Browsing by Author "Duarte, Daniel Filipe Correia"
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- Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposurePublication . Anjos, Catarina; Duarte, Daniel Filipe Correia; Fatsini Fernández, Elvira; Domitília Matias; Cabrita, ElsaBackground The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process. Results Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage. Conclusions The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.
- Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposurePublication . Anjos, Catarina; Duarte, Daniel Filipe Correia; Fatsini Fernández, Elvira; Matias, Domitília; Cabrita, ElsaThe Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process. Results Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage. Conclusions The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.
- Differentially expressed immune genes in response to Streptococcus agalactiae infection in Nile TilapiaPublication . Duarte, Daniel Filipe Correia; Canário, Adelino V. M.; Chen, LiangbiaoAs the world population grows it becomes harder to fulfil the demand for protein. Aquaculture, an activity that consists in the farming of aquatic organisms, is one of the most important global sources of fish. Asia, and particularly China, represent almost 70% of this production, although, one of the biggest obstacles to the development of the aquaculture industry is infections and mortality caused by pathogens. All around the world, Nile tilapia (Oreochromis niloticus) emerges as an economically important species. Even though it is an alien organism in Asia, the Chinese aquaculture of this fish represents almost 50% of the world total production. Also known as group B streptococcus (GBS), Streptococcus agalactiae is a Gram-positive pathogenic bacterium. This pathogen is not only a problem for modern aquaculture, but it affects a broad range of hosts including humans and other mammals, and a wide range of fish species including the Nile tilapia. The fish gills are an important immune barrier, and part of the first line of defence against pathogens as physical contact is the first step for pathogen infection. This study aimed to identify immune related genes and characterize the Nile tilapia immune response to S.agalactiae infection in the gill using RNA-Seq. Nile tilapia gills were collected 6, 9, 15 and 18 hours post infection, and their isolated RNA was sequenced. A differential gene expression and functional enrichment analysis was performed. At 6, 9, 15, and 18 hours post infection 2122, 1851, 1791, 2395 differentially expressed genes were identified. These represented a significant enrichment of different immune related pathways in response to the pathogen infection such as the Cytokine-cytokine signalling pathway, the Toll-like receptor pathway, the NOD-like receptor pathway, the phagosome pathway, and others. These results provide an insight into the response to an important bacterial pathogen as a basis for management of infection in aquaculture.
- Testis transcriptomic analyses reveal the effects of an algae feed on sperm quality in senegalese sole during the breeding seasonPublication . Félix de Azeredo Pinto e Melo, Francisca; Raposo de Magalhães, Cláudia; Marrero Alemán, Carlos; Duarte, Daniel Filipe Correia; Parente, Pedro; Fatsini Fernández, Elvira; Oliveira, Catarina; Cabrita, ElsaThe usage of dietary algae antioxidants to improve fish reproduction is under-explored, especially in terms of the male reproductive system. In this experiment, 6 % of a blended meal of Phaeodactylum tricornutum and Gracilaria gracilis was incorporated in Senegalese sole broodstock feed, to evaluate the effects on sperm quality of F1 males throughout the breeding season. For that, two groups of breeders were fed during 6 months with the control and algae diets (6 % of control wheat meal replaced with 6 % algae blend). Every 2 weeks, fish were sampled for sperm quality evaluation, which included spermatozoa motility (CASA system), lipid peroxidation (MDA quantification), cell viability, reactive oxygen species (ROS), apoptotic status (flow cytometer), and DNA fragmentation (Comet assay). On a final sampling, 6 fish per group were sacrificed to dissect gonadal tissue, extract RNA and perform an RNA sequencing (RNA-seq) for each treatment. Sperm quality variability was high during the breeding season, including within the same month, irrespective of the diet. Cell viability was approximately 80 % during the whole experiment. Nonetheless, in specific sampling points, algae-fed fish showed higher spermatozoa protection against oxidative processes: in the 1st sampling live cells without ROS (%) were 3 times higher than in control group; on the last two samplings, spermatozoa showed half of MDA content; and on the 3rd sampling had less DNA fragmentation. No differences were found regarding apoptotic status. At the end of the reproductive season, gonadal transcriptomic analysis revealed that algae-fed fish were lacking stimuli for sperm production, both in terms of quantity and quality. This fish group seemed to have lipid metabolism and antioxidant capacity enhanced by the diet but, at the same time, were facing a compensatory mechanism due to an unknown algae compound that might be disrupting DNA replication and spermatogenesis. Altogether, this study suggests that algae blends can be used in broodstock feeds for Senegalese sole, however further research is needed to understand how to use only the desirable bioactive compounds and thus obtain higher and consistent sperm quality throughout the breeding season.