Browsing by Author "Power, Deborah Mary"
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- Cartilage acidic protein a novel therapeutic factor to improve skin damage repair?Publication . Félix, Rute; Anjos, Liliana; Costa, Rita; Letsiou, Sophia; Power, Deborah MaryFish skin has been gaining attention due to its efficacy as a human-wound-treatment product and to identify factors promoting its enhanced action. Skin fibroblasts have a central role in maintaining skin integrity and secrete extra cellular matrix (ECM) proteins, growth factors and cytokines to rapidly repair lesions and prevent further damage or infection. The effects on scratch repair of the ubiquitous but poorly characterized ECM protein, cartilage acidic protein 1 (CRTAC1), from piscine and human sources were compared using a zebrafish SJD.1 primary fibroblast cell line. A classic in vitro cell scratch assay, immunofluorescence, biosensor and gene expression analysis were used. Our results demonstrated that the duplicate sea bass Crtac1a and Crtac1b proteins and human CRTAC-1A all promoted SJD.1 primary fibroblast migration in a classic scratch assay and in an electric cell impedance sensing assay. The immunofluorescence analysis revealed that CRTAC1 enhanced cell migration was most likely caused by actin-driven cytoskeletal changes and the cellular transcriptional response was most affected in the early stage (6 h) of scratch repair. In summary, our results suggest that CRTAC1 may be an important factor in fish skin promoting damage repair.
- Core genes of biomineralization and cis-regulatory long non-coding RNA regulate shell growth in bivalvesPublication . Peng, Maoxiao; Cardoso, João; Pearson, Gareth Anthony; Canario, Adelino; Power, Deborah MaryBivalve molluscs are abundant in marine and freshwater systems and contribute essential ecosystem services. They are characterized by an exuberant diversity of biomineralized shells and typically have two symmetric valves (a.k.a shells), but oysters (Ostreidae), some clams (Anomiidae and Chamidae) and scallops (Pectinida) have two asymmetrical valves. Predicting and modelling the likely consequences of ocean acidification on bivalve survival, biodiversity and aquaculture makes understanding shell biomineralization and its regulation a priority. Objectives: This study aimed to a) exploit the atypical asymmetric shell growth of some bivalves and through comparative analysis of the genome and transcriptome pinpoint candidate biomineralization-related genes and regulatory long non-coding RNAs (LncRNAs) and b) demonstrate their roles in regulating shell biomineralization/growth. Methods: Meta-analysis of genomes, de novo generated mantle transcriptomes or transcriptomes and proteomes from public databases for six asymmetric to symmetric bivalve species was used to identify biomineralization-related genes. Bioinformatics filtering uncovered genes and regulatory modules characteristic of bivalves with asymmetric shells and identified candidate biomineralization-related genes and lncRNAs with a biased expression in asymmetric valves. A shell regrowth model in oyster and gene silencing experiments, were used to characterize candidate gene function. Results: Shell matrix genes with asymmetric expression in the mantle of the two valves were identified and unique cis-regulatory lncRNA modules characterized in Ostreidae. LncRNAs that regulate the expression of the tissue inhibitor of metalloproteinases gene family (TIMPDR) and of the shell matrix protein domain family (SMPDR) were identified. In vitro and in vivo silencing experiments revealed the candidate genes and lncRNA were associated with divergent shell growth rates and modified the microstructure of calcium carbonate (CaCO3) crystals. Conclusion: LncRNAs are putative regulatory factors of the bivalve biomineralization toolbox. In the Ostreidae family of bivalves biomineralization-related genes are cis-regulated by lncRNA and modify the planar growth rate and spatial orientation of crystals in the shell.
- Corrigendum: Evidence for a genetic contribution to the ossification of spinal ligaments in ossification of posterior longitudinal ligament and diffuse idiopathic skeletal hyperostosis: a narrative reviewPublication . Couto, Ana Rita; Parreira, Bruna; Power, Deborah Mary; Pinheiro, Luís; Dias, João Madruga; Novofastovski, Irina; Eshed, Iris; Sarzi-Puttini, Piercarlo; Pappone, Nicola; Atzeni, Fabiola; Verlaan, Jorrit-Jan; Kuperus, Jonneke; Bieber, Amir; Ambrosino, Pasquale; Kiefer, David; Khan, Muhammad Asim; Mader, Reuven; Baraliakos, Xenofon; Bruges-Armas, Jácome
- Dual-compartment-gate organic transistors for monitoring biogenic amines from foodPublication . Sergi, Ilenia; Sensi, Matteo; Zanotti, Rian; Tsironi, Theofania; Flemetakis, Emmanouil; Power, Deborah Mary; Bortolotti, Carlo Augusto; Biscarini, FabioAccording to the Food and Agriculture Organization of the United Nations (FAO) more than 14% of the world's food production is lost every year before reaching retail, and another 17% is lost during the retail stage. The use of the expiration date as the main estimator of the life-end of food products creates unjustified food waste. Sensors capable of quantifying the effective food freshness and quality could substantially reduce food waste and enable more effective management of food chain. We propose an electrolyte-gated organic transistor (EGOT) that responds to the release of biogenic amines, like diamines and tyramine, generated by degradation of protein-rich food. The EGOT sensor features a polymeric poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) gate electrode fabricated in the shape of a miniaturized beaker containing an aqueous solution in the inner side (to be exposed to food) and capacitively coupled through a hydrogel to the transistor channel on the outside (not in contact with food). The hydrogen bonds formed by the water-dissolved amines with PEDOT:PSS modulate the EGOT channel across a wide range of amine concentrations. We demonstrate that our sensor can detect different amines by the combinatorial analysis of the response from different channel materials, PEDOT:PSS and the other DPP-DTT, with a limit of detection as low as 100 pM.
- Evolution of chitin-synthase in molluscs and their response to ocean acidificationPublication . Cardoso, João; Power, Deborah Mary; Peng, MaoxiaoChitin-synthase (CHS) is found in most eukaryotes and has a complex evolutionary history. Research into CHS has mainly been in the context of biomineralization of mollusc shells an area of high interest due to the consequences of ocean acidification. Exploration of CHS at the genomic level in molluscs, the evolution of isoforms, their tissue distribution, and response to environmental challenges are largely unknown. Exploiting the extensive molecular resources for mollusc species it is revealed that bivalves possess the largest number of CHS genes (12-22) reported to date in eukaryotes. The evolutionary tree constructed at the class level of molluscs indicates four CHS Type II isoforms (A-D) probably existed in the most recent common ancestor, and Type II-A (Type II-A1/Type II-A-2) and Type II-C (Type II-C-1/Type II-C-2) underwent further differentiation. Non-specific loss of CHS isoforms occurred at the class level, and in some Type II (B-D groups) isoforms the myosin head domain, which is associated with shell formation, was not preserved and highly species-specific tissue expression of CHS isoforms occurred. These observations strongly support the idea of CHS functional diversification with shell biomineralization being one of several important functions. Analysis of transcriptome data uncovered the species-specific potential of CHS isoforms in shell formation and a species-specific response to ocean acidification (OA). The impact of OA was not CHS isoform-dependent although in Mytilus, Type I-B and Type II-D gene expression was down-regulated in both M. galloprovincialis and M. coruscus. In summary, during CHS evolution the gene family expanded in bivalves generating a large diversity of isoforms with different structures and with a ubiquitous tissue distribution suggesting that chitin is involved in many biological functions. These findings provide insight into CHS evolution in molluscs and lay the foundation for research into their function and response to environmental changes.
- Examination of the effects of excess microalgae availability on the disruption of mussel byssus secretionPublication . Ji-Yue Ni; Yan Zhou; Yu-Qing Wang; Shi-Hui Huang; Qian-Wen Cui; Wen-Yi Wang; Xiao-Ying Yang; Power, Deborah Mary; Yi-Feng LiThe present study evaluated the effects of food availability on byssus secretion in the hard-shelled mussel Mytilus coruscus. Byssus production was evaluated, and foot tissue transcriptomes, the site of byssus production, were generated. The results showed that byssus secretion was disrupted in mussels fed high levels of microalgae (HFL, 88.8 mg/L day−1), compared to the control group (p < 0.05), and that more byssus production occurred in the HFL group during the recovery period. Byssus secretion was not affected in mussels fed low levels of microalgae (8.88 × 10−3 mg/L day−1), but the shedding of byssus filaments was significantly increased compared to the control mussels (p < 0.05). Transcriptome data of the foot tissue revealed that lysosome, FoxO signaling, and autophagy pathways involved in autophagic cell death and apoptosis were significantly affected (p < 0.05) and may explain differences in byssus growth under modified food availability in M. coruscus. High feed levels modified metabolic pathways, such as sphingolipid, tyrosine, and phenylalanine, and downregulated genes coding for mussel foot proteins, which may explain reduced byssus production. The study found that contrary to expectation increased food availability reduced mussel byssus production by altering foot metabolism and promoting autophagy of foot tissue.
- Extracting protein from microalgae (Tetraselmis chuii) for proteome analysisPublication . L, Anjos; Estêvão, J.; Infante, Carlos; Mantecón, Lalia; Power, Deborah MaryMicroalgae have high potential as a resource for sustainable and green protein for food or bioactive molecules. Nonetheless, despite the high protein content of microalgae (40 - 70% dry weight) progress in the characterization of their protein composition remains challenging. This is due to the highly variable chemical composition of microalgae strains and factors such as their rigid thick cell wall, polysaccharide content, protein stability, pH. The method described herein was developed to optimize protein extraction for proteome analysis of microalgae (Tetraselmis chuii) biomass. The effects on protein solubility of solvent type (organic, denaturing, and non-denaturing) combined with three customized microalgae disruption methods were investigated. The proteome targeted high quality protein extracts were for hydro-soluble proteins recovered by cell disruption using bead milling coupled to centrifugation (protein yield approximate to 13%). The developed method is inexpensive, efficient (yielding high-quality protein extracts with a low content of interfering compounds) and from an industrial perspective easily scalable and compatible with other applications. To add value to the end product we additionally propose the use of stabilizing agents to maintain protein solubility during refrigerated storage and a method targeting the fractionation of low molecular weight proteins. An inexpensive easy-to-do 5 step protocol for microalgae protein extracts. A protein extraction method free from dangerous or highly polluting chemicals. Production of high yield aqueous protein extracts suitable for proteomics. (C) 2022 The Authors. Published by Elsevier B.V.
- Factors driving bacterial microbiota of eggs from commercial hatcheries of European Seabass and Gilthead SeabreamPublication . Najafpour, Babak; Pinto, Patricia IS; Moutou, Katerina A.; Canario, A.V.M.; Power, Deborah MaryA comprehensive understanding of how bacterial community abundance changes in fishes during their lifecycle and the role of the microbiota on health and production is still lacking. From this perspective, the egg bacterial communities of two commercially farmed species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), from different aquaculture sites were compared, and the potential effect of broodstock water microbiota and disinfectants on the egg microbiota was evaluated. Moreover, 16S ribosomal RNA gene sequencing was used to profile the bacterial communities of the eggs and broodstock water from three commercial hatcheries. Proteobacteria were the most common and dominant phyla across the samples (49.7% on average). Vibrio sp. was the most highly represented genus (7.1%), followed by Glaciecola (4.8%), Pseudoalteromonas (4.4%), and Colwellia (4.2%), in eggs and water across the sites. Routinely used iodine-based disinfectants slightly reduced the eggs’ bacterial load but did not significantly change their composition. Site, species, and type of sample (eggs or water) drove the microbial community structure and influenced microbiome functional profiles. The egg and seawater microbiome composition differed in abundance but shared similar functional profiles. The strong impact of site and species on egg bacterial communities indicates that disease management needs to be site-specific and highlights the need for species- and site-specific optimization of disinfection protocols.
- Gene expression comparison between the injured tubercule skin of turbot (Scophthalmus maximus) and the scale skin of brill (Scophthalmus rhombus)Publication . Estêvão, João; Blanco-Hortas, Andrés; Rubiolo, Juan A.; Aramburu, Óscar; Fernández, Carlos; Gómez-Tato, Antonio; Power, Deborah Mary; Martínez, PaulinoTurbot and brill are two congeneric commercial flatfish species with striking differences in skin organization. The calcified appendages in turbot skin are conical tubercles, while in brill, they are elasmoid scales. A skin injury involving epidermal and dermal levels was evaluated 72 h post-injury to compare the skin regeneration processes between both species. An immune-enriched 4x44k turbot oligo-microarray was used to characterize the skin transcriptome and gene expression profiles in both species. RNA-seq was also performed on the brill samples to improve transcriptome characterization and validate the microarray results. A total of 15,854 and 12,447 expressed genes were identified, respectively, in the turbot and brill skin (10,101 shared) using the oligo-microarray (11,953 and 9629 annotated). RNA-seq enabled the identification of 11,838 genes in brill skin (11,339 annotated). Functional annotation of skin transcriptomes was similar in both species, but in turbot, it was enriched on mechanisms related to maintenance of epithelial structure, mannosidase activity, phospholipid binding, and cell membranes, while in brill, it was enriched on biological and gene regulation mechanisms, tissue development, and transferase and catalytic activities. The number of DEGs identified after skin damage in brill and turbot was 439 and 143, respectively (only 14 shared). Functions related to catabolic and metabolic processes, visual and sensorial perception, response to wounding, and wound healing were enriched in turbot DEGs, while metabolism, immune response, oxidative stress, phospholipid binding, and response to stimulus were enriched in brill. The results indicate that differences may be related to the stage of wound repair due to their different skin architecture. This work provides a foundation for future studies directed at skin defense mechanisms, with practical implications in flatfish aquaculture.
- Insights into core molecular changes associated with metamorphosis in gilthead seabream larvae across diverse hatcheriesPublication . NAJAFPOUR, BABAK; Santos, Soraia; Manchado, Manuel; Vidal, Aurora; Tsipourlianos, Andreas; Canario, Adelino; Moutou, Katerina A.; Power, Deborah MaryEarly development is a critical period in fish aquaculture and is influenced by biotic and abiotic factors (e.g., temperature, feed) that can vary significantly between hatcheries, making it difficult to identify core factors determining quality. Many of the existing larval transcriptome studies are small-scale and occur under specific rearing conditions that do not mirror the diversity of larviculture practices at an industrial level. In the present transcriptome study, gilthead seabream at the larval to juvenile transition (metamorphosis) from several hatcheries in Europe (Greece, Italy, and France) were analysed in a large-scale RNA-seq study. The aim was to uncover the most significant molecular modifications occurring during metamorphosis, irrespective of differences in biotic or abiotic factors, to address knowledge gaps associated with critical early developmental stages under industrial hatchery conditions. Commonly modified gene transcripts between larval stages were identified based on the clustering of gene expression profiles of 25 gilthead seabream libraries from different hatcheries in a PCA analysis. When larvae at flexion were compared to larvae at mid-metamorphosis, 2243 differentially expressed genes (DEGs) were identified, and when larvae at early to mid-metamorphosis were compared to mid to late-metamorphosis, 2299 DEGs were identified. Comparative analysis across the developmental stages of gilthead seabream revealed genes of importance for the metamorphic transition and adaptation to rearing conditions, including genes related to the nervous system at flexion (24 days post hatch), enteroendocrine cell differentiation, and lipid homeostasis at early to mid-metamorphosis (46 dph), and enrichment of genes indicative of immune competence at mid to late-metamorphosis (51-54 dph). The differential expression of some endocrine-associated genes, dio1, dio2, cldn1, ing4, Pou3f4, and fgf22, highlights their importance in metamorphosis. Meta-analysis of the transcriptomes from two species, the gilthead seabream and Senegalese sole, that have differing symmetry and ecology uncovered common molecular expression patterns that underlie larvae maturation during metamorphosis, and we propose that these represent core gene markers of metamorphosis in these two fish species.