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Zou J, Ma Q, Gao C, Yang M, Wen J, Xu L, Guo X, Zhong X, Duan Y. WTAP promotes proliferation of esophageal squamous cell carcinoma via m 6A-dependent epigenetic promoting of PTP4A1. Cancer Sci 2024; 115:2254-2268. [PMID: 38746998 PMCID: PMC11247548 DOI: 10.1111/cas.15924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/04/2023] [Accepted: 06/18/2023] [Indexed: 07/13/2024] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) represents a frequently seen malignancy with high prevalence worldwide. Although current studies have shown that Wilms' tumor 1-associated protein (WTAP), a major part in the methyltransferase complex, is involved in various tumor pathological processes, its specific role in ESCC remains unclear. Therefore, the present work focused on exploring WTAP's function and mechanism in ESCC progression using clinical ESCC specimens, ESCC cells, and mammalian models. Firstly, we proved WTAP was significantly upregulated within ESCC, and WTAP mRNA expression showed a good diagnostic performance for ESCC. Functionally, WTAP positively regulated in-vivo and in-vitro ESCC cells' malignant phenotype through the AKT-mTOR signaling pathway. Meanwhile, WTAP positively regulated the N6-methyladenosine (m6A) modification levels in ESCC cells. Protein tyrosine phase type IVA member 1 (PTP4A1) was confirmed to be the m6A target of WTAP, and WTAP positively regulated the expression of PTP4A1. Further study revealed that PTP4A1 showed high expression within ESCC. Silencing PTP4A1 inhibited the AKT-mTOR signaling pathway to suppress ESCC cells' proliferation. Rescue experiments showed that silencing PTP4A1 partially reversed the WTAP-promoting effect on ESCC cells' proliferation ability. Mechanistically, WTAP regulated PTP4A1 expression to activate the AKT-mTOR pathway, promoting the proliferation of ESCC cells. Our study demonstrated that WTAP regulates the progression of ESCC through the m6A-PTP4A1-AKT-mTOR signaling axis and that WTAP is a potential target for diagnosing and treating ESCC.
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Affiliation(s)
- Jiang Zou
- Research Center of Analytical Instrumentation, Key Laboratory of Bio‐resource and Eco‐environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeNanchongChina
- Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchongChina
| | - Qiang Ma
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeNanchongChina
- Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchongChina
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Chuanli Gao
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Miyuan Yang
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Jilin Wen
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Lei Xu
- Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchongChina
| | - Xiaolan Guo
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeNanchongChina
- Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchongChina
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Xiaowu Zhong
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeNanchongChina
- Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchongChina
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio‐resource and Eco‐environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
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Venkataraman YR, White SJ, Roberts SB. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics 2022; 23:556. [PMID: 35927609 PMCID: PMC9351233 DOI: 10.1186/s12864-022-08781-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/13/2022] [Indexed: 12/30/2022] Open
Abstract
Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08781-5.
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Affiliation(s)
- Yaamini R Venkataraman
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543, USA. .,School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA.
| | - Samuel J White
- School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
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Kenny NJ, McCarthy SA, Dudchenko O, James K, Betteridge E, Corton C, Dolucan J, Mead D, Oliver K, Omer AD, Pelan S, Ryan Y, Sims Y, Skelton J, Smith M, Torrance J, Weisz D, Wipat A, Aiden EL, Howe K, Williams ST. The gene-rich genome of the scallop Pecten maximus. Gigascience 2020; 9:giaa037. [PMID: 32352532 PMCID: PMC7191990 DOI: 10.1093/gigascience/giaa037] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/26/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. FINDINGS Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. CONCLUSIONS The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
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Affiliation(s)
- Nathan J Kenny
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | - Shane A McCarthy
- University of Cambridge, Department of Genetics,Cambridge CB2 3EH, UK
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
| | - Katherine James
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | | | - Craig Corton
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Jale Dolucan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Dan Mead
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Pelan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Yan Ryan
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Institute of Infection and Global Health, Liverpool University, iC2, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | | | | | | | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Erez L Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China
- School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Kerstin Howe
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Suzanne T Williams
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
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Silliman K. Population structure, genetic connectivity, and adaptation in the Olympia oyster ( Ostrea lurida) along the west coast of North America. Evol Appl 2019; 12:923-939. [PMID: 31080505 PMCID: PMC6503834 DOI: 10.1111/eva.12766] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/28/2018] [Accepted: 12/02/2018] [Indexed: 01/02/2023] Open
Abstract
Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent with a null model of no population structure. To distinguish between these hypotheses in O. lurida, 13,424 single nucleotide polymorphisms (SNPs) were used to characterize rangewide population structure, genetic connectivity, and adaptive divergence. Samples were collected across the species range on the west coast of North America, from southern California to Vancouver Island. A conservative approach for detecting putative loci under selection identified 235 SNPs across 129 GBS loci, which were functionally annotated and analyzed separately from the remaining neutral loci. While strong population structure was observed on a regional scale in both neutral and outlier markers, neutral markers had greater power to detect fine-scale structure. Geographic regions of reduced gene flow aligned with known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay, and the currents around Cape Flattery. The outlier loci identified as under putative selection included genes involved in developmental regulation, sensory information processing, energy metabolism, immune response, and muscle contraction. These loci are excellent candidates for future research and may provide targets for genetic monitoring programs. Beyond specific applications for restoration and management of the Olympia oyster, this study lends to the growing body of evidence for both population structure and adaptive differentiation across a range of marine species exhibiting the potential for panmixia. Computational notebooks are available to facilitate reproducibility and future open-sourced research on the population structure of O. lurida.
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Flores-Herrera P, Farlora R, González R, Brokordt K, Schmitt P. De novo assembly, characterization of tissue-specific transcriptomes and identification of immune related genes from the scallop Argopecten purpuratus. FISH & SHELLFISH IMMUNOLOGY 2019; 89:505-515. [PMID: 30940577 DOI: 10.1016/j.fsi.2019.03.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
The scallop Argopecten purpuratus is one of the most economically important cultured mollusks on the coasts from Chile and Peru but its production has declined, in part, due to the emergence of mass mortality events of unknown origin. Driven by this scenario, increasing progress has been made in recent years in the comprehension of immune response mechanisms in this species. However, it is still not entirely understood how different mucosal interfaces participate and cooperate with the immune competent cells, the hemocytes, in the immune defense. Thus, in this work we aimed to characterize the transcriptome of three tissues with immune relevance from A. purpuratus by next-generation sequencing and de novo transcriptome assembly. For this, 18 cDNA libraries were constructed from digestive gland, gills and hemocytes tissues of scallops from different immune conditions and sequenced by the Illumina HiSeq4000 platform. A total of 967.964.884 raw reads were obtained and 967.432.652 clean reads were generated. The clean reads were de novo assembled into 46.601 high quality contigs and 32.299 (69.31%) contigs were subsequently annotated. In addition, three de novo specific assemblies were performed from clean reads obtained from each tissue cDNA libraries for their comparison. Gene ontology (GO) and KEGG analyses revealed that annotated sequences from digestive gland, gills and hemocytes could be classified into both general and specific subcategory terms and known biological pathways, respectively, according to the tissue nature. Finally, several immune related candidate genes were identified, and the differential expression of tissue-specific genes was established, suggesting they could display specific roles in the host defense. The data presented in this study provide the first insight into the tissue specific transcriptome profiles of A. purpuratus, which should be considered for further research on the interplay between the hemocytes and mucosal immune responses.
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Affiliation(s)
- Patricio Flores-Herrera
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Chile
| | - Rodolfo Farlora
- Laboratorio de Biotecnología Acuática y Genómica Reproductiva, Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Chile
| | - Roxana González
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Chile
| | - Katherina Brokordt
- Laboratory of Marine Physiology and Genetics (FIGEMA), Centro de Estudios Avanzados en Zonas Áridas (CEAZA) and Universidad Católica Del Norte, Chile
| | - Paulina Schmitt
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Chile.
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Alharris E, Singh NP, Nagarkatti PS, Nagarkatti M. Role of miRNA in the regulation of cannabidiol-mediated apoptosis in neuroblastoma cells. Oncotarget 2019; 10:45-59. [PMID: 30713602 PMCID: PMC6343753 DOI: 10.18632/oncotarget.26534] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/13/2018] [Indexed: 12/28/2022] Open
Abstract
Neuroblastoma (NBL) is one of the most common childhood cancers that originate from the immature nerve cells of the sympathetic system. Studies with NBL cancers have also shown that miRNAs are dysregulated and may play a critical role in pathogenesis. Cannabidiol (CBD) is a non-psychoactive compound found in marijuana which has been previously shown by our laboratory and others to induce apoptosis in cancer cells. However, there are no studies reported to test if CBD mediates these effects through regulation of miRNA. In the current study, therefore, we investigated if CBD induces apoptosis in human NBL cell lines, SH SY5Y and IMR-32, and if it is regulated by miRNA. Our data demonstrated that CBD induces apoptosis in NBL cells through activation of serotonin and vanilloid receptors. We also found that caspase-2 and -3 played an important role in the induction of apoptosis. CBD also significantly reduced NBL cell migration and invasion in vitro. Furthermore, CBD blocked mitochondrial respiration and caused a shift in metabolism towards glycolysis. CBD altered the expression of miRNA specifically, down-regulating hsa-let-7a and upregulating hsa-mir-1972. Downregulation of let-7a increased expression of target caspase-3, and growth arrest specific-7 (GAS-7) genes. Upregulation of hsa-mir-1972 caused decreased expression of BCL2L1 and SIRT2 genes. Together, our studies suggest that CBD-mediated apoptosis in NBL cells is regulated by miRNA.
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Affiliation(s)
- Esraah Alharris
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA
| | - Narendra P Singh
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA
| | - Prakash S Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA
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Moreira R, Pereiro P, Balseiro P, Milan M, Pauletto M, Bargelloni L, Novoa B, Figueras A. Revealing Mytilus galloprovincialis transcriptomic profiles during ontogeny. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 84:292-306. [PMID: 29481906 DOI: 10.1016/j.dci.2018.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Mediterranean mussels are a worldwide spread bivalve species with extraordinary biological success. One of the reasons of this success could be the reproduction strategy of bivalves, characterized by the presence of trochophore larvae. Larval development in bivalves has been a topic of raising interest in the scientific community but it deserves much more attention. The principal objective of this work was to study the transcriptomic profile of the ontogeny of Mytilus galloprovincialis analyzing the gene expression in different developmental stages, from oocytes to juveniles. For this purpose, after conducting a 454 sequencing of the transcriptomes of mussel hemocytes, adult tissues and larvae, a new DNA microarray was designed and developed. The studied developmental stages: unfertilized oocytes, veliger, pediveliger, settled larvae and juveniles, showed very different transcriptomic profiles and clustered in groups defining their characteristic gene expression along ontogeny. Our results show that oocytes present a distinct and characteristic transcriptome. After metamorphosis, both settled larvae and juveniles showed a very similar transcriptome, with no enriched GO terms found between these two stages. This suggests: 1.- the progressive loss of RNA of maternal origin through larval development and 2.- the stabilization of the gene expression after settlement. On the other hand during metamorphosis a specific profile of differentially expressed genes was found. These genes were related to processes such as differentiation and biosynthesis. Processes related to the immune response were strongly down regulated. These suggest a development commitment at the expense of other non-essential functions, which are temporary set aside. Immune genes such as antimicrobial peptides suffer a decreased expression during metamorphosis. In fact, we found that the oocytes which express a higher quantity of genes such as myticins are more likely to reach success of the offspring, compared to oocytes poor in such mRNAs, whose progeny died before reaching metamorphosis.
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Affiliation(s)
- Rebeca Moreira
- Instituto de Investigaciones Marinas, IIM - CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain.
| | - Patricia Pereiro
- Instituto de Investigaciones Marinas, IIM - CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain.
| | - Pablo Balseiro
- Instituto de Investigaciones Marinas, IIM - CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain; Uni Research Environment, Uni Research AS, Nygårdsgaten 112, 5008 Bergen, Norway.
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science (BCA) University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy.
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science (BCA) University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy.
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA) University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy.
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas, IIM - CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain.
| | - Antonio Figueras
- Instituto de Investigaciones Marinas, IIM - CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain.
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