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- An enhanced static-list scheduling algorithm for temporal partitioning onto RPUsPublication . Cardoso, João; Neto, H. C.; Silveira, L. M.; Devadas, S.; Reis, R.This paper presents a novel algorithm for temporal partitioning of graphs representing a behavioral description. The algorithm is based on an extension of the traditional static-list scheduling that tailors it to resolve both scheduling and temporal partitioning. The nodes to be mapped into a partition are selected based on a statically computed cost model. The cost for each node integrates communication effects, the critical path length, and the possibility of the critical path to hide the delay of parallel nodes. In order to alleviate the runtime there is no dynamic update of the costs. A comparison of the algorithm to other schedulers and with close-to-optimum results obtained with a simulated annealing approach is shown. The presented algorithm has been implemented and the results show that it is robust, effective, and efficient, and when compared to other methods finds very good results in small amounts of CPU time.
- Revisiting the evolution of family B1 GPCRs and ligands: insights from molluscaPublication . Cardoso, João; Mc Shane, Jennifer; Li, Zhi; Peng, Maoxiao; Power, Deborah MaryFamily B1 G protein-coupled receptors (GPCRs) are one of the most well studied neuropeptide receptor families since they play a central role in many biological processes including endocrine, gastrointestinal, cardiovascular and reproduction in animals. The genes for these receptors emerged from a common ancestral gene in bilaterian genomes and evolved via gene/genome duplications and deletions in vertebrate and invertebrate genomes. Their existence and function have mostly been characterized in vertebrates and few studies exist in invertebrate species. Recently, an increased interest in molluscs, means a series of genomes have become available, and since they are less modified than insect and nematode genomes, they are ideal to explore the origin and evolution of neuropeptide gene families. This review provides an overview of Family B1 GPCRs and their peptide ligands and incorporates new data obtained from Mollusca genomes and taking a comparative approach challenges existing models on their origin and evolution.
- 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.
- 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.
- Neuropeptides regulate shell growth in the Mediterranean mussel (Mytilus galloprovincialis)Publication . Li, Zhi; Peng, Maoxiao; Félix, Rute; Cardoso, João; Power, Deborah MaryIn bivalves, which are molluscs enclosed in a biomineralized shell, a diversity of neuropeptide precursors has been described but their involvement in shell growth has been largely neglected. Here, using a symmetric marine bivalve, the Mediterranean mussel (Mytilus galloprovincialis), we uncover a role for the neuroendocrine system and neuropeptides in shell production. We demonstrate that the mantle is rich in neuropeptide precursors and that a complex network of neuropeptide-secreting fibres innervates the mantle edge a region highly involved in shell growth. We show that shell damage and shell repair significantly modify neuropeptide gene expression in the mantle edge and the nervous ganglia (cerebropleural ganglia, CPG). When the CPG nerve commissure was severed, shell production was impaired after shell damage, and modified neuropeptide gene expression, the spatial organization of nerve fibres in the ganglia and mantle and biomineralization enzyme activity in the mantle edge. Injection of CALCIa and CALCIIa peptides rescued the impaired shell repair phenotype providing further support for their role in biomineralization. We propose that the regulatory mechanisms identified are likely to be conserved across bivalves and other shelled molluscs since they all share a similar nervous system, a common mantle biomineralization toolbox, and shell structure.
- Activation profile of the Atlantic salmon (Salmo salar) calcium-sensing receptor (Casr) by selected L-amino acidsPublication . Gomes, Ana; Gélébart, Virginie; Félix, Rute; Cardoso, João; Zimmermann, Fabian; Lai, Floriana; Power, Deborah Mary; Ronnestad, IvarIn mammals, the calcium-sensing receptor (CaSR) is involved in nutrient sensing and modulated by several amino acids. In teleosts, sequence homologues of the mammalian CaSR have been described but their function in sensing amino acids remains elusive, including in Atlantic salmon (Salmo salar), an important aquaculture species. This study investigated the activation of Atlantic salmon Casr (asCasr)-mediated signaling pathways-Gq, Gi, and ERK1/2-by six selected L-amino acids (histidine, tryptophan, phenylalanine, isoleucine, leucine and valine) and by Ca2+. Using a Flp-In-HEK293 cell line stably expressing asCasr, we confirmed activation of all three pathways. L-histidine, L-phenylalanine, and L-tryptophan triggered Gi signaling independent of Ca-2(+). Notably, no Ca-2(+) concentrations induced Gi activation, but IP1 production increased in a concentration-dependent manner. L-histidine was the only amino acid to activate the Gq pathway without Ca-2(+), and this response was amplified by the presence of Ca-2(+). In the presence of 2.5 mM Ca-2(+), L-phenylalanine and L-tryptophan also activated Gq signaling in a concentration-dependent manner. Additionally, in the presence of 10 mM Ca-2(+), L-histidine, L-phenylalanine, and L-tryptophan triggered ERK phosphorylation. These findings establish asCasr as a functional homologue of mammalian CaSR, activated in a concentration-dependent manner by L-amino acids with an aromatic ring.