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. |
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. |
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. |
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. |
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. |
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} } |
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. |
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. |
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} } |
Karamanlidis, Alexandros A; Skrbinšek, Tomaž; Amato, George; Dendrinos, Panagiotis; Gaughran, Stephen; Kasapidis, Panagiotis; Kopatz, Alexander; Stronen, Astrid Vik Sci Rep, 11 (1), pp. 373, 2021, ISSN: 2045-2322. @article{karamanlidis_genetic_2021, title = {Genetic and demographic history define a conservation strategy for earth’s most endangered pinniped, the Mediterranean monk seal Monachus monachus}, author = {Alexandros A Karamanlidis and Tomaž Skrbinšek and George Amato and Panagiotis Dendrinos and Stephen Gaughran and Panagiotis Kasapidis and Alexander Kopatz and Astrid Vik Stronen}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Karamanlidis-SciRep-3.pdf http://www.nature.com/articles/s41598-020-79712-1}, doi = {10.1038/s41598-020-79712-1}, issn = {2045-2322}, year = {2021}, date = {2021-12-01}, urldate = {2021-02-02}, journal = {Sci Rep}, volume = {11}, number = {1}, pages = {373}, abstract = {Abstract The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species’ unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species’ unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival. |
Nousias, Orestis; Tzokas, Konstantinos; Papaharisis, Leonidas; Ekonomaki, Katerina; Chatziplis, Dimitrios; Batargias, Costas; Tsigenopoulos, Costas S Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes Journal Article Fishes, 6 (4), pp. 78, 2021, ISSN: 2410-3888. @article{nousias_genetic_2021, title = {Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes}, author = {Orestis Nousias and Konstantinos Tzokas and Leonidas Papaharisis and Katerina Ekonomaki and Dimitrios Chatziplis and Costas Batargias and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Nousias-Fishes-85.pdf}, doi = {10.3390/fishes6040078}, issn = {2410-3888}, year = {2021}, date = {2021-12-01}, urldate = {2022-01-12}, journal = {Fishes}, volume = {6}, number = {4}, pages = {78}, abstract = {This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes. |
Reitmeier, Sandra; Hitch, Thomas C A; Treichel, Nicole; Fikas, Nikolaos; Hausmann, Bela; Ramer-Tait, Amanda E; Neuhaus, Klaus; Berry, David; Haller, Dirk; Lagkouvardos, Ilias; Clavel, Thomas Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling Journal Article ISME Communications, 1 (1), pp. 31, 2021, ISSN: 2730-6151. @article{reitmeier_handling_2021, title = {Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling}, author = {Sandra Reitmeier and Thomas C A Hitch and Nicole Treichel and Nikolaos Fikas and Bela Hausmann and Amanda E Ramer-Tait and Klaus Neuhaus and David Berry and Dirk Haller and Ilias Lagkouvardos and Thomas Clavel}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/07/2021-Reitmer-ISME-52-1.pdf http://www.nature.com/articles/s43705-021-00033-z}, doi = {10.1038/s43705-021-00033-z}, issn = {2730-6151}, year = {2021}, date = {2021-12-01}, urldate = {2021-07-26}, journal = {ISME Communications}, volume = {1}, number = {1}, pages = {31}, abstract = {Abstract 16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta -diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha -diversity across studies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract 16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta -diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha -diversity across studies. |
Papadaki, Maria; Mandalakis, Manolis; Anastasiou, Thekla I; Pouli, Marina; Asderis, Michalis; Katharios, Pantelis; Papandroulakis, Nikos; Mylonas, Constantinos C Fish Physiology and Biochemistry, 47 (6), pp. 1777–1792, 2021, ISSN: 1573-5168. @article{papadaki_histological_2021b, title = {Histological evaluation of sex differentiation and early sex identification in hatchery-produced greater amberjack (Seriola dumerili) reared in sea cages}, author = {Maria Papadaki and Manolis Mandalakis and Thekla I Anastasiou and Marina Pouli and Michalis Asderis and Pantelis Katharios and Nikos Papandroulakis and Constantinos C Mylonas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Papadaki-FFB-82-pre-print.pdf https://doi.org/10.1007/s10695-021-01007-7}, doi = {10.1007/s10695-021-01007-7}, issn = {1573-5168}, year = {2021}, date = {2021-12-01}, urldate = {2021-12-04}, journal = {Fish Physiology and Biochemistry}, volume = {47}, number = {6}, pages = {1777--1792}, abstract = {The histological process of gonadal differentiation, together with the endocrine changes of sex steroid hormones and some of their precursors, was studied in hatchery-produced greater amberjack Seriola dumerili from 101 until 408 days post-hatching (dph), with samplings conducted every 50 days. Histological processing showed that sex differentiation began at 101 dph with the formation of the ovarian cavity in females, while the presumptive males did not yet contain any germ cells in their gonad. At 150 dph, we observed the first germ cells in the developing testes. Sex differentiation in almost all sampled individuals was complete at 408 dph. No size dimorphism was observed between the sexes, and the sex ratio was 1:1, suggesting that there was no influence of early rearing in captivity on sex differentiation. Plasma concentrations of adrenosterone (Ad), androstenedione (Δ4), 11-ketotestosterone (11ΚΤ), testosterone (Τ), estradiol (Ε2), progesterone (P4) and 17,20β-dihydroxy-4-pregnen-3-one (17,20βP) were measured in males and females with the use of liquid chromatography tandem mass spectrometry (LC–MS/MS) to examine their role in the sex differentiation process. From the seven hormones, the only one that exhibited differences between the sexes was 11-KT and the plasma 11-KT concentration was found to be a useful indication of greater amberjack sex. Variations were observed in the mean values of Ad, Δ4, 11-KT, T, P4 and 17,20βP over time in one or both sexes, indicating their involvement in the sex differentiation process.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The histological process of gonadal differentiation, together with the endocrine changes of sex steroid hormones and some of their precursors, was studied in hatchery-produced greater amberjack Seriola dumerili from 101 until 408 days post-hatching (dph), with samplings conducted every 50 days. Histological processing showed that sex differentiation began at 101 dph with the formation of the ovarian cavity in females, while the presumptive males did not yet contain any germ cells in their gonad. At 150 dph, we observed the first germ cells in the developing testes. Sex differentiation in almost all sampled individuals was complete at 408 dph. No size dimorphism was observed between the sexes, and the sex ratio was 1:1, suggesting that there was no influence of early rearing in captivity on sex differentiation. Plasma concentrations of adrenosterone (Ad), androstenedione (Δ4), 11-ketotestosterone (11ΚΤ), testosterone (Τ), estradiol (Ε2), progesterone (P4) and 17,20β-dihydroxy-4-pregnen-3-one (17,20βP) were measured in males and females with the use of liquid chromatography tandem mass spectrometry (LC–MS/MS) to examine their role in the sex differentiation process. From the seven hormones, the only one that exhibited differences between the sexes was 11-KT and the plasma 11-KT concentration was found to be a useful indication of greater amberjack sex. Variations were observed in the mean values of Ad, Δ4, 11-KT, T, P4 and 17,20βP over time in one or both sexes, indicating their involvement in the sex differentiation process. |
Christidis, Georgios; Mandalakis, Manolis; Anastasiou, Thekla I; Tserpes, George; Peristeraki, Panagiota; Somarakis, Stylianos Keeping Lagocephalus sceleratus off the Table: Sources of Variation in the Quantity of TTX, TTX Analogues, and Risk of Tetrodotoxication Journal Article Toxins, 13 (12), pp. 896, 2021, ISSN: 2072-6651, (BIODIV). @article{christidis_keeping_2021b, title = {Keeping Lagocephalus sceleratus off the Table: Sources of Variation in the Quantity of TTX, TTX Analogues, and Risk of Tetrodotoxication}, author = {Georgios Christidis and Manolis Mandalakis and Thekla I Anastasiou and George Tserpes and Panagiota Peristeraki and Stylianos Somarakis}, url = {https://www.mdpi.com/2072-6651/13/12/896}, doi = {10.3390/toxins13120896}, issn = {2072-6651}, year = {2021}, date = {2021-12-01}, urldate = {2022-01-17}, journal = {Toxins}, volume = {13}, number = {12}, pages = {896}, abstract = {The invasion of the tetrodotoxin (TTX)-bearing silver-cheeked toadfish and potential poisoning due to its consumption (tetrodotoxication) threatens public safety in the Mediterranean Sea. In this study, TTX and TTX analogues of Lagocephalus sceleratus (Gmelin, 1789) were measured using liquid chromatography tandem mass spectrometry (LC-MS/MS) in fish collected off the island of Crete (Southern Mediterranean). We tested the synergistic effect of a suite of factors potentially affecting toxins’ levels and tetrodotoxication risk using general and generalized linear models, respectively. The type of tissue, geographic origin (Cretan Sea, Libyan Sea), sex, and fish maturity stage were significant predictors of toxin concentrations. Mean TTX was higher in gonads and lower in muscles, higher in the Libyan Sea and in female fish, and lower in juvenile (virgin) fish. The concentration of TTX was also significantly and positively correlated with the concentration of several TTX analogues (4-epiTTX, 4,9-anhydroTTX, 11-deoxyTTX, 5,11/6,11-dideoxyTTX, 5,6,11-trideoxyTTX, 11-norTTX-6-ol). The analysis showed that fish originating from the Libyan Sea had significantly higher probability to cause tetrodotoxication in case of consumption. The variability explained by the models developed in this study was relatively low, indicating that toxin levels are hard to predict and the consumption of L. sceleratus should therefore be avoided.}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } The invasion of the tetrodotoxin (TTX)-bearing silver-cheeked toadfish and potential poisoning due to its consumption (tetrodotoxication) threatens public safety in the Mediterranean Sea. In this study, TTX and TTX analogues of Lagocephalus sceleratus (Gmelin, 1789) were measured using liquid chromatography tandem mass spectrometry (LC-MS/MS) in fish collected off the island of Crete (Southern Mediterranean). We tested the synergistic effect of a suite of factors potentially affecting toxins’ levels and tetrodotoxication risk using general and generalized linear models, respectively. The type of tissue, geographic origin (Cretan Sea, Libyan Sea), sex, and fish maturity stage were significant predictors of toxin concentrations. Mean TTX was higher in gonads and lower in muscles, higher in the Libyan Sea and in female fish, and lower in juvenile (virgin) fish. The concentration of TTX was also significantly and positively correlated with the concentration of several TTX analogues (4-epiTTX, 4,9-anhydroTTX, 11-deoxyTTX, 5,11/6,11-dideoxyTTX, 5,6,11-trideoxyTTX, 11-norTTX-6-ol). The analysis showed that fish originating from the Libyan Sea had significantly higher probability to cause tetrodotoxication in case of consumption. The variability explained by the models developed in this study was relatively low, indicating that toxin levels are hard to predict and the consumption of L. sceleratus should therefore be avoided. |
Chatzinikolaou, Eva; Keklikoglou, Kleoniki; Grigoriou, Panagiotis; Arvanitidis, Christos Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells Journal Article Biodiversity Data Journal, 9 , pp. e75358, 2021, ISSN: 1314-2828, 1314-2836, (BIODIV). @article{chatzinikolaou_micro-ct_2021c, title = {Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells}, author = {Eva Chatzinikolaou and Kleoniki Keklikoglou and Panagiotis Grigoriou and Christos Arvanitidis}, url = {https://bdj.pensoft.net/article/75358/}, doi = {10.3897/BDJ.9.e75358}, issn = {1314-2828, 1314-2836}, year = {2021}, date = {2021-12-01}, urldate = {2022-01-17}, journal = {Biodiversity Data Journal}, volume = {9}, pages = {e75358}, abstract = {Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lack of universal standards concerning the publication and curation of micro-CT datasets. The aim of the current project was to create a virtual gallery with micro-CT scans of individuals of the marine gastropod Hexaplex trunculus , which were maintained under a combination of increased temperature and low pH conditions, thus simulating future climate change scenarios. The 3D volume-rendering models created were used to visualise the structure properties of the gastropods shells. Finally, the 3D analysis performed on the micro-CT scans was used to investigate potential changes in the shell properties of the gastropods. The derived micro-CT 3D images were annotated with detailed metadata and can be interactively displayed and manipulated using online tools through the micro-CT virtual laboratory, which was developed under the LifeWatchGreece Research Infrastructure for the dissemination of virtual image galleries collection supporting the principles of FAIR data.}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lack of universal standards concerning the publication and curation of micro-CT datasets. The aim of the current project was to create a virtual gallery with micro-CT scans of individuals of the marine gastropod Hexaplex trunculus , which were maintained under a combination of increased temperature and low pH conditions, thus simulating future climate change scenarios. The 3D volume-rendering models created were used to visualise the structure properties of the gastropods shells. Finally, the 3D analysis performed on the micro-CT scans was used to investigate potential changes in the shell properties of the gastropods. The derived micro-CT 3D images were annotated with detailed metadata and can be interactively displayed and manipulated using online tools through the micro-CT virtual laboratory, which was developed under the LifeWatchGreece Research Infrastructure for the dissemination of virtual image galleries collection supporting the principles of FAIR data. |
Andreadis, Stefanos S; Panteli, Nikolas; Mastoraki, Maria; Rizou, Eleftheria; Stefanou, Vassilia; Tzentilasvili, Sofia; Sarrou, Eirini; Chatzifotis, Stavros; Krigas, Nikos; Antonopoulou, Efthimia Antioxidants, 11 (1), pp. 68, 2021, ISSN: 2076-3921. @article{andreadis_towards_2021, title = {Towards Functional Insect Feeds: Agri-Food By-Products Enriched with Post-Distillation Residues of Medicinal Aromatic Plants in Tenebrio molitor (Coleoptera: Tenebrionidae) Breeding}, author = {Stefanos S Andreadis and Nikolas Panteli and Maria Mastoraki and Eleftheria Rizou and Vassilia Stefanou and Sofia Tzentilasvili and Eirini Sarrou and Stavros Chatzifotis and Nikos Krigas and Efthimia Antonopoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Αndreadis-antioxidants-22.pdf https://www.mdpi.com/2076-3921/11/1/68}, doi = {10.3390/antiox11010068}, issn = {2076-3921}, year = {2021}, date = {2021-12-01}, urldate = {2022-05-09}, journal = {Antioxidants}, volume = {11}, number = {1}, pages = {68}, abstract = {Sustainability, circular economy and alternative production systems are urgent imperatives for humanity and animal husbandry. Unless wasted, agri-food by-products can offer a promising source of high value. We evaluated the effect of rice bran (RB), corncob (CC), potato peels (PP), solid biogas residues (BR), and olive-oil processing residuals (OR), as alternative substrates to wheat bran (WB as control), on the growth and nutritional value of Tenebrio molitor during its breeding for animal feeds and/or human consumption. Innovation-wise, we further investigated the substrate supplementation (0, 10, 20%) with post-distillation residues of Mediterranean aromatic-medicinal plants (MAPs: lavender, Greek oregano, rosemary, olive; 1:1:1:1 ratio). Tenebrio molitor larvae (TML) were reared in all the studied substrates, and TML and diets’ proximate and fatty acid compositions as well as total phenol and flavonoid content and antioxidant potential were assessed using standard procedures. After statistical analysis of correlations, we observed that CC promoted oviposition and progeny survival; larval weight and dry matter were positively affected mainly by dietary energy and fat content; number of TML and/or larval weight increased using 10% MAPs inclusion in WB, RB and OR or RB, OR, BR and PP, respectively, which did not affect protein content; TML fatty acid composition decreased the content of saturated ones and increased that of mono-unsaturated ones; MAPs residues had an apparent favorable impact on total phenolic content and antioxidant activity of each substrate, with RB displaying the highest capacity and content. These findings indicate that alternative substrates can be exploited and their enrichment with natural phenolics is able to influence T. molitor growth, offering highly beneficial and nutritional value.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sustainability, circular economy and alternative production systems are urgent imperatives for humanity and animal husbandry. Unless wasted, agri-food by-products can offer a promising source of high value. We evaluated the effect of rice bran (RB), corncob (CC), potato peels (PP), solid biogas residues (BR), and olive-oil processing residuals (OR), as alternative substrates to wheat bran (WB as control), on the growth and nutritional value of Tenebrio molitor during its breeding for animal feeds and/or human consumption. Innovation-wise, we further investigated the substrate supplementation (0, 10, 20%) with post-distillation residues of Mediterranean aromatic-medicinal plants (MAPs: lavender, Greek oregano, rosemary, olive; 1:1:1:1 ratio). Tenebrio molitor larvae (TML) were reared in all the studied substrates, and TML and diets’ proximate and fatty acid compositions as well as total phenol and flavonoid content and antioxidant potential were assessed using standard procedures. After statistical analysis of correlations, we observed that CC promoted oviposition and progeny survival; larval weight and dry matter were positively affected mainly by dietary energy and fat content; number of TML and/or larval weight increased using 10% MAPs inclusion in WB, RB and OR or RB, OR, BR and PP, respectively, which did not affect protein content; TML fatty acid composition decreased the content of saturated ones and increased that of mono-unsaturated ones; MAPs residues had an apparent favorable impact on total phenolic content and antioxidant activity of each substrate, with RB displaying the highest capacity and content. These findings indicate that alternative substrates can be exploited and their enrichment with natural phenolics is able to influence T. molitor growth, offering highly beneficial and nutritional value. |
Katsika, Lydia; Tasbozan, Oguz; Mastoraki, Maria; Karapanagiotis, Stelios; Zalamitsou, Chrysa; Feidantsis, Konstantinos; Antonopoulou, Efthimia; Chatzifotis, Stavros Aquaculture Research, 52 (11), pp. 5760–5776, 2021, ISSN: 1355-557X, 1365-2109. @article{katsika_effects_2021, title = {Effects of fish oil substitution by hazelnut oil on growth performance, whole‐body fatty acid composition and enzymes of intermediary metabolism of juvenile meagre ( textitArgyrosomus regius Asso, 1801)}, author = {Lydia Katsika and Oguz Tasbozan and Maria Mastoraki and Stelios Karapanagiotis and Chrysa Zalamitsou and Konstantinos Feidantsis and Efthimia Antonopoulou and Stavros Chatzifotis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/12/2021-Katsika-ARE-pre-print-78.pdf https://onlinelibrary.wiley.com/doi/10.1111/are.15452}, doi = {10.1111/are.15452}, issn = {1355-557X, 1365-2109}, year = {2021}, date = {2021-11-01}, urldate = {2021-12-01}, journal = {Aquaculture Research}, volume = {52}, number = {11}, pages = {5760--5776}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Brambila‐Souza, Gabriela; Mylonas, Constantinos Chrysanthos; de Mello, Paulo Henrique; Kuradomi, Rafael Yutaka; Batlouni, Sergio Ricardo; Tolussi, Carlos Eduardo; Moreira, Renata Guimarães Aquaculture Research, 52 (11), pp. 5595–5605, 2021, ISSN: 1355-557X, 1365-2109. @article{brambilasouza_gnrha_2021, title = {GnRHa implants and temperature modulate Lambari‐do‐rabo‐amarelo, textitAstyanax altiparanae (Characiformes: Characidae) induced reproduction out of the reproductive season}, author = {Gabriela Brambila‐Souza and Constantinos Chrysanthos Mylonas and Paulo Henrique de Mello and Rafael Yutaka Kuradomi and Sergio Ricardo Batlouni and Carlos Eduardo Tolussi and Renata Guimarães Moreira}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/12/2021-Brambila-ARE-pre-print-77.pdf https://onlinelibrary.wiley.com/doi/10.1111/are.15435}, doi = {10.1111/are.15435}, issn = {1355-557X, 1365-2109}, year = {2021}, date = {2021-11-01}, urldate = {2021-12-01}, journal = {Aquaculture Research}, volume = {52}, number = {11}, pages = {5595--5605}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bompoti, Andreana; Papazoglou, Andreas S; Moysidis, Dimitrios V; Otountzidis, Nikolaos; Karagiannidis, Efstratios; Stalikas, Nikolaos; Panteris, Eleftherios; Ganesh, Vijayakumar; Sanctuary, Thomas; Arvanitidis, Christos; Sianos, Georgios; Michaelson, James S; Herrmann, Markus D Volumetric Imaging of Lung Tissue at Micrometer Resolution: Clinical Applications of Micro-CT for the Diagnosis of Pulmonary Diseases Journal Article Diagnostics, 11 (11), pp. 2075, 2021, ISSN: 2075-4418, (BIODIV). @article{bompoti_volumetric_2021, title = {Volumetric Imaging of Lung Tissue at Micrometer Resolution: Clinical Applications of Micro-CT for the Diagnosis of Pulmonary Diseases}, author = {Andreana Bompoti and Andreas S Papazoglou and Dimitrios V Moysidis and Nikolaos Otountzidis and Efstratios Karagiannidis and Nikolaos Stalikas and Eleftherios Panteris and Vijayakumar Ganesh and Thomas Sanctuary and Christos Arvanitidis and Georgios Sianos and James S Michaelson and Markus D Herrmann}, url = {https://www.mdpi.com/2075-4418/11/11/2075}, doi = {10.3390/diagnostics11112075}, issn = {2075-4418}, year = {2021}, date = {2021-11-01}, urldate = {2022-01-17}, journal = {Diagnostics}, volume = {11}, number = {11}, pages = {2075}, abstract = {Micro-computed tomography (micro-CT) is a promising novel medical imaging modality that allows for non-destructive volumetric imaging of surgical tissue specimens at high spatial resolution. The aim of this study is to provide a comprehensive assessment of the clinical applications of micro-CT for the tissue-based diagnosis of lung diseases. This scoping review was conducted in accordance with the PRISMA Extension for Scoping Reviews, aiming to include every clinical study reporting on micro-CT imaging of human lung tissues. A literature search yielded 570 candidate articles, out of which 37 were finally included in the review. Of the selected studies, 9 studies explored via micro-CT imaging the morphology and anatomy of normal human lung tissue; 21 studies investigated microanatomic pulmonary alterations due to obstructive or restrictive lung diseases, such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and cystic fibrosis; and 7 studies examined the utility of micro-CT imaging in assessing lung cancer lesions (n = 4) or in transplantation-related pulmonary alterations (n = 3). The selected studies reported that micro-CT could successfully detect several lung diseases providing three-dimensional images of greater detail and resolution than routine optical slide microscopy, and could additionally provide valuable volumetric insight in both restrictive and obstructive lung diseases. In conclusion, micro-CT-based volumetric measurements and qualitative evaluations of pulmonary tissue structures can be utilized for the clinical management of a variety of lung diseases. With micro-CT devices becoming more accessible, the technology has the potential to establish itself as a core diagnostic imaging modality in pathology and to enable integrated histopathologic and radiologic assessment of lung cancer and other lung diseases.}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } Micro-computed tomography (micro-CT) is a promising novel medical imaging modality that allows for non-destructive volumetric imaging of surgical tissue specimens at high spatial resolution. The aim of this study is to provide a comprehensive assessment of the clinical applications of micro-CT for the tissue-based diagnosis of lung diseases. This scoping review was conducted in accordance with the PRISMA Extension for Scoping Reviews, aiming to include every clinical study reporting on micro-CT imaging of human lung tissues. A literature search yielded 570 candidate articles, out of which 37 were finally included in the review. Of the selected studies, 9 studies explored via micro-CT imaging the morphology and anatomy of normal human lung tissue; 21 studies investigated microanatomic pulmonary alterations due to obstructive or restrictive lung diseases, such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and cystic fibrosis; and 7 studies examined the utility of micro-CT imaging in assessing lung cancer lesions (n = 4) or in transplantation-related pulmonary alterations (n = 3). The selected studies reported that micro-CT could successfully detect several lung diseases providing three-dimensional images of greater detail and resolution than routine optical slide microscopy, and could additionally provide valuable volumetric insight in both restrictive and obstructive lung diseases. In conclusion, micro-CT-based volumetric measurements and qualitative evaluations of pulmonary tissue structures can be utilized for the clinical management of a variety of lung diseases. With micro-CT devices becoming more accessible, the technology has the potential to establish itself as a core diagnostic imaging modality in pathology and to enable integrated histopathologic and radiologic assessment of lung cancer and other lung diseases. |
Baltoumas, Fotis A; Zafeiropoulou, Sofia; Karatzas, Evangelos; Paragkamian, Savvas; Thanati, Foteini; Iliopoulos, Ioannis; Eliopoulos, Aristides G; Schneider, Reinhard; Jensen, Lars Juhl; Pafilis, Evangelos; Pavlopoulos, Georgios A NAR Genomics and Bioinformatics, 3 (4), pp. lqab090, 2021, ISSN: 2631-9268. @article{baltoumas_onthefly20_2021, title = {OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis}, author = {Fotis A Baltoumas and Sofia Zafeiropoulou and Evangelos Karatzas and Savvas Paragkamian and Foteini Thanati and Ioannis Iliopoulos and Aristides G Eliopoulos and Reinhard Schneider and Lars Juhl Jensen and Evangelos Pafilis and Georgios A Pavlopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/12/2021-Baltoumas-NAR-74.pdf https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqab090/6382333}, doi = {10.1093/nargab/lqab090}, issn = {2631-9268}, year = {2021}, date = {2021-10-01}, urldate = {2021-12-01}, journal = {NAR Genomics and Bioinformatics}, volume = {3}, number = {4}, pages = {lqab090}, abstract = {Abstract Extracting and processing information from documents is of great importance as lots of experimental results and findings are stored in local files. Therefore, extracting and analyzing biomedical terms from such files in an automated way is absolutely necessary. In this article, we present OnTheFly2.0, a web application for extracting biomedical entities from individual files such as plain texts, office documents, PDF files or images. OnTheFly2.0 can generate informative summaries in popup windows containing knowledge related to the identified terms along with links to various databases. It uses the EXTRACT tagging service to perform named entity recognition (NER) for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and gene ontology terms. Multiple files can be analyzed, whereas identified terms such as proteins or genes can be explored through functional enrichment analysis or be associated with diseases and PubMed entries. Finally, protein–protein and protein–chemical networks can be generated with the use of STRING and STITCH services. To demonstrate its capacity for knowledge discovery, we interrogated published meta-analyses of clinical biomarkers of severe COVID-19 and uncovered inflammatory and senescence pathways that impact disease pathogenesis. OnTheFly2.0 currently supports 197 species and is available at http://bib.fleming.gr:3838/OnTheFly/ and http://onthefly.pavlopouloslab.info.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Extracting and processing information from documents is of great importance as lots of experimental results and findings are stored in local files. Therefore, extracting and analyzing biomedical terms from such files in an automated way is absolutely necessary. In this article, we present OnTheFly2.0, a web application for extracting biomedical entities from individual files such as plain texts, office documents, PDF files or images. OnTheFly2.0 can generate informative summaries in popup windows containing knowledge related to the identified terms along with links to various databases. It uses the EXTRACT tagging service to perform named entity recognition (NER) for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and gene ontology terms. Multiple files can be analyzed, whereas identified terms such as proteins or genes can be explored through functional enrichment analysis or be associated with diseases and PubMed entries. Finally, protein–protein and protein–chemical networks can be generated with the use of STRING and STITCH services. To demonstrate its capacity for knowledge discovery, we interrogated published meta-analyses of clinical biomarkers of severe COVID-19 and uncovered inflammatory and senescence pathways that impact disease pathogenesis. OnTheFly2.0 currently supports 197 species and is available at http://bib.fleming.gr:3838/OnTheFly/ and http://onthefly.pavlopouloslab.info. |
Fraschetti, Simonetta; McOwen, Chris; Papa, Loredana; Papadopoulou, Nadia; Bilan, Meri; Boström, Christoffer; Capdevila, Pol; Carreiro-Silva, Marina; Carugati, Laura; Cebrian, Emma; Coll, Marta; Dailianis, Thanos; Danovaro, Roberto; Leo, Francesco De; Fiorentino, Dario; Gagnon, Karine; Gambi, Cristina; Garrabou, Joaquim; Gerovasileiou, Vasilis; Hereu, Bernat; Kipson, Silvija; Kotta, Jonne; Ledoux, Jean-Baptiste; Linares, Cristina; Martin, Juliette; Medrano, Alba; Montero-Serra, I; Morato, Telmo; Pusceddu, Antonio; Sevastou, Katerina; Smith, Christopher J; Verdura, Jana; Guarnieri, Giuseppe Where Is More Important Than How in Coastal and Marine Ecosystems Restoration Journal Article Frontiers in Marine Science, 8 , pp. 626843, 2021, ISSN: 2296-7745. @article{fraschetti_where_2021, title = {Where Is More Important Than How in Coastal and Marine Ecosystems Restoration}, author = {Simonetta Fraschetti and Chris McOwen and Loredana Papa and Nadia Papadopoulou and Meri Bilan and Christoffer Boström and Pol Capdevila and Marina Carreiro-Silva and Laura Carugati and Emma Cebrian and Marta Coll and Thanos Dailianis and Roberto Danovaro and Francesco De Leo and Dario Fiorentino and Karine Gagnon and Cristina Gambi and Joaquim Garrabou and Vasilis Gerovasileiou and Bernat Hereu and Silvija Kipson and Jonne Kotta and Jean-Baptiste Ledoux and Cristina Linares and Juliette Martin and Alba Medrano and I Montero-Serra and Telmo Morato and Antonio Pusceddu and Katerina Sevastou and Christopher J Smith and Jana Verdura and Giuseppe Guarnieri}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/12/2021-Fraschetti-fmars-75.pdf https://www.frontiersin.org/articles/10.3389/fmars.2021.626843/full}, doi = {10.3389/fmars.2021.626843}, issn = {2296-7745}, year = {2021}, date = {2021-10-01}, urldate = {2021-12-01}, journal = {Frontiers in Marine Science}, volume = {8}, pages = {626843}, abstract = {Restoration is considered an effective strategy to accelerate the recovery of biological communities at local scale. However, the effects of restoration actions in the marine ecosystems are still unpredictable. We performed a global analysis of published literature to identify the factors increasing the probability of restoration success in coastal and marine systems. Our results confirm that the majority of active restoration initiatives are still concentrated in the northern hemisphere and that most of information gathered from restoration efforts derives from a relatively small subset of species. The analysis also indicates that many studies are still experimental in nature, covering small spatial and temporal scales. Despite the limits of assessing restoration effectiveness in absence of a standardized definition of success, the context (degree of human impact, ecosystem type, habitat) of where the restoration activity is undertaken is of greater relevance to a successful outcome than how (method) the restoration is carried out. Contrary to expectations, we found that restoration is not necessarily more successful closer to protected areas (PA) and in areas of moderate human impact. This result can be motivated by the limits in assessing the success of interventions and by the tendency of selecting areas in more obvious need of restoration, where the potential of actively restoring a degraded site is more evident. Restoration sites prioritization considering human uses and conservation status present in the region is of vital importance to obtain the intended outcomes and galvanize further actions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Restoration is considered an effective strategy to accelerate the recovery of biological communities at local scale. However, the effects of restoration actions in the marine ecosystems are still unpredictable. We performed a global analysis of published literature to identify the factors increasing the probability of restoration success in coastal and marine systems. Our results confirm that the majority of active restoration initiatives are still concentrated in the northern hemisphere and that most of information gathered from restoration efforts derives from a relatively small subset of species. The analysis also indicates that many studies are still experimental in nature, covering small spatial and temporal scales. Despite the limits of assessing restoration effectiveness in absence of a standardized definition of success, the context (degree of human impact, ecosystem type, habitat) of where the restoration activity is undertaken is of greater relevance to a successful outcome than how (method) the restoration is carried out. Contrary to expectations, we found that restoration is not necessarily more successful closer to protected areas (PA) and in areas of moderate human impact. This result can be motivated by the limits in assessing the success of interventions and by the tendency of selecting areas in more obvious need of restoration, where the potential of actively restoring a degraded site is more evident. Restoration sites prioritization considering human uses and conservation status present in the region is of vital importance to obtain the intended outcomes and galvanize further actions. |
Chatzinikolaou, Eva; Keklikoglou, Kleoniki Micro-CT protocols for scanning and 3D analysis of Hexaplex trunculus during its different life stages Journal Article 9 , pp. e71542, 2021, ISSN: 1314-2828. @article{chatzinikolaou_micro-ct_2021, title = {Micro-CT protocols for scanning and 3D analysis of Hexaplex trunculus during its different life stages}, author = {Eva Chatzinikolaou and Kleoniki Keklikoglou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Chatzinikolaou-and-Keklikoglou-BDJournal-70.pdf https://bdj.pensoft.net/article/71542/}, doi = {10.3897/BDJ.9.e71542}, issn = {1314-2828}, year = {2021}, date = {2021-09-15}, urldate = {2021-09-22}, volume = {9}, pages = {e71542}, abstract = {Micro-computed tomography (micro-CT) is a high-resolution 3D-imaging technique which is now increasingly applied in biological studies focusing on taxonomy and functional morphology. The creation of virtual representations of specimens can increase availability of otherwise underexploited and inaccessible samples. The 3D model dataset can be also further processed through volume rendering and morphometric analysis. The success of micro-CT as a visualisation technique depends on several methodological manipulations, including the use of contrast enhancing staining agents, filters, scanning mediums, containers, exposure time and frame averaging. The aim of this study was to standardise a series of micro-CT scanning and 3D analysis protocols for a marine gastropod species, Hexaplex trunculus. The analytical protocols have followed all the developmental stages of this gastropod, from egg capsules and embryos to juveniles and adults.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Micro-computed tomography (micro-CT) is a high-resolution 3D-imaging technique which is now increasingly applied in biological studies focusing on taxonomy and functional morphology. The creation of virtual representations of specimens can increase availability of otherwise underexploited and inaccessible samples. The 3D model dataset can be also further processed through volume rendering and morphometric analysis. The success of micro-CT as a visualisation technique depends on several methodological manipulations, including the use of contrast enhancing staining agents, filters, scanning mediums, containers, exposure time and frame averaging. The aim of this study was to standardise a series of micro-CT scanning and 3D analysis protocols for a marine gastropod species, Hexaplex trunculus. The analytical protocols have followed all the developmental stages of this gastropod, from egg capsules and embryos to juveniles and adults. |
Oikonomou, Stavroula; Tsakogiannis, Alexandros; Kriaridou, Christina; Danis, Theodoros; Manousaki, Tereza; Chatziplis, Dimitris; Papandroulakis, Nikos; Mylonas, Constantinos C; Triantafyllidis, Alexandros; Tsigenopoulos, Costas S 21 , pp. 100855, 2021, ISSN: 23525134. @article{oikonomou_first_2021, title = {First linkage maps and a pilot QTL analysis for early growth performance in common dentex (Dentex dentex) and sharpsnout seabream (Diplodus puntazzo)}, author = {Stavroula Oikonomou and Alexandros Tsakogiannis and Christina Kriaridou and Theodoros Danis and Tereza Manousaki and Dimitris Chatziplis and Nikos Papandroulakis and Constantinos C Mylonas and Alexandros Triantafyllidis and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Oikonomou-AquaReports-68.pdf https://linkinghub.elsevier.com/retrieve/pii/S2352513421002714}, doi = {10.1016/j.aqrep.2021.100855}, issn = {23525134}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-22}, volume = {21}, pages = {100855}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Cascarano, Maria Chiara; Stavrakidis-Zachou, Orestis; Mladineo, Ivona; Thompson, Kim D; Papandroulakis, Nikos; Katharios, Pantelis Mediterranean Aquaculture in a Changing Climate: Temperature Effects on Pathogens and Diseases of Three Farmed Fish Species Journal Article 10 (9), pp. 1205, 2021. @article{cascarano_mediterranean_2021, title = {Mediterranean Aquaculture in a Changing Climate: Temperature Effects on Pathogens and Diseases of Three Farmed Fish Species}, author = {Maria Chiara Cascarano and Orestis Stavrakidis-Zachou and Ivona Mladineo and Kim D Thompson and Nikos Papandroulakis and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Cascarano-pathogens-71.pdf https://www.mdpi.com/2076-0817/10/9/1205}, doi = {10.3390/pathogens10091205}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-22}, volume = {10}, number = {9}, pages = {1205}, abstract = {Climate change is expected to have a drastic effect on aquaculture worldwide. As we move forward with the agenda to increase and diversify aquaculture production, rising temperatures will have a progressively relevant impact on fish farming, linked to a multitude of issues associated with fish welfare. Temperature affects the physiology of both fish and pathogens, and has the potential to lead to significant increases in disease outbreaks within aquaculture systems, resulting in severe financial impacts. Significant shifts in future temperature regimes are projected for the Mediterranean Sea. We therefore aim to review and discuss the existing knowledge relating to disease outbreaks in the context of climate change in Mediterranean finfish aquaculture. The objective is to describe the effects of temperature on the physiology of both fish and pathogens, and moreover to list and discuss the principal diseases of the three main fish species farmed in the Mediterranean, namely gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), and meagre (Argyrosomus regius). We will attempt to link the pathology of each disease to a specific temperature range, while discussing potential future disease threats associated with the available climate change trends for the Mediterranean Sea.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Climate change is expected to have a drastic effect on aquaculture worldwide. As we move forward with the agenda to increase and diversify aquaculture production, rising temperatures will have a progressively relevant impact on fish farming, linked to a multitude of issues associated with fish welfare. Temperature affects the physiology of both fish and pathogens, and has the potential to lead to significant increases in disease outbreaks within aquaculture systems, resulting in severe financial impacts. Significant shifts in future temperature regimes are projected for the Mediterranean Sea. We therefore aim to review and discuss the existing knowledge relating to disease outbreaks in the context of climate change in Mediterranean finfish aquaculture. The objective is to describe the effects of temperature on the physiology of both fish and pathogens, and moreover to list and discuss the principal diseases of the three main fish species farmed in the Mediterranean, namely gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), and meagre (Argyrosomus regius). We will attempt to link the pathology of each disease to a specific temperature range, while discussing potential future disease threats associated with the available climate change trends for the Mediterranean Sea. |
Keklikoglou, Kleoniki; Arvanitidis, Christos; Chatzigeorgiou, Georgios; Chatzinikolaou, Eva; Karagiannidis, Efstratios; Koletsa, Triantafyllia; Magoulas, Antonios; Makris, Konstantinos; Mavrothalassitis, George; Papanagnou, Eleni-Dimitra; Papazoglou, Andreas S; Pavloudi, Christina; Trougakos, Ioannis P; Vasileiadou, Katerina; Vogiatzi, Angeliki Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques Journal Article 7 (9), pp. 172, 2021, ISSN: 2313-433X. @article{keklikoglou_micro-ct_2021, title = {Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques}, author = {Kleoniki Keklikoglou and Christos Arvanitidis and Georgios Chatzigeorgiou and Eva Chatzinikolaou and Efstratios Karagiannidis and Triantafyllia Koletsa and Antonios Magoulas and Konstantinos Makris and George Mavrothalassitis and Eleni-Dimitra Papanagnou and Andreas S Papazoglou and Christina Pavloudi and Ioannis P Trougakos and Katerina Vasileiadou and Angeliki Vogiatzi}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Keklikoglou-jimaging-66-1.pdf https://www.mdpi.com/2313-433X/7/9/172}, doi = {10.3390/jimaging7090172}, issn = {2313-433X}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-22}, volume = {7}, number = {9}, pages = {172}, abstract = {Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised. |
Stavrakidis-Zachou, Orestis; Lika, Konstadia; Michail, Pavlidis; Tsalafouta, Aleka; Mohamed, Asaad H; Nikos, Papandroulakis Thermal tolerance, metabolic scope and performance of meagre, Argyrosomus regius, reared under high water temperatures Journal Article 100 , pp. 103063, 2021, ISSN: 03064565. @article{stavrakidis-zachou_thermal_2021, title = {Thermal tolerance, metabolic scope and performance of meagre, Argyrosomus regius, reared under high water temperatures}, author = {Orestis Stavrakidis-Zachou and Konstadia Lika and Pavlidis Michail and Aleka Tsalafouta and Asaad H Mohamed and Papandroulakis Nikos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Stavrakidis-JoTB-65-pre-print.pdf https://linkinghub.elsevier.com/retrieve/pii/S030645652100231X}, doi = {10.1016/j.jtherbio.2021.103063}, issn = {03064565}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-16}, volume = {100}, pages = {103063}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Nikolopoulou, Stamatina; Berov, Dimitar; Klayn, Stefania; Dimitrov, Lyubomir; Velkovsky, Kiril; Chatzinikolaou, Eva; Chatzigeorgiou, Giorgos; Karamfilov, Ventzislav; Pavloudi, Christina Benthic habitat mapping of Plazh Gradina – Zlatna ribka (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea) Journal Article 9 , pp. e71972, 2021, ISSN: 1314-2828, 1314-2836. @article{nikolopoulou_benthic_2021, title = {Benthic habitat mapping of Plazh Gradina – Zlatna ribka (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea)}, author = {Stamatina Nikolopoulou and Dimitar Berov and Stefania Klayn and Lyubomir Dimitrov and Kiril Velkovsky and Eva Chatzinikolaou and Giorgos Chatzigeorgiou and Ventzislav Karamfilov and Christina Pavloudi}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Nikolopoulou-BDJ-64.pdf https://bdj.pensoft.net/article/71972/}, doi = {10.3897/BDJ.9.e71972}, issn = {1314-2828, 1314-2836}, year = {2021}, date = {2021-08-23}, urldate = {2021-09-16}, volume = {9}, pages = {e71972}, abstract = {Habitat mapping is nеcessary for the efficient conservation and protection of marine ecosystems. In addition, it is a requirement for EU Member States as stated in the European Union (EU) Habitats Directive (92/43/EEC), as well as necessary for the achievement and maintenance of 'good environmental status (GES)' of benthic marine habitats in the framework of the EU Marine Strategy Framework Directive (2008/56/EC). This study provides baseline information on the marine benthic habitats of Sozopol Bay (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea). These two Natura 2000 sites were selected as study sites of the RECONNECT project, which aimed at creating a transnational cooperative network to confront the environmental threats of ecosystems with a high natural and cultural interest, by the establishment of common practices and a joint regional strategy. The specific objective was to map the marine habitats using a defined a priori classification (EUNIS), with the ultimate purpose of supporting government marine spatial planning, management and decision-making processes through the development of a Decision Support System.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Habitat mapping is nеcessary for the efficient conservation and protection of marine ecosystems. In addition, it is a requirement for EU Member States as stated in the European Union (EU) Habitats Directive (92/43/EEC), as well as necessary for the achievement and maintenance of 'good environmental status (GES)' of benthic marine habitats in the framework of the EU Marine Strategy Framework Directive (2008/56/EC). This study provides baseline information on the marine benthic habitats of Sozopol Bay (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea). These two Natura 2000 sites were selected as study sites of the RECONNECT project, which aimed at creating a transnational cooperative network to confront the environmental threats of ecosystems with a high natural and cultural interest, by the establishment of common practices and a joint regional strategy. The specific objective was to map the marine habitats using a defined a priori classification (EUNIS), with the ultimate purpose of supporting government marine spatial planning, management and decision-making processes through the development of a Decision Support System. |
