiers in Marine Science, 9 , pp. 886335, 2022, ISSN: 2296-7745. @article{dimitriou_benthicpelagic_2022, title = {Benthic–Pelagic Coupling in the Oligotrophic Eastern Mediterranean: A Synthesis of the HYPOXIA Project Results}, author = {Panagiotis D Dimitriou and Ioulia Santi and Manos L Moraitis and Irini Tsikopoulou and Paraskevi Pitta and Ioannis Karakassis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Dimitriou-FMS-47.pdf https://www.frontiersin.org/articles/10.3389/fmars.2022.886335/full}, doi = {10.3389/fmars.2022.886335}, issn = {2296-7745}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Frontiers in Marine Science}, volume = {9}, pages = {886335}, abstract = {Benthic–pelagic coupling studies have shown that the response of the benthic system to eutrophication is subject to complex nonlinear dynamics with specific thresholds beyond which abrupt changes in the response of the ecosystem occur and time lags between inputs and responses. The “HYPOXIA: Benthic–pelagic coupling and regime shifts ” project aimed to investigate how nutrient input in the water column results in ecological processes of eutrophication, which may lead to significant, irreversible changes in the eastern Mediterranean marine ecosystems within a short period of time. The project included analysis of historical water and benthic data, field sampling, and mesocosm experiments. From the project results, it can be concluded that nutrient inputs are quickly capitalized by small phytoplankton species in the water column resulting in the bloom of specific species with high nutrient uptake capabilities. When Eutrophic Index values (calculated using nutrient and chlorophyll- a concentrations) cross the moderate-to-poor threshold, the precipitating organic matter can cause observable effects on the benthic system. Depending on eutrophication intensity and persistence, the effects can start from microbenthos, meiofauna, and macrofauna increase in abundance and biomass to significant changes in the community structure. The latter includes the proliferation of macrofaunal opportunistic species, an increase in deposit feeders, and the high risk of ecosystem quality degradation. However, contrary to other regions of the world, no water hypoxia or benthic dead zones were observed as chlorophyll- a and O 2 concentrations showed a positive correlation. This is caused by the high photosynthetic activity of the phytoplankton and microphytobenthos, the increased bioturbation of macrofauna, and the increased abundance of sediment deposit-feeding species, which quickly consume the excess organic matter. Eastern Mediterranean coastal ecosystems show high resilience to the adverse effects of eutrophication, preventing hypoxia and azoic conditions when eutrophication is the only source of environmental disturbance.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Benthic–pelagic coupling studies have shown that the response of the benthic system to eutrophication is subject to complex nonlinear dynamics with specific thresholds beyond which abrupt changes in the response of the ecosystem occur and time lags between inputs and responses. The “HYPOXIA: Benthic–pelagic coupling and regime shifts ” project aimed to investigate how nutrient input in the water column results in ecological processes of eutrophication, which may lead to significant, irreversible changes in the eastern Mediterranean marine ecosystems within a short period of time. The project included analysis of historical water and benthic data, field sampling, and mesocosm experiments. From the project results, it can be concluded that nutrient inputs are quickly capitalized by small phytoplankton species in the water column resulting in the bloom of specific species with high nutrient uptake capabilities. When Eutrophic Index values (calculated using nutrient and chlorophyll- a concentrations) cross the moderate-to-poor threshold, the precipitating organic matter can cause observable effects on the benthic system. Depending on eutrophication intensity and persistence, the effects can start from microbenthos, meiofauna, and macrofauna increase in abundance and biomass to significant changes in the community structure. The latter includes the proliferation of macrofaunal opportunistic species, an increase in deposit feeders, and the high risk of ecosystem quality degradation. However, contrary to other regions of the world, no water hypoxia or benthic dead zones were observed as chlorophyll- a and O 2 concentrations showed a positive correlation. This is caused by the high photosynthetic activity of the phytoplankton and microphytobenthos, the increased bioturbation of macrofauna, and the increased abundance of sediment deposit-feeding species, which quickly consume the excess organic matter. Eastern Mediterranean coastal ecosystems show high resilience to the adverse effects of eutrophication, preventing hypoxia and azoic conditions when eutrophication is the only source of environmental disturbance. |
Tsertou, M I; Papandroulakis, N; Keklikoglou, K; Kalantzi, I; Tsapakis, M; Tsalafouta, A; Pavlidis, M; Antonopoulou, E; Katharios, P Comparative study of Chronic Ulcerative Dermatopathy in cultured meagre, Argyrosomus regius Journal Article Aquaculture, 556 , pp. 738301, 2022, ISSN: 00448486. @article{tsertou_comparative_2022, title = {Comparative study of Chronic Ulcerative Dermatopathy in cultured meagre, Argyrosomus regius}, author = {M I Tsertou and N Papandroulakis and K Keklikoglou and I Kalantzi and M Tsapakis and A Tsalafouta and M Pavlidis and E Antonopoulou and P Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Tsertou-AQUA-pre-print-34.pdf https://linkinghub.elsevier.com/retrieve/pii/S0044848622004173}, doi = {10.1016/j.aquaculture.2022.738301}, issn = {00448486}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Aquaculture}, volume = {556}, pages = {738301}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gisbert, Enric; Luz, Ronald Kennedy; Fernández, Ignacio; Pradhan, Pravata K; Salhi, Maria; Mozanzadeh, Mansour T; Kumar, Aditya; Kotzamanis, Yannis; Castro‐Ruiz, Diana; Bessonart, Martin; Darias, Maria J Development, nutrition, and rearing practices of relevant catfish species (Siluriformes) at early stages Journal Article Reviews in Aquaculture, 14 (1), pp. 73–105, 2022, ISSN: 1753-5123, 1753-5131. @article{gisbert_development_2022, title = {Development, nutrition, and rearing practices of relevant catfish species (Siluriformes) at early stages}, author = {Enric Gisbert and Ronald Kennedy Luz and Ignacio Fernández and Pravata K Pradhan and Maria Salhi and Mansour T Mozanzadeh and Aditya Kumar and Yannis Kotzamanis and Diana Castro‐Ruiz and Martin Bessonart and Maria J Darias}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2022-Kotzamanis-RAqua-preprint-2.pdf https://onlinelibrary.wiley.com/doi/10.1111/raq.12586}, doi = {10.1111/raq.12586}, issn = {1753-5123, 1753-5131}, year = {2022}, date = {2022-01-01}, urldate = {2022-01-12}, journal = {Reviews in Aquaculture}, volume = {14}, number = {1}, pages = {73--105}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bianchi, Carlo Nike; Gerovasileiou, Vasilis; Morri, Carla; Froglia, Carlo Distribution and Ecology of Decapod Crustaceans in Mediterranean Marine Caves: A Review Journal Article Diversity, 14 (3), pp. 176, 2022, ISSN: 1424-2818. @article{bianchi_distribution_2022, title = {Distribution and Ecology of Decapod Crustaceans in Mediterranean Marine Caves: A Review}, author = {Carlo Nike Bianchi and Vasilis Gerovasileiou and Carla Morri and Carlo Froglia}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Bolgan-AqCon-15-pre-print-1.pdf https://www.mdpi.com/1424-2818/14/3/176}, doi = {10.3390/d14030176}, issn = {1424-2818}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Diversity}, volume = {14}, number = {3}, pages = {176}, abstract = {Decapod crustaceans are important components of the fauna of marine caves worldwide, yet information on their ecology is still scarce. Mediterranean marine caves are perhaps the best known of the world and may offer paradigms to the students of marine cave decapods from other geographic regions. This review summarizes and updates the existing knowledge about the decapod fauna of Mediterranean marine caves on the basis of a dataset of 76 species from 133 caves in 13 Mediterranean countries. Most species were found occasionally, while 15 species were comparatively frequent (found in at least seven caves). They comprise cryptobiotic and bathyphilic species that only secondarily colonize caves (secondary stygobiosis). Little is known about the population biology of cave decapods, and quantitative data are virtually lacking. The knowledge on Mediterranean marine cave decapods is far from being complete. Future research should focus on filling regional gaps and on the decapod ecological role: getting out at night to feed and resting in caves during daytime, decapods may import organic matter to the cave ecosystem. Some decapod species occurring in caves are protected by law. Ecological interest and the need for conservation initiatives combine to claim for intensifying research on the decapod fauna of the Mediterranean Sea caves.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Decapod crustaceans are important components of the fauna of marine caves worldwide, yet information on their ecology is still scarce. Mediterranean marine caves are perhaps the best known of the world and may offer paradigms to the students of marine cave decapods from other geographic regions. This review summarizes and updates the existing knowledge about the decapod fauna of Mediterranean marine caves on the basis of a dataset of 76 species from 133 caves in 13 Mediterranean countries. Most species were found occasionally, while 15 species were comparatively frequent (found in at least seven caves). They comprise cryptobiotic and bathyphilic species that only secondarily colonize caves (secondary stygobiosis). Little is known about the population biology of cave decapods, and quantitative data are virtually lacking. The knowledge on Mediterranean marine cave decapods is far from being complete. Future research should focus on filling regional gaps and on the decapod ecological role: getting out at night to feed and resting in caves during daytime, decapods may import organic matter to the cave ecosystem. Some decapod species occurring in caves are protected by law. Ecological interest and the need for conservation initiatives combine to claim for intensifying research on the decapod fauna of the Mediterranean Sea caves. |
Dimitriou, Andreas C; Antoniou, Aglaia; Alexiou, Ioannis; Poulakakis, Nikos; Parmakelis, Aristeidis; Sfenthourakis, Spyros Diversification within an oceanic Mediterranean island: Insights from a terrestrial isopod Journal Article Molecular Phylogenetics and Evolution, 175 , pp. 107585, 2022, ISSN: 10557903. @article{dimitriou_diversification_2022, title = {Diversification within an oceanic Mediterranean island: Insights from a terrestrial isopod}, author = {Andreas C Dimitriou and Aglaia Antoniou and Ioannis Alexiou and Nikos Poulakakis and Aristeidis Parmakelis and Spyros Sfenthourakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Dimitriou-52.pdf https://linkinghub.elsevier.com/retrieve/pii/S1055790322001981}, doi = {10.1016/j.ympev.2022.107585}, issn = {10557903}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Molecular Phylogenetics and Evolution}, volume = {175}, pages = {107585}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Oikonomou, Stavroula; Kazlari, Zoi; Papapetrou, Maria; Papanna, Kantham; Papaharisis, Leonidas; Manousaki, Tereza; Loukovitis, Dimitrios; Dimitroglou, Arkadios; Kottaras, Lefteris; Gourzioti, Evgenia; Pagonis, Charalampos; Kostandis, Andreas; Tsigenopoulos, Costas S; Chatziplis, Dimitiros Genome Wide Association (GWAS) Analysis and genomic heritability for parasite resistance and growth in European seabass Journal Article Aquaculture Reports, 24 , pp. 101178, 2022, ISSN: 23525134. @article{oikonomou_genome_2022, title = {Genome Wide Association (GWAS) Analysis and genomic heritability for parasite resistance and growth in European seabass}, author = {Stavroula Oikonomou and Zoi Kazlari and Maria Papapetrou and Kantham Papanna and Leonidas Papaharisis and Tereza Manousaki and Dimitrios Loukovitis and Arkadios Dimitroglou and Lefteris Kottaras and Evgenia Gourzioti and Charalampos Pagonis and Andreas Kostandis and Costas S Tsigenopoulos and Dimitiros Chatziplis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Oikonomou-AqRep-45.pdf https://linkinghub.elsevier.com/retrieve/pii/S2352513422001740}, doi = {10.1016/j.aqrep.2022.101178}, issn = {23525134}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Aquaculture Reports}, volume = {24}, pages = {101178}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Oikonomou, Stavroula; Samaras, Athanasios; Tekeoglou, Maria; Loukovitis, Dimitrios; Dimitroglou, Arkadios; Kottaras, Lefteris; Papanna, Kantham; Papaharisis, Leonidas; Tsigenopoulos, Costas S; Pavlidis, Michail; Chatziplis, Dimitrios Genomic Selection and Genome-Wide Association Analysis for Stress Response, Disease Resistance and Body Weight in European Seabass Journal Article Animals, 12 (3), pp. 277, 2022, ISSN: 2076-2615. @article{oikonomou_genomic_2022, title = {Genomic Selection and Genome-Wide Association Analysis for Stress Response, Disease Resistance and Body Weight in European Seabass}, author = {Stavroula Oikonomou and Athanasios Samaras and Maria Tekeoglou and Dimitrios Loukovitis and Arkadios Dimitroglou and Lefteris Kottaras and Kantham Papanna and Leonidas Papaharisis and Costas S Tsigenopoulos and Michail Pavlidis and Dimitrios Chatziplis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Oikonomou-ANIMALS-9.pdf https://www.mdpi.com/2076-2615/12/3/277}, doi = {10.3390/ani12030277}, issn = {2076-2615}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Animals}, volume = {12}, number = {3}, pages = {277}, abstract = {The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its future use to select broodstock whose offspring may potentially be less affected by handling. A total of 865 European seabass offspring were used to measure body weight and stress response. Moreover, a disease challenge experiment with Vibrio anguillarum was conducted in a subset (332) of the above fish to study disease resistance. Fish were genotyped with a 57k SNP array, and a Genome-Wide Association study (GWAS) was performed. Five SNPs were found to be statistically significant, three of which affect stress indicators and body weight (in a subgroup of the population), and a putative SNP affects growth performance, while no SNP associated with resistance to Vibrio was found. A moderate to high genomic heritability regarding stress indicators and body weight was estimated using the Restricted Maximum Likelihood (REML) process. Finally, the accuracy, along with the correlation between Estimated Breeding Values (EBVs) and Genomic Estimated Breeding Values (GEBVs), were calculated for all the traits.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its future use to select broodstock whose offspring may potentially be less affected by handling. A total of 865 European seabass offspring were used to measure body weight and stress response. Moreover, a disease challenge experiment with Vibrio anguillarum was conducted in a subset (332) of the above fish to study disease resistance. Fish were genotyped with a 57k SNP array, and a Genome-Wide Association study (GWAS) was performed. Five SNPs were found to be statistically significant, three of which affect stress indicators and body weight (in a subgroup of the population), and a putative SNP affects growth performance, while no SNP associated with resistance to Vibrio was found. A moderate to high genomic heritability regarding stress indicators and body weight was estimated using the Restricted Maximum Likelihood (REML) process. Finally, the accuracy, along with the correlation between Estimated Breeding Values (EBVs) and Genomic Estimated Breeding Values (GEBVs), were calculated for all the traits. |
García-Escudero, Catalina A; Tsigenopoulos, Costas S; Gerakaris, Vasilis; Tsakogiannis, Alexandros; Apostolaki, Eugenia T ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea Journal Article Diversity, 14 (2), pp. 76, 2022, ISSN: 1424-2818. @article{garcia-escudero_its_2022, title = {ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea}, author = {Catalina A García-Escudero and Costas S Tsigenopoulos and Vasilis Gerakaris and Alexandros Tsakogiannis and Eugenia T Apostolaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Garcia-Escudero-DIVERSITY-8.pdf https://www.mdpi.com/1424-2818/14/2/76}, doi = {10.3390/d14020076}, issn = {1424-2818}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Diversity}, volume = {14}, number = {2}, pages = {76}, abstract = {Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions. |
Nousias, O; Oikonomou, S; Manousaki, T; Papadogiannis, V; Angelova, N; Tsaparis, D; Tsakogiannis, A; Duncan, N; Estevez, A; Tzokas, K; Pavlidis, M; Chatziplis, D; Tsigenopoulos, C S Scientific Reports, 12 (1), pp. 5301, 2022, ISSN: 2045-2322. @article{nousias_linkage_2022, title = {Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing}, author = {O Nousias and S Oikonomou and T Manousaki and V Papadogiannis and N Angelova and D Tsaparis and A Tsakogiannis and N Duncan and A Estevez and K Tzokas and M Pavlidis and D Chatziplis and C S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Nousias-Sci-Report-27.pdf https://www.nature.com/articles/s41598-022-09289-4}, doi = {10.1038/s41598-022-09289-4}, issn = {2045-2322}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Scientific Reports}, volume = {12}, number = {1}, pages = {5301}, abstract = {Abstract Meagre ( Argyrosomus regius ), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax , traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Meagre ( Argyrosomus regius ), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax , traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production. |
Charisi, C; Kodonas, K; Keklikoglou, K; Arhakis, A; Arapostathis, K A; Kotsanos, N Morphological, histological, and chemical analysis of first permanent molars with molar incisor malformation Journal Article European Archives of Paediatric Dentistry, 2022, ISSN: 1818-6300, 1996-9805. @article{charisi_morphological_2022, title = {Morphological, histological, and chemical analysis of first permanent molars with molar incisor malformation}, author = {C Charisi and K Kodonas and K Keklikoglou and A Arhakis and K A Arapostathis and N Kotsanos}, url = {https://link.springer.com/10.1007/s40368-022-00723-9https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Charisi-EAPD-50-pre-print.pdf https://link.springer.com/10.1007/s40368-022-00723-9}, doi = {10.1007/s40368-022-00723-9}, issn = {1818-6300, 1996-9805}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {European Archives of Paediatric Dentistry}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Solís, Francisco Javier Toledo; Fernandes, Jorge M O; Sarropoulou, Elena; Monzón, Ignacio Fernández Noncoding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks Incollection Cellular and Molecular Approaches in Fish Biology, pp. 105–159, Elsevier, 2022, ISBN: 978-0-12-822273-7. @incollection{toledo_solis_noncoding_2022, title = {Noncoding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks}, author = {Francisco Javier Toledo Solís and Jorge M O Fernandes and Elena Sarropoulou and Ignacio Fernández Monzón}, url = {https://linkinghub.elsevier.com/retrieve/pii/B9780128222737000124}, doi = {10.1016/B978-0-12-822273-7.00012-4}, isbn = {978-0-12-822273-7}, year = {2022}, date = {2022-01-01}, urldate = {2022-02-17}, booktitle = {Cellular and Molecular Approaches in Fish Biology}, pages = {105--159}, publisher = {Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Koulouri, Panayota; Mogias, Athanasios; Gerovasileiou, Vasilis Mediterranean Marine Science, 23 (2), pp. 266–269, 2022, ISSN: 1791-6763, 1108-393X. @article{koulouri_ocean_2022, title = {Ocean Literacy across the Mediterranean Sea region in the Era of 2030 Agenda and the Decade of Ocean Science for Sustainable Development (2021-2030)}, author = {Panayota Koulouri and Athanasios Mogias and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Koulouri-editorial-MedMarSci-29.pdf}, doi = {10.12681/mms.30099}, issn = {1791-6763, 1108-393X}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Mediterranean Marine Science}, volume = {23}, number = {2}, pages = {266--269}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Demetriou, Monica; Raitsos, Dionysios E; Kournopoulou, Antonia; Mandalakis, Manolis; Sfenthourakis, Spyros; Psarra, Stella Phytoplankton Phenology in the Coastal Zone of Cyprus, Based on Remote Sensing and In Situ Observations Journal Article Remote Sensing, 14 (1), pp. 12, 2022, ISSN: 2072-4292. @article{demetriou_phytoplankton_2022, title = {Phytoplankton Phenology in the Coastal Zone of Cyprus, Based on Remote Sensing and In Situ Observations}, author = {Monica Demetriou and Dionysios E Raitsos and Antonia Kournopoulou and Manolis Mandalakis and Spyros Sfenthourakis and Stella Psarra}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Demetriou-RemSensing-4.pdf https://www.mdpi.com/2072-4292/14/1/12}, doi = {10.3390/rs14010012}, issn = {2072-4292}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Remote Sensing}, volume = {14}, number = {1}, pages = {12}, abstract = {Alterations in phytoplankton biomass, community structure and timing of their growth (phenology), are directly implicated in the carbon cycle and energy transfer to higher trophic levels of the marine food web. Due to the lack of long-term in situ datasets, there is very little information on phytoplankton seasonal succession in Cyprus (eastern Mediterranean Sea). On the other hand, satellite-derived measurements of ocean colour can only provide long-term time series of chlorophyll (an index of phytoplankton biomass) up to the first optical depth (surface waters). The coupling of both means of observations is essential for understanding phytoplankton dynamics and their response to environmental change. Here, we use 23 years of remotely sensed, regionally tuned ocean-colour observations, along with a unique time series of in situ phytoplankton pigment composition data, collected in coastal waters of Cyprus during 2016. The satellite observations show an initiation of phytoplankton growth period in November, a peak in February and termination in April, with an overall mean duration of textasciitilde4 months. An in-depth exploration of in situ total Chl-a concentration and phytoplankton pigments revealed that pico- and nano-plankton cells dominated the phytoplankton community. The growth peak in February was dominated by nanophytoplankton and potentially larger diatoms (pigments of 19’ hexanoyloxyfucoxanthin and fucoxanthin, respectively), in the 0–20 m layer. The highest total Chl-a concentration was recorded at a station off Akrotiri peninsula in the south, where strong coastal upwelling has been reported. Another station in the southern part, located next to a fish farm, showed a higher contribution of picophytoplankton during the most oligotrophic period (summer). Our results highlight the importance of using available in situ data coupled to ocean-colour remote sensing, for monitoring marine ecosystems in areas with limited in situ data availability.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Alterations in phytoplankton biomass, community structure and timing of their growth (phenology), are directly implicated in the carbon cycle and energy transfer to higher trophic levels of the marine food web. Due to the lack of long-term in situ datasets, there is very little information on phytoplankton seasonal succession in Cyprus (eastern Mediterranean Sea). On the other hand, satellite-derived measurements of ocean colour can only provide long-term time series of chlorophyll (an index of phytoplankton biomass) up to the first optical depth (surface waters). The coupling of both means of observations is essential for understanding phytoplankton dynamics and their response to environmental change. Here, we use 23 years of remotely sensed, regionally tuned ocean-colour observations, along with a unique time series of in situ phytoplankton pigment composition data, collected in coastal waters of Cyprus during 2016. The satellite observations show an initiation of phytoplankton growth period in November, a peak in February and termination in April, with an overall mean duration of textasciitilde4 months. An in-depth exploration of in situ total Chl-a concentration and phytoplankton pigments revealed that pico- and nano-plankton cells dominated the phytoplankton community. The growth peak in February was dominated by nanophytoplankton and potentially larger diatoms (pigments of 19’ hexanoyloxyfucoxanthin and fucoxanthin, respectively), in the 0–20 m layer. The highest total Chl-a concentration was recorded at a station off Akrotiri peninsula in the south, where strong coastal upwelling has been reported. Another station in the southern part, located next to a fish farm, showed a higher contribution of picophytoplankton during the most oligotrophic period (summer). Our results highlight the importance of using available in situ data coupled to ocean-colour remote sensing, for monitoring marine ecosystems in areas with limited in situ data availability. |
Zafeiropoulos, Haris; Paragkamian, Savvas; Ninidakis, Stelios; Pavlopoulos, Georgios A; Jensen, Lars Juhl; Pafilis, Evangelos PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types Journal Article Microorganisms, 10 (2), pp. 293, 2022, ISSN: 2076-2607. @article{zafeiropoulos_prego_2022, title = {PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types}, author = {Haris Zafeiropoulos and Savvas Paragkamian and Stelios Ninidakis and Georgios A Pavlopoulos and Lars Juhl Jensen and Evangelos Pafilis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Zafeiropoulos-Micro-12.pdf https://www.mdpi.com/2076-2607/10/2/293}, doi = {10.3390/microorganisms10020293}, issn = {2076-2607}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {293}, abstract = {To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO’s capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO’s capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes. |
Kaitetzidou, Elisavet; Gilfillan, Gregor D; Antonopoulou, Efthimia; Sarropoulou, Elena Sex-biased dynamics of three-spined stickleback (Gasterosteus aculeatus) gene expression patterns Journal Article Genomics, 114 (1), pp. 266–277, 2022, ISSN: 08887543. @article{kaitetzidou_sex-biased_2022b, title = {Sex-biased dynamics of three-spined stickleback (Gasterosteus aculeatus) gene expression patterns}, author = {Elisavet Kaitetzidou and Gregor D Gilfillan and Efthimia Antonopoulou and Elena Sarropoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Kaitetzidou-Genomics-3.pdf https://linkinghub.elsevier.com/retrieve/pii/S0888754321004377}, doi = {10.1016/j.ygeno.2021.12.010}, issn = {08887543}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Genomics}, volume = {114}, number = {1}, pages = {266--277}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Escalas, Arthur; Auguet, Jean-Christophe; Avouac, Amandine; Belmaker, Jonathan; Dailianis, Thanos; Kiflawi, Moshe; Pickholtz, Renanel; Skouradakis, Grigorios; Villéger, Sébastien Shift and homogenization of gut microbiome during invasion in marine fishes Journal Article Animal Microbiome, 4 (1), pp. 37, 2022, ISSN: 2524-4671. @article{escalas_shift_2022, title = {Shift and homogenization of gut microbiome during invasion in marine fishes}, author = {Arthur Escalas and Jean-Christophe Auguet and Amandine Avouac and Jonathan Belmaker and Thanos Dailianis and Moshe Kiflawi and Renanel Pickholtz and Grigorios Skouradakis and Sébastien Villéger}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Escalas-AniMicro-48.pdf https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-022-00181-0}, doi = {10.1186/s42523-022-00181-0}, issn = {2524-4671}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Animal Microbiome}, volume = {4}, number = {1}, pages = {37}, abstract = {Abstract Biological invasion is one of the main components of global changes in aquatic ecosystems. Unraveling how establishment in novel environments affects key biological features of animals is a key step towards understanding invasion. Gut microbiome of herbivorous animals is important for host health but has been scarcely assessed in invasive species. Here, we characterized the gut microbiome of two invasive marine herbivorous fishes ( Siganus rivulatus and Siganus luridus ) in their native (Red Sea) and invaded (Mediterranean Sea) ranges. The taxonomic and phylogenetic diversity of the microbiome increased as the fishes move away from the native range and its structure became increasingly different from the native microbiome. These shifts resulted in homogenization of the microbiome in the invaded range, within and between the two species. The shift in microbial diversity was associated with changes in its functions related with the metabolism of short-chain fatty acids. Altogether, our results suggest that the environmental conditions encountered by Siganidae during their expansion in Mediterranean ecosystems strongly modifies the composition of their gut microbiome along with its putative functions. Further studies should pursue to identify the precise determinants of these modifications (e.g. changes in host diet or behavior, genetic differentiation) and whether they participate in the ecological success of these species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Biological invasion is one of the main components of global changes in aquatic ecosystems. Unraveling how establishment in novel environments affects key biological features of animals is a key step towards understanding invasion. Gut microbiome of herbivorous animals is important for host health but has been scarcely assessed in invasive species. Here, we characterized the gut microbiome of two invasive marine herbivorous fishes ( Siganus rivulatus and Siganus luridus ) in their native (Red Sea) and invaded (Mediterranean Sea) ranges. The taxonomic and phylogenetic diversity of the microbiome increased as the fishes move away from the native range and its structure became increasingly different from the native microbiome. These shifts resulted in homogenization of the microbiome in the invaded range, within and between the two species. The shift in microbial diversity was associated with changes in its functions related with the metabolism of short-chain fatty acids. Altogether, our results suggest that the environmental conditions encountered by Siganidae during their expansion in Mediterranean ecosystems strongly modifies the composition of their gut microbiome along with its putative functions. Further studies should pursue to identify the precise determinants of these modifications (e.g. changes in host diet or behavior, genetic differentiation) and whether they participate in the ecological success of these species. |
Angelova, Nelina; Danis, Theodoros; Lagnel, Jacques; Tsigenopoulos, Costas S; Manousaki, Tereza SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments Journal Article BMC Research Notes, 15 (1), pp. 98, 2022, ISSN: 1756-0500. @article{angelova_snakecube_2022, title = {SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments}, author = {Nelina Angelova and Theodoros Danis and Jacques Lagnel and Costas S Tsigenopoulos and Tereza Manousaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Angelova-BMC-18.pdf https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-022-05978-5}, doi = {10.1186/s13104-022-05978-5}, issn = {1756-0500}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {BMC Research Notes}, volume = {15}, number = {1}, pages = {98}, abstract = {Abstract Objective The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. Results Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Objective The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. Results Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field. |
Kioukis, Antonios; Pourjam, Mohsen; Neuhaus, Klaus; Lagkouvardos, Ilias Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling Journal Article Frontiers in Bioinformatics, 2 , pp. 864597, 2022, ISSN: 2673-7647. @article{kioukis_taxonomy_2022, title = {Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling}, author = {Antonios Kioukis and Mohsen Pourjam and Klaus Neuhaus and Ilias Lagkouvardos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Kioukis-Frontiers-in-Bioinfo-39.pdf https://www.frontiersin.org/articles/10.3389/fbinf.2022.864597/full}, doi = {10.3389/fbinf.2022.864597}, issn = {2673-7647}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Frontiers in Bioinformatics}, volume = {2}, pages = {864597}, abstract = {Bacterial diversity is often analyzed using 16S rRNA gene amplicon sequencing. Commonly, sequences are clustered based on similarity cutoffs to obtain groups reflecting molecular species, genera, or families. Due to the amount of the generated sequencing data, greedy algorithms are preferred for their time efficiency. Such algorithms rely only on pairwise sequence similarities. Thus, sometimes sequences with diverse phylogenetic background are clustered together. In contrast, taxonomic classifiers use position specific taxonomic information in assigning a probable taxonomy to a given sequence. Here we introduce Taxonomy Informed Clustering (TIC), a novel approach that utilizes classifier-assigned taxonomy to restrict clustering to only those sequences that share the same taxonomic path. Based on this concept, we offer a complete and automated pipeline for processing of 16S rRNA amplicon datasets in diversity analyses. First, raw reads are processed to form denoised amplicons. Next, the denoised amplicons are taxonomically classified. Finally, the TIC algorithm progressively assigning clusters at molecular species, genus and family levels. TIC outperforms greedy clustering algorithms like USEARCH and VSEARCH in terms of clusters’ purity and entropy, when using data from the Living Tree Project as test samples. Furthermore, we applied TIC on a dataset containing all Bifidobacteriaceae -classified sequences from the IMNGS database. Here, TIC identified evidence for 1000s of novel molecular genera and species. These results highlight the straightforward application of the TIC pipeline and superior results compared to former methods in diversity studies. The pipeline is freely available at: https://github.com/Lagkouvardos/TIC .}, keywords = {}, pubstate = {published}, tppubtype = {article} } Bacterial diversity is often analyzed using 16S rRNA gene amplicon sequencing. Commonly, sequences are clustered based on similarity cutoffs to obtain groups reflecting molecular species, genera, or families. Due to the amount of the generated sequencing data, greedy algorithms are preferred for their time efficiency. Such algorithms rely only on pairwise sequence similarities. Thus, sometimes sequences with diverse phylogenetic background are clustered together. In contrast, taxonomic classifiers use position specific taxonomic information in assigning a probable taxonomy to a given sequence. Here we introduce Taxonomy Informed Clustering (TIC), a novel approach that utilizes classifier-assigned taxonomy to restrict clustering to only those sequences that share the same taxonomic path. Based on this concept, we offer a complete and automated pipeline for processing of 16S rRNA amplicon datasets in diversity analyses. First, raw reads are processed to form denoised amplicons. Next, the denoised amplicons are taxonomically classified. Finally, the TIC algorithm progressively assigning clusters at molecular species, genus and family levels. TIC outperforms greedy clustering algorithms like USEARCH and VSEARCH in terms of clusters’ purity and entropy, when using data from the Living Tree Project as test samples. Furthermore, we applied TIC on a dataset containing all Bifidobacteriaceae -classified sequences from the IMNGS database. Here, TIC identified evidence for 1000s of novel molecular genera and species. These results highlight the straightforward application of the TIC pipeline and superior results compared to former methods in diversity studies. The pipeline is freely available at: https://github.com/Lagkouvardos/TIC . |
García-Pérez, Isabel; Molsosa-Solanas, Anna; Perelló-Amorós, Miquel; Sarropoulou, Elena; Blasco, Josefina; Gutiérrez, Joaquim; de la serrana, Daniel Garcia The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream (Sparus aurata) Fast Skeletal Muscle Journal Article Cells, 11 (3), pp. 428, 2022, ISSN: 2073-4409. @article{garcia-perez_emerging_2022, title = {The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream (Sparus aurata) Fast Skeletal Muscle}, author = {Isabel García-Pérez and Anna Molsosa-Solanas and Miquel Perelló-Amorós and Elena Sarropoulou and Josefina Blasco and Joaquim Gutiérrez and Daniel Garcia de la serrana}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Garcia-Perez-CELLS-13.pdf https://www.mdpi.com/2073-4409/11/3/428}, doi = {10.3390/cells11030428}, issn = {2073-4409}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Cells}, volume = {11}, number = {3}, pages = {428}, abstract = {Long non-coding RNAs (lncRNAs) are an emerging group of ncRNAs that can modulate gene expression at the transcriptional or translational levels. In the present work, previously published transcriptomic data were used to identify lncRNAs expressed in gilthead sea bream skeletal muscle, and their transcription levels were studied under different physiological conditions. Two hundred and ninety lncRNAs were identified and, based on transcriptomic differences between juveniles and adults, a total of seven lncRNAs showed potential to be important for muscle development. Our data suggest that the downregulation of most of the studied lncRNAs might be linked to increased myoblast proliferation, while their upregulation might be necessary for differentiation. However, with these data, as it is not possible to propose a formal mechanism to explain their effect, bioinformatic analysis suggests two possible mechanisms. First, the lncRNAs may act as sponges of myoblast proliferation inducers microRNAs (miRNAs) such as miR-206, miR-208, and miR-133 (binding energy MEF textless −25.0 kcal). Secondly, lncRNA20194 had a strong predicted interaction towards the myod1 mRNA (ndG = −0.17) that, based on the positive correlation between the two genes, might promote its function. Our study represents the first characterization of lncRNAs in gilthead sea bream fast skeletal muscle and provides evidence regarding their involvement in muscle development.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Long non-coding RNAs (lncRNAs) are an emerging group of ncRNAs that can modulate gene expression at the transcriptional or translational levels. In the present work, previously published transcriptomic data were used to identify lncRNAs expressed in gilthead sea bream skeletal muscle, and their transcription levels were studied under different physiological conditions. Two hundred and ninety lncRNAs were identified and, based on transcriptomic differences between juveniles and adults, a total of seven lncRNAs showed potential to be important for muscle development. Our data suggest that the downregulation of most of the studied lncRNAs might be linked to increased myoblast proliferation, while their upregulation might be necessary for differentiation. However, with these data, as it is not possible to propose a formal mechanism to explain their effect, bioinformatic analysis suggests two possible mechanisms. First, the lncRNAs may act as sponges of myoblast proliferation inducers microRNAs (miRNAs) such as miR-206, miR-208, and miR-133 (binding energy MEF textless −25.0 kcal). Secondly, lncRNA20194 had a strong predicted interaction towards the myod1 mRNA (ndG = −0.17) that, based on the positive correlation between the two genes, might promote its function. Our study represents the first characterization of lncRNAs in gilthead sea bream fast skeletal muscle and provides evidence regarding their involvement in muscle development. |
Droubogiannis, Stavros; Pavlidi, Lydia; Tsertou, Maria Ioanna; Kokkari, Constantina; Skliros, Dimitrios; Flemetakis, Emmanouil; Katharios, Pantelis Vibrio Phage Artemius, a Novel Phage Infecting Vibrio alginolyticus Journal Article Pathogens, 11 (8), pp. 848, 2022, ISSN: 2076-0817. @article{droubogiannis_vibrio_2022, title = {Vibrio Phage Artemius, a Novel Phage Infecting Vibrio alginolyticus}, author = {Stavros Droubogiannis and Lydia Pavlidi and Maria Ioanna Tsertou and Constantina Kokkari and Dimitrios Skliros and Emmanouil Flemetakis and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Droubogiannis-pathogen-54.pdf https://www.mdpi.com/2076-0817/11/8/848}, doi = {10.3390/pathogens11080848}, issn = {2076-0817}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Pathogens}, volume = {11}, number = {8}, pages = {848}, abstract = {Vibrio alginolyticus is an important pathogen of marine animals and has been the target of phage therapy applications in marine aquaculture for many years. Here, we report the isolation and partial characterization of a novel species of the Siphoviridae family, the Vibrio phage Artemius. The novel phage was species-specific and could only infect strains of V. alginolyticus. It could efficiently reduce the growth of the host bacterium at various multiplicities of infection as assessed by an in vitro lysis assay. It had a genome length of 43,349 base pairs. The complete genome has double-stranded DNA with a G + C content of 43.61%. In total, 57 ORFs were identified, of which 19 were assigned a predicted function. A genomic analysis indicated that Vibrio phage Artemius is lytic and does not harbor genes encoding toxins and antibiotic resistance determinants.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Vibrio alginolyticus is an important pathogen of marine animals and has been the target of phage therapy applications in marine aquaculture for many years. Here, we report the isolation and partial characterization of a novel species of the Siphoviridae family, the Vibrio phage Artemius. The novel phage was species-specific and could only infect strains of V. alginolyticus. It could efficiently reduce the growth of the host bacterium at various multiplicities of infection as assessed by an in vitro lysis assay. It had a genome length of 43,349 base pairs. The complete genome has double-stranded DNA with a G + C content of 43.61%. In total, 57 ORFs were identified, of which 19 were assigned a predicted function. A genomic analysis indicated that Vibrio phage Artemius is lytic and does not harbor genes encoding toxins and antibiotic resistance determinants. |
Gabed, Noujoud; Verret, Frédéric; Peticca, Aurélie; Kryvoruchko, Igor; Gastineau, Romain; Bosson, Orlane; Séveno, Julie; Davidovich, Olga; Davidovich, Nikolai; Witkowski, Andrzej; Kristoffersen, Jon Bent; Benali, Amel; Ioannou, Efstathia; Koutsaviti, Aikaterini; Roussis, Vassilios; Gâteau, Hélène; Phimmaha, Suliya; Leignel, Vincent; Badawi, Myriam; Khiar, Feriel; Francezon, Nellie; Fodil, Mostefa; Pasetto, Pamela; Mouget, Jean-Luc What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age Journal Article Marine Drugs, 20 (4), pp. 234, 2022, ISSN: 1660-3397. @article{gabed_what_2022, title = {What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age}, author = {Noujoud Gabed and Frédéric Verret and Aurélie Peticca and Igor Kryvoruchko and Romain Gastineau and Orlane Bosson and Julie Séveno and Olga Davidovich and Nikolai Davidovich and Andrzej Witkowski and Jon Bent Kristoffersen and Amel Benali and Efstathia Ioannou and Aikaterini Koutsaviti and Vassilios Roussis and Hélène Gâteau and Suliya Phimmaha and Vincent Leignel and Myriam Badawi and Feriel Khiar and Nellie Francezon and Mostefa Fodil and Pamela Pasetto and Jean-Luc Mouget}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Gabed-N-Mar-Drugs-33.pdf https://www.mdpi.com/1660-3397/20/4/234}, doi = {10.3390/md20040234}, issn = {1660-3397}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Marine Drugs}, volume = {20}, number = {4}, pages = {234}, abstract = {The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).}, keywords = {}, pubstate = {published}, tppubtype = {article} } The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest). |
2021 |
Kotzamanis, Yannis; Fawole, Femi J; Brezas, Andreas; Kumar, Vikas; Fontanillas, Ramon; Antonopoulou, Efthimia; Kouroupakis, Emmanouil; Ilia, Vassiliki Dietary lysine requirement of greater amberjack juvenile ( textitSeriola dumerili , Risso, 1810) Journal Article Aquaculture Nutrition, 27 (6), pp. 2107–2118, 2021, ISSN: 1353-5773, 1365-2095. @article{kotzamanis_dietary_2021, title = {Dietary lysine requirement of greater amberjack juvenile ( textitSeriola dumerili , Risso, 1810)}, author = {Yannis Kotzamanis and Femi J Fawole and Andreas Brezas and Vikas Kumar and Ramon Fontanillas and Efthimia Antonopoulou and Emmanouil Kouroupakis and Vassiliki Ilia}, url = {https://onlinelibrary.wiley.com/doi/10.1111/anu.13344}, doi = {10.1111/anu.13344}, issn = {1353-5773, 1365-2095}, year = {2021}, date = {2021-12-01}, urldate = {2022-01-12}, journal = {Aquaculture Nutrition}, volume = {27}, number = {6}, pages = {2107--2118}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
