Agostinho Antunes's research while affiliated with University of Porto and other places

Publications (423)

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The shortfin mako, Isurus oxyrinchus, is an oceanic pelagic shark species found worldwide in tropical and subtropical waters. It is frequently caught by pelagic longline fisheries, but despite its commercial importance and ecological significance, little is still known about its biology and ecology at the molecular level. Therefore, we combined two...
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Cyanobacteria, ancient prokaryotes, interfere with ecosystem water quality through the production of cyanotoxins and bloom formation. Therefore, for water safety and public health reasons, the application of faster, sensitive, and specific tools on its risk assessment is demanded. Polymerase chain reaction (PCR) coupled with DNA sequencing can be a...
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In the last two decades many reports have addressed the application of artificial intelligence (AI) in the search and design of antimicrobial peptides (AMPs). AI has been represented by machine learning (ML) algorithms that use sequence-based features for the discovery of new peptidic scaffolds with promising biological activity. From AI perspectiv...
Article
Sex chromosomes recombine restrictly in their homologous area, the pseudoautosomal region (PAR), represented by PAR1 and PAR2, which behave like an autosome in both pairing and recombination. The PAR1, common to most of the eutherian mammals, is located at the terminus of the sex chromosomes short arm and exhibit recombination rates ~20 times highe...
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Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here we use whole genome sequences of five species from the genus Leopardus, a recently diversified Neotropical lineage with species bearing distinctive morphological, ecological and behavi...
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Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species,...
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Peptide-based drugs are promising anticancer candidates due to their biocompatibility and low toxicity. In particular, tumor-homing peptides (THPs) have the ability to bind specifically to cancer cell receptors and tumor vasculature. Despite their potential to develop antitumor drugs, there are few available prediction tools to assist the discovery...
Preprint
Antimicrobial peptides (AMPs) have appeared as promising compounds to treat a wide range of diseases. Their clinical potentialities reside in the wide range of mechanisms they can use for both killing microbes and modulating immune responses. However, the hugeness of the AMPs’ chemical space (AMPCS), represented by more than 1065 unique sequences o...
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Cyanobacteria are ancient prokaryotes responsible for bloom formation in many freshwater resources worldwide. These dense agglomerations are a result of the rise of nutrient input (N and P) or temperature. The toxin content and illness associated with contact impair human health with repercussions in water quality. Produced by a wide variety of cya...
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We are an international group of biological scientists, conservationists, and environmentalists who have been closely following the plight and conservation of pangolins over a number of years. Pangolins comprise the mammalian Order Pholidota, which contains eight living species found in diverse habitats in Africa (4 species) and Asia (4 species), w...
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Sexual reproduction is a diverse and widespread process. In gonochoristic species, the differentiation of sexes occurs through diverse mechanisms, influenced by environmental and genetic factors. In most vertebrates, a master-switch gene is responsible for triggering a sex determination network. However, only a few genes have acquired master-switch...
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Within the Conidae family, the piscivorous Conus species have been a hotspot target for drug discovery. Here, we assess the relevance of Conus and their other feeding habits, and thus under distinctive evolutionary constraints, to highlight the potential of neglected molluscivorous and vermivorous species in biomedical research and pharmaceutical i...
Preprint
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Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 MYA, yet the genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remain largely unknown. Additionally, many populations have declined drastically due to anthropogenic...
Preprint
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Antimicrobial peptides (AMPs) are small bioactive chemicals that have appeared as promising compounds to treat a wide range of diseases. The effectiveness of AMPs resides in the wide range of mechanisms they can use for both killing microbes and modulating immune responses. However, the AMPs’ chemical space (AMPCS) is huge, it is estimated that the...
Preprint
Antimicrobial peptides (AMPs) are small bioactive chemicals that have appeared as promising compounds to treat a wide range of diseases. The effectiveness of AMPs resides in the wide range of mechanisms they can use for both killing microbes and modulating immune responses. However, the AMPs’ chemical space (AMPCS) is huge, it is estimated that the...
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Aim How historical and contemporary eco-evolutionary processes shape the patterns of genetic diversity and differentiation across species’ distribution range remains an open question with strong conservation implications. Focusing on the orange stony coral, Astroides calycularis, we (a) characterized the pattern of neutral genetic diversity across...
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Associations between different organisms have been extensively described in terrestrial and marine environments. These associations are involved in roles as diverse as nutrient exchanges, shelter or adaptation to adverse conditions. Ascidians are widely dispersed marine invertebrates associated to invasive behaviours. Studying their microbiomes has...
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The human β-coronavirus SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China. It causes Covid-19 disease which has become pandemic. Each of the five-known human β-coronaviruses has four major structural proteins (E, M, N and S) and 16 non-structural proteins encoded by ORF1a and ORF1b together (ORF1ab) that are involved in virus pathog...
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Over the last years, many studies have reported the challenge of precisely identifying shark and ray species from the fin trade. In Asia, the high demand for shark fin soup has resulted in correspondingly high prices for fins. This, in turn, has caused overexploitation of elasmobranch populations worldwide. Fin processing can cause the loss of morp...
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Cyanobacteria are a group of microorganisms that can be found in a diverse range of biogeographical areas and produce potent and damaging cyanotoxins, which reveal importance for continuous studies and surveillance efforts. In this study, we analyzed worldwide two-month culture-enriched water samples collected from 12 distinct countries (Costa Rica...
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Marine protected areas (MPAs) are one of the most efficient conservation tools to buffer marine biodiversity loss induced by human activities. Beside effective enforcement, an accurate understanding of the eco-evolutionary processes underlying the patterns of biodiversity is needed to reap the benefits of management policies. In this context, integ...
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Cyanobacteria have long been associated with harmful effects on humans, animals and aquatic biota. Cyanotoxins are their most toxic metabolite. This review summarizes the current research, impacts and future needs in cyanobacterial studies undertaken in Portugal, the south-ernmost country of Europe, and with a recent multiplication of cyanotoxicity...
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Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging and pursued by different teams lacking connection with each other. This lack of coordination hampers the full development of venom...
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We focus on the stalked goose barnacle L. anatifera adhesive system, an opportunistic less selective species for the substrate, found attached to a variety of floating objects at seas. Adhesion is an adaptative character in barnacles, ensuring adequate positioning in the habitat for feeding and reproduction. The protein composition of the cement mu...
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Background Molecular phylogenetic algorithms frequently disagree with the approaches considering reproductive compatibility and morphological criteria for species delimitation. The question stems if the resulting species boundaries from molecular, reproductive and/or morphological data are definitively not reconcilable; or if the existing phylogene...
Article
Enzyme subunit interfaces have remarkable potential in drug design as both target and scaffold for their own inhibitors. We show an evolution-driven strategy for the de novo design of peptide inhibitors targeting interfaces of the Escherichia coli FoF1-ATP synthase as a case study. The evolutionary algorithm ROSE was applied to generate diversity-o...
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We report here the genome sequences of six Vibrio strains isolated from an Atlantic intertidal marine sponge, Ophlitaspongia papilla . Genome mining and comparative genomics will assist in deciphering the bioactive potential of the symbiotic microbes and molecular mechanisms of sponge-microbial symbioses.
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Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predati...
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High levels of population differentiation are a common demographic pattern in syngnathids, even at small geographical scales. This is probably the end result of the common life history traits observed within the family, involving limited dispersal capabilities and strong habitat dependency. The worm pipefish, Nerophis lumbriciformis, which displays...
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Here we provide all datasets and details applied in the construction of a composite protein database required for the proteogenomic analyses of the article "Putative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database". All data, subdivided into six datasets...
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Cephalopods, successful predators, can use a mixture of substances to subdue their prey, becoming interesting sources of bioactive compounds. In addition to neurotoxins and enzymes, the presence of antimicrobial compounds has been reported. Recently, the transcriptome and the whole proteome of the Octopus vulgaris salivary apparatus were released,...
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The COVID-19 outbreak has sickened over six million people across the world. The origin of COVID-19 coronavirus (CoV) remains unknown although pangolins have been suggested as potential hosts. We investigated two pangolins seized in Guangdong Province, China. Molecular screening revealed CoV in one pangolin (“Dahu”), while another (“Meidong”) was i...
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Lung cancer is the type of cancer causing most deaths in humans, with 234,030 new cases of lung cancer diagnosed in the United States in 2018. Recently, Tumor suppressor genes (TSGs) or the control of its pathway became promising drug targets for cancer therapy. A diverse group of TSGs is involved in progression and metastasis of lung cancer. Here,...
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The octocoral, Paramuricea clavata , is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have diffe...
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Ascidians are marine invertebrates associated with diverse microbial communities, embedded in their tunic, conferring special ecological and biotechnological relevance to these model organisms used in evolutionary and developmental studies. Next-generation sequencing tools have increased the knowledge of ascidians’ associated organisms and their pr...
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Horizontal gene transfer (HGT) plays an important role for evolutionary innovations within prokaryotic communities and is a crucial event for their survival. Several computational approaches have arisen to identify HGT events in recipient genomes. However, this has been proven to be a complex task due to the generation of a great number of false po...
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Studying the diet of crustaceans based on the direct visual inspection of the gut contents can be difficult because they can ingest only a portion of the prey and further crush it into very small pieces, making a very few food items identifiable. Here, the usefulness of molecular methods to identify the species present in the gut contents of two cr...
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Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions ( Panthera leo spelaea ), 12 historic lions ( Panthera leo leo/Panthera leo melanochaita ) that lived between the...
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Adhesive secretion has a fundamental role in barnacles’ survival, keeping them in an adequate position on the substrate under a variety of hydrologic regimes. It arouses special interest for industrial applications, such as antifouling strategies, underwater industrial and surgical glues, and dental composites. This study was focused on the goose b...
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• Understanding the interactions among demographic parameters, mating system and population dynamics is key to predict the response of populations to global change. The Mediterranean red coral is a precious octocoral suffering from population decline due to overfishing and warming‐driven mass mortality events. • While the demographic consequences o...
Article
Cnidaria is a phylum of predominantly marine organisms that evolved into two basic body forms: “polyp” characterized by a tubular body; and “medusa” the free-floating stage characterized by a bell-shaped body. A fast increase in the abundance of the free-living stage of cnidarians known as “jellyfish”, can produce huge impacts on fisheries, public...
Article
Formyl peptide receptors (FPRs) were firstly detected in immune cells where they act as key mediators of leukocyte chemotaxis, promoting the host defense against pathogens. Recently, three paralogs were reported in Homo sapiens (FPR1–3) and seven paralogs in Mus musculus (FPR1, FPRrs1–4, FPRrs6 and FPRrs7), but information from other mammalian line...
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Historical reports show that in Portugal, cyanotoxins reports were mainly in the Center (cylindrospermopsins) and South (cylindrospermopsins, saxitoxins) regions of the country apart from the well distributed microcystins. Therefore, in our study, seven freshwater ecosystems located in the North and Center Regions of Portugal were screened between...
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The acquisition of UCP1-mediated non-shivering thermogenesis (NST) was an important event during the evolution of mammals. Here, we assessed the thermogenic neofunctionalization that occurred in the mammalian UCP1, by performing detailed comparative evolutionary genomics analyses (including phylogenetic and selection analyses) of the UCP family mem...
Article
Described as "junk" DNA, pseudogenes are dead structures of previously active genes present in genomes. Pseudogenes are categorized into two main classes: processed pseudogenes, formed through retrotransposition, and non-processed pseudogenes, typically originated from gene decay following duplication events. The term "processed pseudogene" has cha...
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Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending ev...
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As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. The cause of its extinction remains contentious: besides excessive mortality associated to habitat destructio...
Chapter
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Cyanobacteria are an ancient and diverse group of microorganisms that are of major ecotoxicological relevance since they produce harmful algal blooms, as well as toxic and natural molecules with distinct effects on human health. In water quality management, several methods can be applied and in these molecular tools through genomics research can se...
Book
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Cylindrospermopsis raciborskii is a freshwater cyanobacterium species known for its invasion from tropical to temperate environments. Some strains of this species are able to produce cyanotoxins. In Portugal (Southern Europe) its occurrence was firstly recorded in the South Region (Alqueva Reservoir, 2000) in where it is known to form blooms and wh...
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Background: Recent advances in genome sequencing technologies and the cost drop in high-throughput sequencing continue to give rise to a deluge of data available for downstream analyses. Among others, evolutionary biologists often make use of genomic data to uncover phenotypic diversity and adaptive evolution in protein-coding genes. Therefore, mu...
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Alignment-free (AF) methodologies have increased in popularity in the last decades as alternative tools to alignment-based (AB) algorithms for performing comparative sequence analyses. They have been especially useful to detect remote homologs within the twilight zone of highly diverse gene/protein families and superfamilies. The most popular align...
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Corbicula fluminea and Dreissena polymorpha are two non-indigenous species (NIS), known to provoke biodiversity loss of the existent native communities and alterations in the ecosystem functioning structure. Both of these NIS have successfully founded well established populations in Lakes Maggiore and Garda (Northern Italy). Here, we evaluated the...
Preprint
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The octocoral, Paramuricea clavata , is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have diffe...
Article
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The vertebrate toll-like receptor (TLRs) supergene family is a first-line immune defense against viral and non-viral pathogens. Here, comparative evolutionary-genomics of 79 vertebrate species (8 mammals, 48 birds, 11 reptiles, 1 amphibian, and 11 fishes) revealed differential gain/loss of 26 TLRs, including 6 (TLR3, TLR7, TLR8, TLR14, TLR21, and T...
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Typical avian eyes are phenotypically engineered for photopic vision (daylight). In contrast, the highly-derived eyes of the barn owl (Tyto alba) are adapted for scotopic vision (dim light). The dramatic modifications distinguishing barn owl eyes from other birds include: (i) shifts in frontal orientation to improve binocularity; (ii) rod-dominated...
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Conus ateralbus is a cone snail endemic to the west side of the island of Sal, in the Cabo Verde Archipelago off West Africa. We describe the isolation and characterization of the first bioactive peptide from the venom of this species. This 30AA venom peptide is named conotoxin AtVIA (δ-conotoxin-like). An excitatory activity was manifested by the...