6 research outputs found

    Unpublished Mediterranean and Black Sea records of marine alien, cryptogenic, and neonative species

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    To enrich spatio-temporal information on the distribution of alien, cryptogenic, and neonative species in the Mediterranean and the Black Sea, a collective effort by 173 marine scientists was made to provide unpublished records and make them open access to the scientific community. Through this effort, we collected and harmonized a dataset of 12,649 records. It includes 247 taxa, of which 217 are Animalia, 25 Plantae and 5 Chromista, from 23 countries surrounding the Mediterranean and the Black Sea. Chordata was the most abundant taxonomic group, followed by Arthropoda, Mollusca, and Annelida. In terms of species records, Siganus luridus, Siganus rivulatus, Saurida lessepsianus, Pterois miles, Upeneus moluccensis, Charybdis (Archias) longicollis, and Caulerpa cylindracea were the most numerous. The temporal distribution of the records ranges from 1973 to 2022, with 44% of the records in 2020–2021. Lethrinus borbonicus is reported for the first time in the Mediterranean Sea, while Pomatoschistus quagga, Caulerpa cylindracea, Grateloupia turuturu, and Misophria pallida are first records for the Black Sea; Kapraunia schneideri is recorded for the second time in the Mediterranean and for the first time in Israel; Prionospio depauperata and Pseudonereis anomala are reported for the first time from the Sea of Marmara. Many first country records are also included, namely: Amathia verticillata (Montenegro), Ampithoe valida (Italy), Antithamnion amphigeneum (Greece), Clavelina oblonga (Tunisia and Slovenia), Dendostrea cf. folium (Syria), Epinephelus fasciatus (Tunisia), Ganonema farinosum (Montenegro), Macrorhynchia philippina (Tunisia), Marenzelleria neglecta (Romania), Paratapes textilis (Tunisia), and Botrylloides diegensis (Tunisia).Stelios Katsanevakis, Michail Ragkousis, Maria Sini, Markos Digenis and Vasilis Gerovasileiou were supported by the Hellenic Foundation for Research and Innovation (HFRI) under the “First Call for HFRI Research Projects to support Faculty members and Researchers and the procurement of high-cost research equipment grant” (Project ALAS – “ALiens in the Aegean – a Sea under siege” (Katsanevakis et al. 2020b); Project Number: HFRI-FM17-1597). Konstantinos Tsirintanis was co-financed by Greece and the European Union (European Social Fund-ESF) through the Operational Programme “Human Resources Development, Education and Lifelong Learning”, 2014-2020, in the context of the Act “Enhancing Human Resources Research Potential by undertaking a Doctoral Research” Sub-action 2: IKY Scholarship Programme for PhD candidates in the Greek Universities. Maria Zotou was supported by the project “Coastal Environment Observatory and Risk Management in Island Regions AEGIS+” (MIS 5047038), implemented within the Operational Programme “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014-2020), co financed by the Hellenic Government (Ministry of Development and Investments) and the European Union (European Regional Development Fund, Cohesion Fund). Razy Hoffman was supported by Yad-Hanadiv Foundation, through the Israel Society of Ecology and Environmental Sciences and Israel Nature and Parks Authority, an integrated program for establishing biological baselines and monitoring protocols for marine reserves in the Israeli Mediterranean Sea (Grant #10669). Tatiana Begun, Adrian Teaca and Mihaela Muresan were supported by the European Union’s Horizon 2020 BRIDGE-BS project under grant agreement no. 101000240. Fiona Tomas was supported by the project “Invasion of the tropical alga Halimeda incrassata in the Balearic Islands: ecology and invasion dynamics (AAEE119/2017)”, funded by the Vicepresidencia y Consejería de Innovación, Investigación y Turismo del Govern de les Illes Balears, with support from the European Union and FEDER funds, and the project “Una nueva alga invasora en el Mediterráneo: invasibilidad, detección y erradicación del alga tropical Halimeda incrassata (INVHALI)”, funded by the Fundación Biodiversidad, del Ministerio para la Transición Ecológica y el Reto Demográfico. Simonetta Fraschetti, Laura Tamburello, Antonia Chiarore were supported by the project PO FEAMP 2014-2020 - DRD n. 35/2019, “Innovazione, sviluppo e sostenibilità nel settore della pesca e dell'acquacoltura per la Regione Campania” (ISSPA 2.51) and the EU EASME - EMFF (Sustainable Blue Econ-omy) Project AFRIMED (http://afrimed-project.eu/, grant agreement N. 789059). Carlos Jimenez, Louis Hadjioannou, Vasilis Resaikos, Valentina Fossati, Magdalene Papatheodoulou, and Antonis Petrou were supported by MedPan Small Projects, Mava, and LIFE-IP. Louis Hadjioannou, Manos L. Moraitis and Neophytos Agrotis received funding from the European Union’s Horizon 2020 research and innovation program within the framework of the CMMI/MaRITeC-X project under grant agreement No. 857586. Ernesto Azzurro was supported by the project USEIt - Utilizzo di Sinergie operative per la gestione integrata specie aliene Invasive in Italia, funded by the research programme @CNR. Antonietta Rosso and Francesco Sciuto were supported by the University of Catania through “PiaCeRi-Piano Incentivi per la Ricerca di Ateneo 2020–22 linea di intervento 2.” This is the Catania Paleoecological Research Group contribution n. 484. Diego K. Kersting was supported by the Beatriu de Pinós programme funded by the Secretary of Universities and Research (Government of Catalonia) and the Horizon 2020 programme of research and innovation of the European Union under the Marie Sklodowska-Curie grant agreement No 801370. Francesco Tiralongo was supported by the AlienFish project of Ente Fauna Marina Mediterranea (Scientific Organization for Research and Conservation of Marine Biodiversity, 96012 Avola, Italy), a citizen science project for monitoring and studying rare and non-indigenous fish in Italian waters. Adriana Vella, was supported by funds through the BioCon_Innovate Research Excellence Grant from the University of Malta awarded to her. Noel Vella was supported by REACH HIGH Scholars Programme-Post Doctoral Grant for the FINS project. Some of the records provided by Victor Surugiu were obtained during surveys carried out within the framework of the project “Adequate management of invasive species in Romania, in accordance with EU Regulation 1143/2014 on the prevention and management of the introduction and spread of invasive alien species”, SMIS 2014+ 120008, coordinated by the Romanian Ministry of Environment, Water and Forests in partnership with the University of Bucharest (2018–2022). Alan Deidun and Alessio Marrone were supported by the “Spot The Alien” citizen science campaign for the monitoring of the Alien species in the Maltese archipelago and by the Interreg Italia-Malta Harmony project. The authors from the National Institute of Biology (Slovenia) acknowledge the financial support of the Slovenian Research Agency (Research Core Funding No. P1-0237) and of the Ministry of Agriculture, Forestry and Food (project “Survey of the species richness and abundance of alien species in the Slovenian Sea”). Emanuele Mancini and Fabio Collepardo Coccia were supported by the project PO-FEAMP 2014-2020 “BIOBLITZ: research, knowledge and participation for the sustainable management of marine resources (BioBlitz Blu 2020)” coordinated by CURSA for MIPAAF, the Italian Ministry of Agricultural, Food and Forestry Policies, Measure 1.40 - Protection and restoration of biodiversity and marine ecosystems and compensation schemes in the context of sustainable fishing activities. Daniele Grech was supported by the PO-FEAMP 2014-2020 project ECOGESTOCK “Approccio ECOsistemico per la tutela e la GEStione delle risorse biologiche e STOCK ittici nelle acque interne”, the citizen science project Progetto Fucales: chi le ha viste? and the Paralenz Every dive counts sponsor. Jamila Rizgalla was supported by the project Snowball for the monitoring of alien species in Libyan waters له اهتفش له اهتدطصا ؟) have you seen it have you fished it?). Gerasimos Kondylatos and Dimitrios Mavrouleas were supported by the project “EXPLIAS” (MIS (ΟΠΣ): 5049912), design and piloting methods of commercial exploitation of invasive alien species with a view to contributing to their population control, coordinated by the National Technical University of Athens with the collaboration of the Hellenic Centre for Marine Research and the University of the Aegean and co-founded by Greece and the European Union. G. Kondylatos and Savvas Nikolidakis were supported by the project “SAMOS” (ID CODE: 32.2072004/001), a study for a submarine productive park in Marathokampos of Samos. Paraskevi K. Karachle, Aikaterini Dogrammatzi, Giorgos A. Apostolopoulos, Kassiani Konida and Melina Nalmpanti were supported by the project “4ALIEN: Biology and the potential economic exploitation of four alien species in the Hellenic Seas”, funded by NRSF 2017-2020 (MIS (ΟΠΣ): 5049511). Fabio Crocetta and Riccardo Virgili were partially funded by the project PO FEAMP Campania 2014–2020, DRD n. 35 of 15th March 2018, Innovazione, sviluppo e sostenibilità nel settore della pesca e dell’acquacoltura per la regione Campania, Misura 2.51, WP5, Task 5.5 Presenza e distribuzione di specie non indigene del macrozoobenthos e del necton in Campania. Michel Bariche was partially funded by the University Research Board of the American University of Beirut (DDF 103951/2592). Constantinos G. Georgiadis, Dimitra Lida Rammou, Paschalis Papadamakis and Sotiris Orfanidis were supported by the MSFD monitoring program. Sonia Smeraldo was supported by the MPA-Engage project, led by the Institute of Marine Sciences of the Spanish National Research Council and funded by the Interreg MED program. Evgeniia Karpova acknowledge that the publication of this article was in part carried out within the framework of the state assignment of the FRC IBSS “Patterns of Formation and Anthropogenic Transformation of Biodiversity and Bioresources of the Azov– Black Sea Basin and Other Regions of the World Ocean” (No. 121030100028-0). Elena Slynko’s work was carried out within the framework of a State Assignment no. 121051100109-1 of IBIW RAS. Manuela Falautano and Luca Castriota were supported by ISPRA citizen science campaigns for the monitoring of alien species through the dedicated institutional project ([email protected]). María Altamirano was supported by the project RUGULOPTERYX funded by Fundación Biodiversidad-Ministerio para la Transición Ecológica y el reto Demográfico (Spain) and the project UMA20-FEDERJA-006 with support from the European Union and FEDER funds and Junta de Andalucía. Records provided by L. Mangialajo were collected in the framework of projects funded by the Pew Charitable Trust, by the European Commission (AFRIMED, http://afrimed-project.eu/, grant agreement N. 789059) and by the Académie 3 de l’Université Côte d’Azur (projet CONVOST).Peer reviewe

    Unpublished Mediterranean and Black Sea records of marine alien, cryptogenic, and neonative species

    Get PDF
    To enrich spatio-temporal information on the distribution of alien, cryptogenic, and neonative species in the Mediterranean and the Black Sea, a collective effort by 173 marine scientists was made to provide unpublished records and make them open access to the scientific community. Through this effort, we collected and harmonized a dataset of 12,649 records. It includes 247 taxa, of which 217 are Animalia, 25 Plantae and 5 Chromista, from 23 countries surrounding the Mediterranean and the Black Sea. Chordata was the most abundant taxonomic group, followed by Arthropoda, Mollusca, and Annelida. In terms of species records, Siganus luridus, Siganus rivulatus, Saurida lessepsianus, Pterois miles, Upeneus moluccensis, Charybdis (Archias) longicollis, and Caulerpa cylindracea were the most numerous. The temporal distribution of the records ranges from 1973 to 2022, with 44% of the records in 2020–2021. Lethrinus borbonicus is reported for the first time in the Mediterranean Sea, while Pomatoschistus quagga, Caulerpa cylindracea, Grateloupia turuturu, and Misophria pallida are first records for the Black Sea; Kapraunia schneideri is recorded for the second time in the Mediterranean and for the first time in Israel; Prionospio depauperata and Pseudonereis anomala are reported for the first time from the Sea of Marmara. Many first country records are also included, namely: Amathia verticillata (Montenegro), Ampithoe valida (Italy), Antithamnion amphigeneum (Greece), Clavelina oblonga (Tunisia and Slovenia), Dendostrea cf. folium (Syria), Epinephelus fasciatus (Tunisia), Ganonema farinosum (Montenegro), Macrorhynchia philippina (Tunisia), Marenzelleria neglecta (Romania), Paratapes textilis (Tunisia), and Botrylloides diegensis (Tunisia).peer-reviewe

    Βιοπληροφορική ανάλυση ιικών γονιδιωμάτων σε χρωμοσωμικές ενσωματώσεις, με βάση τις τεχνολογίες αλληλούχισης επόμενης γενεάς (NGS)

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    Κατά την διάρκεια μιας ιογενούς λοίμωξης, πολλοί ιοί ενσωματώνουν το γενετικό τους υλικό στο γονιδίωμα του ξενιστή, είτε ως μέρος του κύκλου αναπαραγωγής τους είτε στοχαστικά. Τέτοιες ενσωματώσεις δεν είναι αναγκαία παθολογικές, αλλά έχουν παρουσιαστεί ισχυρά στοιχεία που συνδέουν την απορρύθμιση της έκφρασης καίριων μεταγραφικών παραγόντων, και την επερχόμενη ανάπτυξη καρκίνου, με την παρουσία ιικού γενετικού υλικού στο ανθρώπινο γονιδίωμα (1). Μεταξύ άλλων, ο ανθρώπινος ιός των θηλωμάτων (HPV) προκαλεί τον πιο γνωστό ιογενή καρκίνο αυτό του τράχηλου της μήτρας (1), η ανάπτυξη ηπατοκυτταρικού καρκίνου έχει συσχετιστεί σε μεγάλο βαθμό με την μόλυνση από τον ιό της ηπατίτιδας Β (HBV) (2) και εμφανίζονται στοιχεία για ενσωματώσεις ιικών στελεχών όπως ο Covid-19 (SARS-Cov2), με άγνωστες ακόμα κλινικές συνέπειες (3). Μηχανιστικά οι ιικές ενσωματώσεις διαταράσσουν το τρισδιάστατο επιγενετικό περιβάλλον της περιοχής του DNA στην οποία εισάγονται. Σε κάποιες περιπτώσεις το ιικό γενετικό υλικό μπορεί να περιέχει μοτίβα πρόσδεσης ενδογενών μεταγραφικών παραγόντων οι οποίοι μπορούν να ενεργοποιήσουν ή να απενεργοποιήσουν την έκφραση γειτονικών γονιδίων. Αν αυτά τα γειτονικά γονίδια είναι ογκογόνα ή ογκοκατασταλτικά γονίδια ή ιική ενσωμάτωση μπορεί να αυξήσει τις πιθανότητες ανάπτυξης καρκίνου. Προσπάθειες για την πρόγνωση και πρόληψη παθολογιών που προκαλούνται από ιικές ενσωματώσεις έχουν εμποδιστεί κατά πολύ από την δυσκολία εντοπισμού αυτών με τις τρέχουσες μεθοδολογίες μοριακής βιολογίας (PCR,WGS etc). Η σπανιότητα των γεγονότων αυτών σε συνδυασμό με τον τρόπο δειγματοληψίας (bulk vs single cell) καθιστούν τον έγκαιρο εντοπισμό πιθανά επικίνδυνων ενσωματώσεων ιδιαίτερα δύσκολο (4). Ο πιο διαδεδομένος τρόπος πειραματικής προσέγγισης για τον εντοπισμό τέτοιων ενσωματώσεων (για διαγνωστικούς ή επιστημονικούς λόγους) είναι η αλληλούχιση του πλήρους γονιδιώματος του ασθενή (WGS) ή των περιοχών που πιθανόν περιέχουν ιικές ενσωματώσεις (TS) (4). Και στις δύο περιπτώσεις η βιοπληροφορική ανάλυση των δεδομένων που προκύπτουν από τα πειράματα βασίζεται στον εντοπισμό χιμαιρικών αναγνώσεων (chimeric reads/split reads) οι οποίες περιέχουν γενετικό υλικό και από τους δύο οργανισμούς. Βάση αυτών μπορεί να γίνει η ακριβής χαρτογράφηση μιας ιικής ενσωμάτωσης. Όλοι οι υπάρχοντες αλγόριθμοι εντοπισμού βασίζονται στην ανακάλυψη, χαρτογράφηση και το φιλτράρισμα αυτών των χιμαιρικών αναγνώσεων για να στοιχειοθετήσουν τις προβλέψεις τους. Κύριος στόχος της παρούσας εργασίας είναι η αξιολόγηση (benchmarking) υπαρχόντων αλγορίθμων εντοπισμού ιικών ενσωματώσεων. Για την περάτωση του παραπάνω θα χρησιμοποιηθούν τεχνητά δεδομένα προσομοίωσης με γνωστό αριθμό και συντεταγμένες ενσωματώσεων. Με βάση τα αποτελέσματα του benchmarking, θα ακολουθήσει πρόταση/ανάπτυξη κατάλληλων μεθοδολογιών εντοπισμού ιικών ενσωματώσεων οι οποίες μπορούν να χρησιμοποιηθούν σε bulk και single cell δεδομένα NGS. Τέλος, οι νέοι αλγόριθμοι θα ελεγχθούν σε δημοσιευμένα δεδομένα NGS από δείγματα όγκων ασθενών με παθολογίες όπως ηπατοκυτταρικός καρκίνος (HCC). Με το πέρας της εκπόνησης της διπλωματικής αυτής εργασίας ευελπιστούμε σε μια βαθύτερη κατανόηση των περιορισμών των υπαρχόντων μεθοδολογιών εντοπισμού, και την βελτιστοποίηση αυτών για την πληρέστερη και ακριβέστερη πρόγνωση παθολογιών που προκαλούνται από ιικές ενσωματώσεις.In the span of viral infection, many viruses integrate their genomic material into the host genome. While such events are not necessarily pathogenic, there is strong evidence for correlation between viral integration and development of cancer as a result of ensuing deregulation of oncogenic or tumor-suppressing genes (12). Among others, Human Papilloma Virus (HPV) has been shown to cause cervical cancer (44), Hepatitis B virus (HBV) integrations have been found in 80% of Hepatocellular carcinoma (HCC) cases (12), while recent evidence has emerged suggesting that SARS-CoV2 genomic material has been found integrated in patient genomes with yet unknown clinical consequences (43). Other integrating viruses involved in human pathologies include Epstein–Barr virus (EBV), Human herpesvirus 6 (HHV6), Human immunodeficiency virus (HIV) and Herpes Simplex virus (HSV-1). Mechanistically, viral integrations disturb the three-dimensional epigenetic microenvironment of the genomic region they are found in. In some cases the inserted sequence could contain transcription factor binding motifs that could promote up- or down-regulation of proximal genes. In other cases insertional mutagenesis of target human loci like genes, promoters or enhancers could disrupt host gene expression. If the genes affected are oncogenic or tumor-supressors, cancer development usually ensues. Efforts on the prognosis and early treatment of pathologies caused by viral genome integrations have been stifled by the limitations of current detection methods (PCR based, NGS-based). The rarity of such events, in combination with sampling biases (whole tissue vs single cell samples) render the timely detection of potentially carcinogenic viral integrations particularly challenging (10). The most widespread methods for detecting viral integrations are Whole Genome Sequencing (WGS) of the patient’s genome and Targeted Sequencing (TS) of the patient’s genome, enriched for regions that contain viral genetic material (10). In both cases, the necessary downstream bioinformatic analysis utilizes chimeric and discordantly paired NGS reads that contain DNA sequences of both the host and viral genomes. Based on these reads, an accurate mapping of the integration breakpoints can be achieved. Regardless of possible algorithmic differences, all viral integration detection tools utilize these reads as evidence for viral integration events. The main goal of the present thesis is the benchmarking and evaluation of such viral integration tools using an artificial genome containing random viral integrations as ground truth. Based on the benchmarking results, optimization and future directions for the algorithms evaluated are proposed in order to facilitate the more accurate prognosis of pathologies stemming from viral integration events

    Unpublished Mediterranean and Black Sea records of marine alien, cryptogenic, and neonative species

    Get PDF
    To enrich spatio-temporal information on the distribution of alien, cryptogenic, and neonative species in the Mediterranean and the Black Sea, a collective effort by 173 marine scientists was made to provide unpublished records and make them open access to the scientific community. Through this effort, we collected and harmonized a dataset of 12,649 records. It includes 247 taxa, of which 217 are Animalia, 25 Plantae and 5 Chromista, from 23 countries surrounding the Mediterranean and the Black Sea. Chordata was the most abundant taxonomic group, followed by Arthropoda, Mollusca, and Annelida. In terms of species records, Siganus luridus, Siganus rivulatus, Saurida lessepsianus, Pterois miles, Upeneus moluccensis, Charybdis (Archias) longicollis, and Caulerpa cylindracea were the most numerous. The temporal distribution of the records ranges from 1973 to 2022, with 44% of the records in 2020–2021. Lethrinus borbonicus is reported for the first time in the Mediterranean Sea, while Pomatoschistus quagga, Caulerpa cylindracea, Grateloupia turuturu, and Misophria pallida are first records for the Black Sea; Kapraunia schneideri is recorded for the second time in the Mediterranean and for the first time in Israel; Prionospio depauperata and Pseudonereis anomala are reported for the first time from the Sea of Marmara. Many first country records are also included, namely: Amathia verticillata (Montenegro), Ampithoe valida (Italy), Antithamnion amphigeneum (Greece), Clavelina oblonga (Tunisia and Slovenia), Dendostrea cf. folium (Syria), Epinephelus fasciatus (Tunisia), Ganonema farinosum (Montenegro), Macrorhynchia philippina (Tunisia), Marenzelleria neglecta (Romania), Paratapes textilis (Tunisia), and Botrylloides diegensis (Tunisia)
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