2022 |
Michail, George; Berillis, Panagiotis; Nakas, Christos; Henry, Morgane; Mente, Eleni Haematology reference values for textitDicentrarchus labrax and textitSparus aurata : A systematic review and meta‐analysis Journal Article Journal of Fish Diseases, 45 (10), pp. 1549–1570, 2022, ISSN: 0140-7775, 1365-2761. @article{michail_haematology_2022, title = {Haematology reference values for textitDicentrarchus labrax and textitSparus aurata : A systematic review and meta‐analysis}, author = {George Michail and Panagiotis Berillis and Christos Nakas and Morgane Henry and Eleni Mente}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/09/2022-Michail-FD-61-preprint.pdf https://onlinelibrary.wiley.com/doi/10.1111/jfd.13680}, doi = {10.1111/jfd.13680}, issn = {0140-7775, 1365-2761}, year = {2022}, date = {2022-01-01}, urldate = {2022-09-26}, journal = {Journal of Fish Diseases}, volume = {45}, number = {10}, pages = {1549--1570}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
García-Escudero, Catalina A; Tsigenopoulos, Costas S; Gerakaris, Vasilis; Tsakogiannis, Alexandros; Apostolaki, Eugenia T ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea Journal Article Diversity, 14 (2), pp. 76, 2022, ISSN: 1424-2818. @article{garcia-escudero_its_2022, title = {ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea}, author = {Catalina A García-Escudero and Costas S Tsigenopoulos and Vasilis Gerakaris and Alexandros Tsakogiannis and Eugenia T Apostolaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Garcia-Escudero-DIVERSITY-8.pdf https://www.mdpi.com/1424-2818/14/2/76}, doi = {10.3390/d14020076}, issn = {1424-2818}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Diversity}, volume = {14}, number = {2}, pages = {76}, abstract = {Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions. |
Nousias, O; Oikonomou, S; Manousaki, T; Papadogiannis, V; Angelova, N; Tsaparis, D; Tsakogiannis, A; Duncan, N; Estevez, A; Tzokas, K; Pavlidis, M; Chatziplis, D; Tsigenopoulos, C S Scientific Reports, 12 (1), pp. 5301, 2022, ISSN: 2045-2322. @article{nousias_linkage_2022, title = {Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing}, author = {O Nousias and S Oikonomou and T Manousaki and V Papadogiannis and N Angelova and D Tsaparis and A Tsakogiannis and N Duncan and A Estevez and K Tzokas and M Pavlidis and D Chatziplis and C S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Nousias-Sci-Report-27.pdf https://www.nature.com/articles/s41598-022-09289-4}, doi = {10.1038/s41598-022-09289-4}, issn = {2045-2322}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Scientific Reports}, volume = {12}, number = {1}, pages = {5301}, abstract = {Abstract Meagre ( Argyrosomus regius ), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax , traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Meagre ( Argyrosomus regius ), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax , traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production. |
Charisi, C; Kodonas, K; Keklikoglou, K; Arhakis, A; Arapostathis, K A; Kotsanos, N Morphological, histological, and chemical analysis of first permanent molars with molar incisor malformation Journal Article European Archives of Paediatric Dentistry, 2022, ISSN: 1818-6300, 1996-9805. @article{charisi_morphological_2022, title = {Morphological, histological, and chemical analysis of first permanent molars with molar incisor malformation}, author = {C Charisi and K Kodonas and K Keklikoglou and A Arhakis and K A Arapostathis and N Kotsanos}, url = {https://link.springer.com/10.1007/s40368-022-00723-9https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Charisi-EAPD-50-pre-print.pdf https://link.springer.com/10.1007/s40368-022-00723-9}, doi = {10.1007/s40368-022-00723-9}, issn = {1818-6300, 1996-9805}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {European Archives of Paediatric Dentistry}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Solís, Francisco Javier Toledo; Fernandes, Jorge M O; Sarropoulou, Elena; Monzón, Ignacio Fernández Noncoding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks Incollection Cellular and Molecular Approaches in Fish Biology, pp. 105–159, Elsevier, 2022, ISBN: 978-0-12-822273-7. @incollection{toledo_solis_noncoding_2022, title = {Noncoding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks}, author = {Francisco Javier Toledo Solís and Jorge M O Fernandes and Elena Sarropoulou and Ignacio Fernández Monzón}, url = {https://linkinghub.elsevier.com/retrieve/pii/B9780128222737000124}, doi = {10.1016/B978-0-12-822273-7.00012-4}, isbn = {978-0-12-822273-7}, year = {2022}, date = {2022-01-01}, urldate = {2022-02-17}, booktitle = {Cellular and Molecular Approaches in Fish Biology}, pages = {105--159}, publisher = {Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Koulouri, Panayota; Mogias, Athanasios; Gerovasileiou, Vasilis Mediterranean Marine Science, 23 (2), pp. 266–269, 2022, ISSN: 1791-6763, 1108-393X. @article{koulouri_ocean_2022, title = {Ocean Literacy across the Mediterranean Sea region in the Era of 2030 Agenda and the Decade of Ocean Science for Sustainable Development (2021-2030)}, author = {Panayota Koulouri and Athanasios Mogias and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Koulouri-editorial-MedMarSci-29.pdf}, doi = {10.12681/mms.30099}, issn = {1791-6763, 1108-393X}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Mediterranean Marine Science}, volume = {23}, number = {2}, pages = {266--269}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kazanidis, Georgios; Guido, Adriano; Rosso, Antonietta; Sanfilippo, Rossana; Roberts, Murray J; Gerovasileiou, Vasilis One on Top of the Other: Exploring the Habitat Cascades Phenomenon in Iconic Biogenic Marine Habitats Journal Article Diversity, 14 (4), pp. 290, 2022, ISSN: 1424-2818. @article{kazanidis_one_2022, title = {One on Top of the Other: Exploring the Habitat Cascades Phenomenon in Iconic Biogenic Marine Habitats}, author = {Georgios Kazanidis and Adriano Guido and Antonietta Rosso and Rossana Sanfilippo and Murray J Roberts and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/09/2022-Kazanidis-Diversity-57-1.pdf https://www.mdpi.com/1424-2818/14/4/290}, doi = {10.3390/d14040290}, issn = {1424-2818}, year = {2022}, date = {2022-01-01}, urldate = {2022-09-26}, journal = {Diversity}, volume = {14}, number = {4}, pages = {290}, abstract = {Biogenic habitats often form hot spots of biodiversity. However, the role of epibiosis and the ‘habitat cascades’ phenomenon in enhancing structural heterogeneity and biodiversity in biogenic habitats in remote and difficult-to-access areas is little known. In this work, we provide the first insight by exploring epibiosis across remote habitats that often support high levels of biodiversity, i.e., cold-water coral reefs and marine caves. The present study acts as a stepping-stone for the further exploration of ‘habitat cascades’ in habitats where scientific knowledge about this phenomenon is limited.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Biogenic habitats often form hot spots of biodiversity. However, the role of epibiosis and the ‘habitat cascades’ phenomenon in enhancing structural heterogeneity and biodiversity in biogenic habitats in remote and difficult-to-access areas is little known. In this work, we provide the first insight by exploring epibiosis across remote habitats that often support high levels of biodiversity, i.e., cold-water coral reefs and marine caves. The present study acts as a stepping-stone for the further exploration of ‘habitat cascades’ in habitats where scientific knowledge about this phenomenon is limited. |
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. |
Teixeira, Marcos A L; Langeneck, Joachim; Vieira, Pedro E; Hernández, José Carlos; Sampieri, Bruno R; Kasapidis, Panagiotis; Mucciolo, Serena; Bakken, Torkild; Ravara, Ascensão; Nygren, Arne; Costa, Filipe O Reappraisal of the hyperdiverse Journal Article Invertebrate Systematics, 36 (11), pp. 1017–1061, 2022, ISSN: 1445-5226, 1447-2600. @article{teixeira_reappraisal_2022, title = {Reappraisal of the hyperdiverse}, author = {Marcos A L Teixeira and Joachim Langeneck and Pedro E Vieira and José Carlos Hernández and Bruno R Sampieri and Panagiotis Kasapidis and Serena Mucciolo and Torkild Bakken and Ascensão Ravara and Arne Nygren and Filipe O Costa}, editor = {Greg Rouse}, url = {https://www.publish.csiro.au/IS/IS21084}, doi = {10.1071/IS21084}, issn = {1445-5226, 1447-2600}, year = {2022}, date = {2022-01-01}, urldate = {2023-05-25}, journal = {Invertebrate Systematics}, volume = {36}, number = {11}, pages = {1017--1061}, abstract = {Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D}, keywords = {}, pubstate = {published}, tppubtype = {article} } Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D |
Kaitetzidou, Elisavet; Gilfillan, Gregor D; Antonopoulou, Efthimia; Sarropoulou, Elena Sex-biased dynamics of three-spined stickleback (Gasterosteus aculeatus) gene expression patterns Journal Article Genomics, 114 (1), pp. 266–277, 2022, ISSN: 08887543. @article{kaitetzidou_sex-biased_2022b, title = {Sex-biased dynamics of three-spined stickleback (Gasterosteus aculeatus) gene expression patterns}, author = {Elisavet Kaitetzidou and Gregor D Gilfillan and Efthimia Antonopoulou and Elena Sarropoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Kaitetzidou-Genomics-3.pdf https://linkinghub.elsevier.com/retrieve/pii/S0888754321004377}, doi = {10.1016/j.ygeno.2021.12.010}, issn = {08887543}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Genomics}, volume = {114}, number = {1}, pages = {266--277}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Escalas, Arthur; Auguet, Jean-Christophe; Avouac, Amandine; Belmaker, Jonathan; Dailianis, Thanos; Kiflawi, Moshe; Pickholtz, Renanel; Skouradakis, Grigorios; Villéger, Sébastien Shift and homogenization of gut microbiome during invasion in marine fishes Journal Article Animal Microbiome, 4 (1), pp. 37, 2022, ISSN: 2524-4671. @article{escalas_shift_2022, title = {Shift and homogenization of gut microbiome during invasion in marine fishes}, author = {Arthur Escalas and Jean-Christophe Auguet and Amandine Avouac and Jonathan Belmaker and Thanos Dailianis and Moshe Kiflawi and Renanel Pickholtz and Grigorios Skouradakis and Sébastien Villéger}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Escalas-AniMicro-48.pdf https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-022-00181-0}, doi = {10.1186/s42523-022-00181-0}, issn = {2524-4671}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Animal Microbiome}, volume = {4}, number = {1}, pages = {37}, abstract = {Abstract Biological invasion is one of the main components of global changes in aquatic ecosystems. Unraveling how establishment in novel environments affects key biological features of animals is a key step towards understanding invasion. Gut microbiome of herbivorous animals is important for host health but has been scarcely assessed in invasive species. Here, we characterized the gut microbiome of two invasive marine herbivorous fishes ( Siganus rivulatus and Siganus luridus ) in their native (Red Sea) and invaded (Mediterranean Sea) ranges. The taxonomic and phylogenetic diversity of the microbiome increased as the fishes move away from the native range and its structure became increasingly different from the native microbiome. These shifts resulted in homogenization of the microbiome in the invaded range, within and between the two species. The shift in microbial diversity was associated with changes in its functions related with the metabolism of short-chain fatty acids. Altogether, our results suggest that the environmental conditions encountered by Siganidae during their expansion in Mediterranean ecosystems strongly modifies the composition of their gut microbiome along with its putative functions. Further studies should pursue to identify the precise determinants of these modifications (e.g. changes in host diet or behavior, genetic differentiation) and whether they participate in the ecological success of these species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Biological invasion is one of the main components of global changes in aquatic ecosystems. Unraveling how establishment in novel environments affects key biological features of animals is a key step towards understanding invasion. Gut microbiome of herbivorous animals is important for host health but has been scarcely assessed in invasive species. Here, we characterized the gut microbiome of two invasive marine herbivorous fishes ( Siganus rivulatus and Siganus luridus ) in their native (Red Sea) and invaded (Mediterranean Sea) ranges. The taxonomic and phylogenetic diversity of the microbiome increased as the fishes move away from the native range and its structure became increasingly different from the native microbiome. These shifts resulted in homogenization of the microbiome in the invaded range, within and between the two species. The shift in microbial diversity was associated with changes in its functions related with the metabolism of short-chain fatty acids. Altogether, our results suggest that the environmental conditions encountered by Siganidae during their expansion in Mediterranean ecosystems strongly modifies the composition of their gut microbiome along with its putative functions. Further studies should pursue to identify the precise determinants of these modifications (e.g. changes in host diet or behavior, genetic differentiation) and whether they participate in the ecological success of these species. |
Angelova, Nelina; Danis, Theodoros; Lagnel, Jacques; Tsigenopoulos, Costas S; Manousaki, Tereza SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments Journal Article BMC Research Notes, 15 (1), pp. 98, 2022, ISSN: 1756-0500. @article{angelova_snakecube_2022, title = {SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments}, author = {Nelina Angelova and Theodoros Danis and Jacques Lagnel and Costas S Tsigenopoulos and Tereza Manousaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Angelova-BMC-18.pdf https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-022-05978-5}, doi = {10.1186/s13104-022-05978-5}, issn = {1756-0500}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {BMC Research Notes}, volume = {15}, number = {1}, pages = {98}, abstract = {Abstract Objective The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. Results Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Objective The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. Results Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field. |
Kioukis, Antonios; Pourjam, Mohsen; Neuhaus, Klaus; Lagkouvardos, Ilias Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling Journal Article Frontiers in Bioinformatics, 2 , pp. 864597, 2022, ISSN: 2673-7647. @article{kioukis_taxonomy_2022, title = {Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling}, author = {Antonios Kioukis and Mohsen Pourjam and Klaus Neuhaus and Ilias Lagkouvardos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Kioukis-Frontiers-in-Bioinfo-39.pdf https://www.frontiersin.org/articles/10.3389/fbinf.2022.864597/full}, doi = {10.3389/fbinf.2022.864597}, issn = {2673-7647}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Frontiers in Bioinformatics}, volume = {2}, pages = {864597}, abstract = {Bacterial diversity is often analyzed using 16S rRNA gene amplicon sequencing. Commonly, sequences are clustered based on similarity cutoffs to obtain groups reflecting molecular species, genera, or families. Due to the amount of the generated sequencing data, greedy algorithms are preferred for their time efficiency. Such algorithms rely only on pairwise sequence similarities. Thus, sometimes sequences with diverse phylogenetic background are clustered together. In contrast, taxonomic classifiers use position specific taxonomic information in assigning a probable taxonomy to a given sequence. Here we introduce Taxonomy Informed Clustering (TIC), a novel approach that utilizes classifier-assigned taxonomy to restrict clustering to only those sequences that share the same taxonomic path. Based on this concept, we offer a complete and automated pipeline for processing of 16S rRNA amplicon datasets in diversity analyses. First, raw reads are processed to form denoised amplicons. Next, the denoised amplicons are taxonomically classified. Finally, the TIC algorithm progressively assigning clusters at molecular species, genus and family levels. TIC outperforms greedy clustering algorithms like USEARCH and VSEARCH in terms of clusters’ purity and entropy, when using data from the Living Tree Project as test samples. Furthermore, we applied TIC on a dataset containing all Bifidobacteriaceae -classified sequences from the IMNGS database. Here, TIC identified evidence for 1000s of novel molecular genera and species. These results highlight the straightforward application of the TIC pipeline and superior results compared to former methods in diversity studies. The pipeline is freely available at: https://github.com/Lagkouvardos/TIC .}, keywords = {}, pubstate = {published}, tppubtype = {article} } Bacterial diversity is often analyzed using 16S rRNA gene amplicon sequencing. Commonly, sequences are clustered based on similarity cutoffs to obtain groups reflecting molecular species, genera, or families. Due to the amount of the generated sequencing data, greedy algorithms are preferred for their time efficiency. Such algorithms rely only on pairwise sequence similarities. Thus, sometimes sequences with diverse phylogenetic background are clustered together. In contrast, taxonomic classifiers use position specific taxonomic information in assigning a probable taxonomy to a given sequence. Here we introduce Taxonomy Informed Clustering (TIC), a novel approach that utilizes classifier-assigned taxonomy to restrict clustering to only those sequences that share the same taxonomic path. Based on this concept, we offer a complete and automated pipeline for processing of 16S rRNA amplicon datasets in diversity analyses. First, raw reads are processed to form denoised amplicons. Next, the denoised amplicons are taxonomically classified. Finally, the TIC algorithm progressively assigning clusters at molecular species, genus and family levels. TIC outperforms greedy clustering algorithms like USEARCH and VSEARCH in terms of clusters’ purity and entropy, when using data from the Living Tree Project as test samples. Furthermore, we applied TIC on a dataset containing all Bifidobacteriaceae -classified sequences from the IMNGS database. Here, TIC identified evidence for 1000s of novel molecular genera and species. These results highlight the straightforward application of the TIC pipeline and superior results compared to former methods in diversity studies. The pipeline is freely available at: https://github.com/Lagkouvardos/TIC . |
Papadaki, Maria; Kaitetzidou, Elisavet; Papadakis, Ioannis E; Sfakianakis, Dimitris G; Papandroulakis, Nikos; Mylonas, Constantinos C; Sarropoulou, Elena Temperature-Biased miRNA Expression Patterns during European Sea Bass (Dicentrarchus labrax) Development Journal Article International Journal of Molecular Sciences, 23 (19), pp. 11164, 2022, ISSN: 1422-0067. @article{papadaki_temperature-biased_2022, title = {Temperature-Biased miRNA Expression Patterns during European Sea Bass (Dicentrarchus labrax) Development}, author = {Maria Papadaki and Elisavet Kaitetzidou and Ioannis E Papadakis and Dimitris G Sfakianakis and Nikos Papandroulakis and Constantinos C Mylonas and Elena Sarropoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/09/2022-Papadaki-IJMS-65.pdf https://www.mdpi.com/1422-0067/23/19/11164}, doi = {10.3390/ijms231911164}, issn = {1422-0067}, year = {2022}, date = {2022-01-01}, urldate = {2022-09-27}, journal = {International Journal of Molecular Sciences}, volume = {23}, number = {19}, pages = {11164}, abstract = {Environmental effects and, particularly, temperature changes have been demonstrated to influence the activity, function, and well-being of teleosts. Temperature may change seasonally in the wild, and in captivity under aquaculture operations. Moreover, climate change is expected to shift temperature profiles worldwide. MicroRNAs (miRNA) are important temperature-sensitive gene-expression regulators acting at the post-transcriptional level. They are known to be key regulators in development, reproduction, and immune responses. Therefore, early larval development of the European sea bass (Dicentrarchus labrax), one of the most extensively cultured species in Mediterranean aquaculture, was investigated at early rearing temperatures, i.e., 15, 17.5, and 20 °C, in regard to the impact of temperatures on miRNAs through sncRNA high-throughput sequencing but also at the phenotypic level in terms of growth, sex, vision, and skeletal deformities. Expression profiling revealed stage- and temperature-specific miRNA expression targeting genes with roles in reproduction and immune response mainly at the flexion and all-fins stages. Similar stage- and temperature-specific results were also observed concerning the number of rod cells and lower jaw elongation. The present work presents for the first time highly promising results on the influence of early rearing temperature at the post-transcriptional level during European sea bass development, with a putative impact on reproduction and immune response, as well as regarding teleost vision and larval development.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Environmental effects and, particularly, temperature changes have been demonstrated to influence the activity, function, and well-being of teleosts. Temperature may change seasonally in the wild, and in captivity under aquaculture operations. Moreover, climate change is expected to shift temperature profiles worldwide. MicroRNAs (miRNA) are important temperature-sensitive gene-expression regulators acting at the post-transcriptional level. They are known to be key regulators in development, reproduction, and immune responses. Therefore, early larval development of the European sea bass (Dicentrarchus labrax), one of the most extensively cultured species in Mediterranean aquaculture, was investigated at early rearing temperatures, i.e., 15, 17.5, and 20 °C, in regard to the impact of temperatures on miRNAs through sncRNA high-throughput sequencing but also at the phenotypic level in terms of growth, sex, vision, and skeletal deformities. Expression profiling revealed stage- and temperature-specific miRNA expression targeting genes with roles in reproduction and immune response mainly at the flexion and all-fins stages. Similar stage- and temperature-specific results were also observed concerning the number of rod cells and lower jaw elongation. The present work presents for the first time highly promising results on the influence of early rearing temperature at the post-transcriptional level during European sea bass development, with a putative impact on reproduction and immune response, as well as regarding teleost vision and larval development. |
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. |
Martin, Jon Lapeyra; Santi, Ioulia; Pitta, Paraskevi; John, Uwe; Gypens, Nathalie Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias Journal Article Metabarcoding and Metagenomics, 6 , pp. e85794, 2022, ISSN: 2534-9708. @article{martin_towards_2022, title = {Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias}, author = {Jon Lapeyra Martin and Ioulia Santi and Paraskevi Pitta and Uwe John and Nathalie Gypens}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/09/2022-Santi_MBMG-60.pdf https://mbmg.pensoft.net/article/85794/}, doi = {10.3897/mbmg.6.85794}, issn = {2534-9708}, year = {2022}, date = {2022-01-01}, urldate = {2022-09-26}, journal = {Metabarcoding and Metagenomics}, volume = {6}, pages = {e85794}, abstract = {Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene is the most widely used marker for groups’ and species’ detection and classification within marine eukaryotic microorganisms. These datasets have commonly relied on the acquisition of organismal abundances directly from the number of DNA sequences (i.e. reads). Besides the inherent technical biases in metabarcoding, the largely varying 18S rRNA gene copy numbers (GCN) among marine protists (ranging from tens to thousands) is one of the most important biological biases for species quantification. In this work, we present a gene copy number correction factor (CF) for four marine planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous and flagellated cells. On the basis of the theoretical assumption that ‘1 read’ is equivalent to ‘1 GCN’, we used the GCN median values per plankton group to calculate the corrected cell number and biomass relative abundances. The species-specific absolute GCN per cell were obtained from various studies published in the literature. We contributed to the development of a species-specific 18S rRNA GCN database proposed by previous authors. To assess the efficiency of the correction factor we compared the metabarcoding, morphological and corrected relative abundances (in cell number and biomass) of 15 surface water samples collected in the Belgian Coastal Zone. Results showed that the application of the correction factor over metabarcoding results enables us to significantly improve the estimates of cell abundances for Dinoflagellata, Ciliophora and flagellated cells, but not for Bacillariophyta. This is likely to due to large biovolume plasticity in diatoms not corresponding to genome size and gene copy numbers. C-biomass relative abundance estimations directly from amplicon reads were only improved for Dinoflagellata and Ciliophora. The method is still facing biases related to the low number of species GCN assessed. Nevertheless, the increase of species in the GCN database may lead to the refinement of the proposed correction factor.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene is the most widely used marker for groups’ and species’ detection and classification within marine eukaryotic microorganisms. These datasets have commonly relied on the acquisition of organismal abundances directly from the number of DNA sequences (i.e. reads). Besides the inherent technical biases in metabarcoding, the largely varying 18S rRNA gene copy numbers (GCN) among marine protists (ranging from tens to thousands) is one of the most important biological biases for species quantification. In this work, we present a gene copy number correction factor (CF) for four marine planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous and flagellated cells. On the basis of the theoretical assumption that ‘1 read’ is equivalent to ‘1 GCN’, we used the GCN median values per plankton group to calculate the corrected cell number and biomass relative abundances. The species-specific absolute GCN per cell were obtained from various studies published in the literature. We contributed to the development of a species-specific 18S rRNA GCN database proposed by previous authors. To assess the efficiency of the correction factor we compared the metabarcoding, morphological and corrected relative abundances (in cell number and biomass) of 15 surface water samples collected in the Belgian Coastal Zone. Results showed that the application of the correction factor over metabarcoding results enables us to significantly improve the estimates of cell abundances for Dinoflagellata, Ciliophora and flagellated cells, but not for Bacillariophyta. This is likely to due to large biovolume plasticity in diatoms not corresponding to genome size and gene copy numbers. C-biomass relative abundance estimations directly from amplicon reads were only improved for Dinoflagellata and Ciliophora. The method is still facing biases related to the low number of species GCN assessed. Nevertheless, the increase of species in the GCN database may lead to the refinement of the proposed correction factor. |
Droubogiannis, Stavros; Pavlidi, Lydia; Tsertou, Maria Ioanna; Kokkari, Constantina; Skliros, Dimitrios; Flemetakis, Emmanouil; Katharios, Pantelis Vibrio Phage Artemius, a Novel Phage Infecting Vibrio alginolyticus Journal Article Pathogens, 11 (8), pp. 848, 2022, ISSN: 2076-0817. @article{droubogiannis_vibrio_2022, title = {Vibrio Phage Artemius, a Novel Phage Infecting Vibrio alginolyticus}, author = {Stavros Droubogiannis and Lydia Pavlidi and Maria Ioanna Tsertou and Constantina Kokkari and Dimitrios Skliros and Emmanouil Flemetakis and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Droubogiannis-pathogen-54.pdf https://www.mdpi.com/2076-0817/11/8/848}, doi = {10.3390/pathogens11080848}, issn = {2076-0817}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Pathogens}, volume = {11}, number = {8}, pages = {848}, abstract = {Vibrio alginolyticus is an important pathogen of marine animals and has been the target of phage therapy applications in marine aquaculture for many years. Here, we report the isolation and partial characterization of a novel species of the Siphoviridae family, the Vibrio phage Artemius. The novel phage was species-specific and could only infect strains of V. alginolyticus. It could efficiently reduce the growth of the host bacterium at various multiplicities of infection as assessed by an in vitro lysis assay. It had a genome length of 43,349 base pairs. The complete genome has double-stranded DNA with a G + C content of 43.61%. In total, 57 ORFs were identified, of which 19 were assigned a predicted function. A genomic analysis indicated that Vibrio phage Artemius is lytic and does not harbor genes encoding toxins and antibiotic resistance determinants.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Vibrio alginolyticus is an important pathogen of marine animals and has been the target of phage therapy applications in marine aquaculture for many years. Here, we report the isolation and partial characterization of a novel species of the Siphoviridae family, the Vibrio phage Artemius. The novel phage was species-specific and could only infect strains of V. alginolyticus. It could efficiently reduce the growth of the host bacterium at various multiplicities of infection as assessed by an in vitro lysis assay. It had a genome length of 43,349 base pairs. The complete genome has double-stranded DNA with a G + C content of 43.61%. In total, 57 ORFs were identified, of which 19 were assigned a predicted function. A genomic analysis indicated that Vibrio phage Artemius is lytic and does not harbor genes encoding toxins and antibiotic resistance determinants. |
Gabed, Noujoud; Verret, Frédéric; Peticca, Aurélie; Kryvoruchko, Igor; Gastineau, Romain; Bosson, Orlane; Séveno, Julie; Davidovich, Olga; Davidovich, Nikolai; Witkowski, Andrzej; Kristoffersen, Jon Bent; Benali, Amel; Ioannou, Efstathia; Koutsaviti, Aikaterini; Roussis, Vassilios; Gâteau, Hélène; Phimmaha, Suliya; Leignel, Vincent; Badawi, Myriam; Khiar, Feriel; Francezon, Nellie; Fodil, Mostefa; Pasetto, Pamela; Mouget, Jean-Luc What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age Journal Article Marine Drugs, 20 (4), pp. 234, 2022, ISSN: 1660-3397. @article{gabed_what_2022, title = {What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age}, author = {Noujoud Gabed and Frédéric Verret and Aurélie Peticca and Igor Kryvoruchko and Romain Gastineau and Orlane Bosson and Julie Séveno and Olga Davidovich and Nikolai Davidovich and Andrzej Witkowski and Jon Bent Kristoffersen and Amel Benali and Efstathia Ioannou and Aikaterini Koutsaviti and Vassilios Roussis and Hélène Gâteau and Suliya Phimmaha and Vincent Leignel and Myriam Badawi and Feriel Khiar and Nellie Francezon and Mostefa Fodil and Pamela Pasetto and Jean-Luc Mouget}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Gabed-N-Mar-Drugs-33.pdf https://www.mdpi.com/1660-3397/20/4/234}, doi = {10.3390/md20040234}, issn = {1660-3397}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Marine Drugs}, volume = {20}, number = {4}, pages = {234}, abstract = {The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).}, keywords = {}, pubstate = {published}, tppubtype = {article} } The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest). |
2021 |
Kotzamanis, Yannis; Fawole, Femi J; Brezas, Andreas; Kumar, Vikas; Fontanillas, Ramon; Antonopoulou, Efthimia; Kouroupakis, Emmanouil; Ilia, Vassiliki Dietary lysine requirement of greater amberjack juvenile ( textitSeriola dumerili , Risso, 1810) Journal Article Aquaculture Nutrition, 27 (6), pp. 2107–2118, 2021, ISSN: 1353-5773, 1365-2095. @article{kotzamanis_dietary_2021, title = {Dietary lysine requirement of greater amberjack juvenile ( textitSeriola dumerili , Risso, 1810)}, author = {Yannis Kotzamanis and Femi J Fawole and Andreas Brezas and Vikas Kumar and Ramon Fontanillas and Efthimia Antonopoulou and Emmanouil Kouroupakis and Vassiliki Ilia}, url = {https://onlinelibrary.wiley.com/doi/10.1111/anu.13344}, doi = {10.1111/anu.13344}, issn = {1353-5773, 1365-2095}, year = {2021}, date = {2021-12-01}, urldate = {2022-01-12}, journal = {Aquaculture Nutrition}, volume = {27}, number = {6}, pages = {2107--2118}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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. |
Gasco, L; Józefiak, A; Henry, M Beyond the protein concept: health aspects of using edible insects on animals Journal Article 7 (5), pp. 715–741, 2021, ISSN: 2352-4588. @article{gasco_beyond_2021, title = {Beyond the protein concept: health aspects of using edible insects on animals}, author = {L Gasco and A Józefiak and M Henry}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Gasco-Henry-JIFF-67.pdf https://www.wageningenacademic.com/doi/10.3920/JIFF2020.0077}, doi = {10.3920/JIFF2020.0077}, issn = {2352-4588}, year = {2021}, date = {2021-08-13}, urldate = {2021-09-22}, volume = {7}, number = {5}, pages = {715--741}, abstract = {There is an increasing interest in the use of insects in animal feed since they contain high proteins levels, lipids, vitamins and minerals. In particular, insect-derived proteins are seen as one of the potential solution to face the increasing protein shortage and are able to fully substitute soybean meal or fishmeal in aquaculture or livestock feeds. However, beside their interesting nutritional composition, insects are also rich in bioactive compounds such as chitin, antimicrobial peptides or specific fatty acids with immunostimulating, antimicrobial and/or anti-inflammatory properties able to sustain animal health, increase their resistance to diseases. Further studies will also have to investigate whether insects share similarities with bacterial or parasitical pathogens and may act as immunostimulants. These recent findings may launch insects beyond the protein concept into healthy animal feeds. This review presents the effects of insects and their bioactive compounds on fish and crustaceans, poultry, pigs and rabbits immune system, gut health, microbiota and resistance to diseases.}, keywords = {}, pubstate = {published}, tppubtype = {article} } There is an increasing interest in the use of insects in animal feed since they contain high proteins levels, lipids, vitamins and minerals. In particular, insect-derived proteins are seen as one of the potential solution to face the increasing protein shortage and are able to fully substitute soybean meal or fishmeal in aquaculture or livestock feeds. However, beside their interesting nutritional composition, insects are also rich in bioactive compounds such as chitin, antimicrobial peptides or specific fatty acids with immunostimulating, antimicrobial and/or anti-inflammatory properties able to sustain animal health, increase their resistance to diseases. Further studies will also have to investigate whether insects share similarities with bacterial or parasitical pathogens and may act as immunostimulants. These recent findings may launch insects beyond the protein concept into healthy animal feeds. This review presents the effects of insects and their bioactive compounds on fish and crustaceans, poultry, pigs and rabbits immune system, gut health, microbiota and resistance to diseases. |
Doxa, Chrysa K; Sfakianakis, Dimitris; Sterioti, Aspasia; Kentouri, Maroudio Effect of temperature on the development of deformities during the embryonic stages of Charonia seguenzae (Aradas & Benoit, 1870) Journal Article Journal of Thermal Biology, 100 , pp. 103046, 2021, ISSN: 03064565, (AQUA). @article{doxa_effect_2021-1, title = {Effect of temperature on the development of deformities during the embryonic stages of Charonia seguenzae (Aradas & Benoit, 1870)}, author = {Chrysa K Doxa and Dimitris Sfakianakis and Aspasia Sterioti and Maroudio Kentouri}, url = {https://linkinghub.elsevier.com/retrieve/pii/S030645652100214X}, doi = {10.1016/j.jtherbio.2021.103046}, issn = {03064565}, year = {2021}, date = {2021-08-01}, urldate = {2022-01-17}, journal = {Journal of Thermal Biology}, volume = {100}, pages = {103046}, note = {AQUA}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Medvecky, Matej; Mandalakis, Manolis PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems Journal Article Frontiers in Chemistry, 9 , pp. 722087, 2021, ISSN: 2296-2646. @article{medvecky_pepmandis_2021, title = {PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems}, author = {Matej Medvecky and Manolis Mandalakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Mandalakis-FiChem-62.pdf https://www.frontiersin.org/articles/10.3389/fchem.2021.722087/full}, doi = {10.3389/fchem.2021.722087}, issn = {2296-2646}, year = {2021}, date = {2021-08-01}, urldate = {2021-08-23}, journal = {Frontiers in Chemistry}, volume = {9}, pages = {722087}, abstract = {The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest. |
Fanini, Lucia; Costa, Leonardo Lopes; Zalmon, Ilana Rosental; Riechers, Maraja Social and Ecological Elements for a Perspective Approach to Citizen Science on the Beach Journal Article Frontiers in Ecology and Evolution, 9 , pp. 694487, 2021, ISSN: 2296-701X. @article{fanini_social_2021, title = {Social and Ecological Elements for a Perspective Approach to Citizen Science on the Beach}, author = {Lucia Fanini and Leonardo Lopes Costa and Ilana Rosental Zalmon and Maraja Riechers}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Fanini-fevo-61.pdf https://www.frontiersin.org/articles/10.3389/fevo.2021.694487/full}, doi = {10.3389/fevo.2021.694487}, issn = {2296-701X}, year = {2021}, date = {2021-08-01}, urldate = {2021-08-23}, journal = {Frontiers in Ecology and Evolution}, volume = {9}, pages = {694487}, abstract = {Sandy beaches are ecotonal environments connecting land and sea, hosting exclusive resident organisms and key life stages of (often charismatic) fauna. Humans also visit sandy beaches where tourism, in particular, moves billions of people every year. However, instead of representing a connection to nature, the attitude toward visiting the beach is biased concerning its recreational use. Such “sun, sea, and sand” target and its display seem to be deeply rooted in social systems. How could scientists engage the newest generations and facilitate an exit from this loop, fostering care (including participative beach science), and ultimately sustainable sandy beach use? To tackle this question, we applied the concept of social–ecological systems to the Littoral Active Zone (LAZ). The LAZ is a unit sustaining beach functionalities, though it includes relevant features making a beach attractive to the public. Out of the analysis of the system LAZ in its social and ecological templates, we extracted elements suitable to the planning of citizen science programs. The perspective of leverage points was integrated to the needs identified in the analysis, through reconnecting–restructuring–rethinking the components of the system. Two cross-cutting approaches were marked as important to social and ecological designs and break through the dominant perception of beaches as mere piles of sand: the physical dimension (LAZ) of the beach as a unit, and the use of communication through social media, suitable to both monitoring and scientific data collection, and to data communication and hedonistic display of a day on the beach.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sandy beaches are ecotonal environments connecting land and sea, hosting exclusive resident organisms and key life stages of (often charismatic) fauna. Humans also visit sandy beaches where tourism, in particular, moves billions of people every year. However, instead of representing a connection to nature, the attitude toward visiting the beach is biased concerning its recreational use. Such “sun, sea, and sand” target and its display seem to be deeply rooted in social systems. How could scientists engage the newest generations and facilitate an exit from this loop, fostering care (including participative beach science), and ultimately sustainable sandy beach use? To tackle this question, we applied the concept of social–ecological systems to the Littoral Active Zone (LAZ). The LAZ is a unit sustaining beach functionalities, though it includes relevant features making a beach attractive to the public. Out of the analysis of the system LAZ in its social and ecological templates, we extracted elements suitable to the planning of citizen science programs. The perspective of leverage points was integrated to the needs identified in the analysis, through reconnecting–restructuring–rethinking the components of the system. Two cross-cutting approaches were marked as important to social and ecological designs and break through the dominant perception of beaches as mere piles of sand: the physical dimension (LAZ) of the beach as a unit, and the use of communication through social media, suitable to both monitoring and scientific data collection, and to data communication and hedonistic display of a day on the beach. |
Peñaloza, C; Manousaki, T; Franch, R; Tsakogiannis, A; Sonesson, A K; Aslam, M L; Allal, F; Bargelloni, L; Houston, R D; Tsigenopoulos, C S Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata) Journal Article Genomics, 113 (4), pp. 2096–2107, 2021, ISSN: 08887543. @article{penaloza_development_2021, title = {Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)}, author = {C Peñaloza and T Manousaki and R Franch and A Tsakogiannis and A K Sonesson and M L Aslam and F Allal and L Bargelloni and R D Houston and C S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Penaloza-Genomics-39.pdf https://linkinghub.elsevier.com/retrieve/pii/S0888754321001713}, doi = {10.1016/j.ygeno.2021.04.038}, issn = {08887543}, year = {2021}, date = {2021-07-01}, urldate = {2021-06-24}, journal = {Genomics}, volume = {113}, number = {4}, pages = {2096--2107}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Nikolaivits, Efstratios; Siaperas, Romanos; Agrafiotis, Andreas; Ouazzani, Jamal; Magoulas, Antonios; Gioti, Αnastasia; Topakas, Evangelos Science of The Total Environment, 775 , pp. 145818, 2021, ISSN: 00489697. @article{nikolaivits_functional_2021, title = {Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus}, author = {Efstratios Nikolaivits and Romanos Siaperas and Andreas Agrafiotis and Jamal Ouazzani and Antonios Magoulas and Αnastasia Gioti and Evangelos Topakas}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969721008858}, doi = {10.1016/j.scitotenv.2021.145818}, issn = {00489697}, year = {2021}, date = {2021-06-01}, urldate = {2021-03-17}, journal = {Science of The Total Environment}, volume = {775}, pages = {145818}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kumar, Neeraj; Hitch, Thomas C A; Haller, Dirk; Lagkouvardos, Ilias; Clavel, Thomas MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes Journal Article Microbial Biotechnology, pp. 1751–7915.13845, 2021, ISSN: 1751-7915, 1751-7915. @article{kumar_mimic_2021, title = {MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes}, author = {Neeraj Kumar and Thomas C A Hitch and Dirk Haller and Ilias Lagkouvardos and Thomas Clavel}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/07/2021-Kumar-MicBio-50.pdf https://onlinelibrary.wiley.com/doi/10.1111/1751-7915.13845}, doi = {10.1111/1751-7915.13845}, issn = {1751-7915, 1751-7915}, year = {2021}, date = {2021-06-01}, urldate = {2021-07-26}, journal = {Microbial Biotechnology}, pages = {1751--7915.13845}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kogiannou, Dimitra; Nikoloudaki, Chrysanthi; Katharios, Pantelis; Triga, Adriana; Rigos, George Evaluation of absorption and depletion of florfenicol in European seabass textitDicentrarchus labrax Journal Article Veterinary Medicine and Science, 7 (3), pp. 987–997, 2021, ISSN: 2053-1095, 2053-1095. @article{kogiannou_evaluation_2021, title = {Evaluation of absorption and depletion of florfenicol in European seabass textitDicentrarchus labrax}, author = {Dimitra Kogiannou and Chrysanthi Nikoloudaki and Pantelis Katharios and Adriana Triga and George Rigos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Kogiannou-VetMed-Sci-40.pdf https://onlinelibrary.wiley.com/doi/10.1002/vms3.415}, doi = {10.1002/vms3.415}, issn = {2053-1095, 2053-1095}, year = {2021}, date = {2021-05-01}, urldate = {2021-06-24}, journal = {Veterinary Medicine and Science}, volume = {7}, number = {3}, pages = {987--997}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rigos, George; Kogiannou, Dimitra; Vasilaki, Antigoni; Kotsiri, Mado Evaluation of Praziquantel Efficacy against Zeuxapta seriolae Infections in Greater Amberjack, Seriola dumerili Journal Article Applied Sciences, 11 (10), pp. 4656, 2021, ISSN: 2076-3417. @article{rigos_evaluation_2021, title = {Evaluation of Praziquantel Efficacy against Zeuxapta seriolae Infections in Greater Amberjack, Seriola dumerili}, author = {George Rigos and Dimitra Kogiannou and Antigoni Vasilaki and Mado Kotsiri}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Rigos-ApllSciences-41l.pdf https://www.mdpi.com/2076-3417/11/10/4656}, doi = {10.3390/app11104656}, issn = {2076-3417}, year = {2021}, date = {2021-05-01}, urldate = {2021-06-24}, journal = {Applied Sciences}, volume = {11}, number = {10}, pages = {4656}, abstract = {The aim of this study was to evaluate the efficacy of dietary praziquantel (PZQ), a promising fish anthelminthic, against Zeuxapta seriolae, a lethal ectoparasite of greater amberjack (Seriola dumerili Risso) farmed in the Mediterranean and elsewhere. The trial was carried out in small cages (3 m3) in situ, harbouring fish (125 ± 14 g) naturally infected with Z. seriolae, at 25 ± 1 °C water temperature. Praziquantel-medicated diet (150 mg PZQ/kg fish) was delivered for three days against a control group. Measurement of both adults and oncomiracidia of Z. seriolae in sampled gill arches revealed significant differences between the tested groups (PZQ: 19.3 ± 9.8 vs. Control: 3.8 ± 6.3). Considering an estimated efficacy of 80.4% in the medicated fish, the present study indicates that oral PZQ treatments can confront Z. seriolae infections considerably in farmed greater amberjack and, perhaps, replace the commonly used hydrogen peroxidase baths.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The aim of this study was to evaluate the efficacy of dietary praziquantel (PZQ), a promising fish anthelminthic, against Zeuxapta seriolae, a lethal ectoparasite of greater amberjack (Seriola dumerili Risso) farmed in the Mediterranean and elsewhere. The trial was carried out in small cages (3 m3) in situ, harbouring fish (125 ± 14 g) naturally infected with Z. seriolae, at 25 ± 1 °C water temperature. Praziquantel-medicated diet (150 mg PZQ/kg fish) was delivered for three days against a control group. Measurement of both adults and oncomiracidia of Z. seriolae in sampled gill arches revealed significant differences between the tested groups (PZQ: 19.3 ± 9.8 vs. Control: 3.8 ± 6.3). Considering an estimated efficacy of 80.4% in the medicated fish, the present study indicates that oral PZQ treatments can confront Z. seriolae infections considerably in farmed greater amberjack and, perhaps, replace the commonly used hydrogen peroxidase baths. |
Ragkousis, Michail; Digenis, Markos; Kovačić, Marcelo; Katsanevakis, Stelios; Gerovasileiou, Vasilis Rarely Reported Cryptobenthic Fish in Marine Caves of the Eastern Mediterranean Sea Journal Article Journal of Marine Science and Engineering, 9 (6), pp. 557, 2021, ISSN: 2077-1312. @article{ragkousis_rarely_2021, title = {Rarely Reported Cryptobenthic Fish in Marine Caves of the Eastern Mediterranean Sea}, author = {Michail Ragkousis and Markos Digenis and Marcelo Kovačić and Stelios Katsanevakis and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Ragkousis-jmse-09-00557-43.pdf https://www.mdpi.com/2077-1312/9/6/557}, doi = {10.3390/jmse9060557}, issn = {2077-1312}, year = {2021}, date = {2021-05-01}, urldate = {2021-06-24}, journal = {Journal of Marine Science and Engineering}, volume = {9}, number = {6}, pages = {557}, abstract = {Data on the distribution and ecology of cryptobenthic fish of marine caves in the Mediterranean Sea are extremely scarce but necessary for scientists and marine managers alike in order to understand these fish’s ecological role and assess their conservation status. Broadscale surveys by implementing underwater visual census and photographic sampling in marine caves of the northeastern Mediterranean Sea, within different expeditions during the last 5 years, brought to light new records of eight rarely reported cryptobenthic fish species. To a smaller extent, complementary citizen science data from diving professionals of Crete were used to fill distribution gaps. A total of 36 new records (66 individuals) from 18 marine caves and caverns of the Aegean and northeastern Levantine Seas were assembled, belonging to the gobies Corcyrogobius liechtensteini, Didogobius splechtnai, Gammogobius steinitzi, and Thorogobius ephippiatus, the blenny Microlipophrys nigriceps, the tripterygiid Tripterygion melanurum, the speleophilic bythitid Grammonus ater, and the gobiesocid Lepadogaster cf. lepadogaster. The above species have been rarely reported from the Eastern Mediterranean Sea, with D. splechtnai and G. steinitzi being recorded for the first and second time from Greek waters, respectively, while L. cf. lepadogaster constitutes the second record of a clingfish species in a marine cave of the Aegean Sea. Interesting behavioral and ecological habits were also noted for some species, based on in situ observations and photographic evidence. Our study contributes to filling gaps in the knowledge of cave fish diversity and demonstrates that cryptobenthic mobile species in understudied cryptic habitats are more common than previously thought in the Mediterranean Sea.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Data on the distribution and ecology of cryptobenthic fish of marine caves in the Mediterranean Sea are extremely scarce but necessary for scientists and marine managers alike in order to understand these fish’s ecological role and assess their conservation status. Broadscale surveys by implementing underwater visual census and photographic sampling in marine caves of the northeastern Mediterranean Sea, within different expeditions during the last 5 years, brought to light new records of eight rarely reported cryptobenthic fish species. To a smaller extent, complementary citizen science data from diving professionals of Crete were used to fill distribution gaps. A total of 36 new records (66 individuals) from 18 marine caves and caverns of the Aegean and northeastern Levantine Seas were assembled, belonging to the gobies Corcyrogobius liechtensteini, Didogobius splechtnai, Gammogobius steinitzi, and Thorogobius ephippiatus, the blenny Microlipophrys nigriceps, the tripterygiid Tripterygion melanurum, the speleophilic bythitid Grammonus ater, and the gobiesocid Lepadogaster cf. lepadogaster. The above species have been rarely reported from the Eastern Mediterranean Sea, with D. splechtnai and G. steinitzi being recorded for the first and second time from Greek waters, respectively, while L. cf. lepadogaster constitutes the second record of a clingfish species in a marine cave of the Aegean Sea. Interesting behavioral and ecological habits were also noted for some species, based on in situ observations and photographic evidence. Our study contributes to filling gaps in the knowledge of cave fish diversity and demonstrates that cryptobenthic mobile species in understudied cryptic habitats are more common than previously thought in the Mediterranean Sea. |
Chatzinikolaou, Eva; Damianidis, Panagiotis; Pavloudi, Christina; Vasileiadou, Aikaterini; Faulwetter, Sarah; Keklikoglou, Kleoniki; Plaitis, Wanda; Mavraki, Dimitra; Nikolopoulou, Stamatina; Arvanitidis, Christos Benthic communities in three Mediterranean touristic ports: MAPMED project Journal Article Biodiversity Data Journal, 9 , pp. e66420, 2021, ISSN: 1314-2828. @article{chatzinikolaou_benthic_2021, title = {Benthic communities in three Mediterranean touristic ports: MAPMED project}, author = {Eva Chatzinikolaou and Panagiotis Damianidis and Christina Pavloudi and Aikaterini Vasileiadou and Sarah Faulwetter and Kleoniki Keklikoglou and Wanda Plaitis and Dimitra Mavraki and Stamatina Nikolopoulou and Christos Arvanitidis}, url = {https://bdj.pensoft.net/article/66420/ https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Chatzinikolaou-DioDiv-Data-J-32.pdf}, doi = {10.3897/BDJ.9.e66420}, issn = {1314-2828}, year = {2021}, date = {2021-04-01}, urldate = {2021-04-27}, journal = {Biodiversity Data Journal}, volume = {9}, pages = {e66420}, abstract = {Mediterranean ports are sources of significant economic activity and at the same time they act as recipients of considerable anthropogenic disturbance and pollution. Macrobenthic communities are an important component of the port biota and have been used as environmental quality indicators.Macrobenthic assemblages were recorded in three Mediterranean touristic ports under the framework of the ENPI CBC MED project MAPMED. Samples were collected from Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia) ports during February, May and September 2012. The sampling stations were selected according to the different sectors within each port (i.e. leisure, fishing, passenger/cargo vessels, shipyard). A total number of 277 taxa belonging to 12 phyla were found, of which the 96 taxa were found in all three ports. El Kantaoui port hosted the highest number of macrobenthic taxa. Mollusca were the most abundant group (34%) in all ports. The highest percentage of opportunistic taxa per station was found before the touristic period in the shipyard of Heraklion port (89.3%).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mediterranean ports are sources of significant economic activity and at the same time they act as recipients of considerable anthropogenic disturbance and pollution. Macrobenthic communities are an important component of the port biota and have been used as environmental quality indicators.Macrobenthic assemblages were recorded in three Mediterranean touristic ports under the framework of the ENPI CBC MED project MAPMED. Samples were collected from Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia) ports during February, May and September 2012. The sampling stations were selected according to the different sectors within each port (i.e. leisure, fishing, passenger/cargo vessels, shipyard). A total number of 277 taxa belonging to 12 phyla were found, of which the 96 taxa were found in all three ports. El Kantaoui port hosted the highest number of macrobenthic taxa. Mollusca were the most abundant group (34%) in all ports. The highest percentage of opportunistic taxa per station was found before the touristic period in the shipyard of Heraklion port (89.3%). |
Kourkouta, Chara; Printzi, Alice; Geladakis, George; Mitrizakis, Nikos; Papandroulakis, Nikos; Koumoundouros, George Scientific Reports, 11 (1), pp. 8787, 2021, ISSN: 2045-2322. @article{kourkouta_long_2021, title = {Long lasting effects of early temperature exposure on the swimming performance and skeleton development of metamorphosing Gilthead seabream ( Sparus aurata L.) larvae}, author = {Chara Kourkouta and Alice Printzi and George Geladakis and Nikos Mitrizakis and Nikos Papandroulakis and George Koumoundouros}, url = {https://www.nature.com/articles/s41598-021-88306-4 https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Kourkouta-SciReports-31-1.pdf }, doi = {10.1038/s41598-021-88306-4}, issn = {2045-2322}, year = {2021}, date = {2021-04-01}, urldate = {2021-04-27}, journal = {Scientific Reports}, volume = {11}, number = {1}, pages = {8787}, abstract = {Temperatures experienced during early ontogeny significantly influence fish phenotypes, with clear consequences for the wild and reared stocks. We examined the effect of temperature (17, 20, or 23 °C) during the short embryonic and yolk-sac larval period, on the swimming performance and skeleton of metamorphosing Gilthead seabream larvae. In the following ontogenetic period, all fish were subjected to common temperature (20 °C). The critical swimming speed of metamorphosing larvae was significantly decreased from 9.7 ± 0.6 TL/s (total length per second) at 17 °C developmental temperature (DT) to 8.7 ± 0.6 and 8.8 ± 0.7 TL/s at 20 and 23 °C DT respectively (p textless 0.05). Swimming performance was significantly correlated with fish body shape (p textless 0.05). Compared with the rest groups, fish of 17 °C DT presented a slender body shape, longer caudal peduncle, terminal mouth and ventrally transposed pectoral fins. Moreover, DT significantly affected the relative depth of heart ventricle (VD/TL, p textless 0.05), which was comparatively increased at 17 °C DT. Finally, the incidence of caudal-fin abnormalities significantly decreased (p textless 0.05) with the increase of DT. To our knowledge, this is the first evidence for the significant effect of DT during the short embryonic and yolk-sac larval period on the swimming performance of the later stages.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Temperatures experienced during early ontogeny significantly influence fish phenotypes, with clear consequences for the wild and reared stocks. We examined the effect of temperature (17, 20, or 23 °C) during the short embryonic and yolk-sac larval period, on the swimming performance and skeleton of metamorphosing Gilthead seabream larvae. In the following ontogenetic period, all fish were subjected to common temperature (20 °C). The critical swimming speed of metamorphosing larvae was significantly decreased from 9.7 ± 0.6 TL/s (total length per second) at 17 °C developmental temperature (DT) to 8.7 ± 0.6 and 8.8 ± 0.7 TL/s at 20 and 23 °C DT respectively (p textless 0.05). Swimming performance was significantly correlated with fish body shape (p textless 0.05). Compared with the rest groups, fish of 17 °C DT presented a slender body shape, longer caudal peduncle, terminal mouth and ventrally transposed pectoral fins. Moreover, DT significantly affected the relative depth of heart ventricle (VD/TL, p textless 0.05), which was comparatively increased at 17 °C DT. Finally, the incidence of caudal-fin abnormalities significantly decreased (p textless 0.05) with the increase of DT. To our knowledge, this is the first evidence for the significant effect of DT during the short embryonic and yolk-sac larval period on the swimming performance of the later stages. |
