Repositório Comunidade: CBMACBMAhttps://hdl.handle.net/1822/684642024-03-29T13:59:55Z2024-03-29T13:59:55ZHighly fluorescent 2‐Aminopurine derivatives: synthesis, photo‐physical characterization, and preliminary cytotoxicity evaluationGonçalves, Jorge M.Gonçalves, João N. D.Pêra, Ana S.Senhorães, Nádia R.Rodrigues, Ana Rita OliveiraOliveira, Rui Pedro Soares deCoutinho, Paulo J. G.Castanheira, Elisabete M. S.Dias, Alicehttps://hdl.handle.net/1822/894452024-03-12T21:06:01ZTítulo: Highly fluorescent 2‐Aminopurine derivatives: synthesis, photo‐physical characterization, and preliminary cytotoxicity evaluation
Autor: Gonçalves, Jorge M.; Gonçalves, João N. D.; Pêra, Ana S.; Senhorães, Nádia R.; Rodrigues, Ana Rita Oliveira; Oliveira, Rui Pedro Soares de; Coutinho, Paulo J. G.; Castanheira, Elisabete M. S.; Dias, Alice
Resumo: New fluorescent nucleobase analogues (FBAs) are emerg-ing as extraordinarily useful tools for DNA labelling tech-nologies. The highly fluorescent adenine analogue 2 aminopurine (2AP) is still the most used within the few hundreds of newly FBAs synthesized, but its excitation in the UV region demands for high energy sources endanger-ing living cells. New and highly fluorescent 2AP deriva-tives, 2-amino-6-cyanopurines, were obtained using novel, simpler, but very efficient synthesis method. All the new compounds exhibit advantageous photophysical properties over 2AP, showing absorption and emission bands ranging the visible region (blue-green region), high fluorescence quantum yields and Stokes’ shifts, especially in non-protic organic solvents. Density Functional Theory calculations (DFT) of electronic and vibrational structure were per-formed, allowing to predict absorption and emission spec-tra in accordance with experimental data. The extensive solvatochromism of compounds gives them important microenvironmental sensitivity to be used as superior fluorescent probes, comparing to 2AP. In addition, these newly synthesized 2-amino-6-cyanopurines exhibit little to no toxicity in assays using yeast cells, making them also valuable candidates for fluorescent studies in living cells.
Descrição: First published: 15 March 2023
<b>Tipo</b>: articleMining bioactive molecules from extreme environments using sequence-based metagenomicsSousa, JoanaSantos-Pereira, CátiaCosta, Ângela Maria AraújoGuiet, Andréia Oliveira SantosFranco-Duarte, RicardoRodrigues, L. R.Silvério, Sara Isabel Cruzhttps://hdl.handle.net/1822/891392024-02-28T15:22:06Z2024-02-28T15:22:05ZTítulo: Mining bioactive molecules from extreme environments using sequence-based metagenomics
Autor: Sousa, Joana; Santos-Pereira, Cátia; Costa, Ângela Maria Araújo; Guiet, Andréia Oliveira Santos; Franco-Duarte, Ricardo; Rodrigues, L. R.; Silvério, Sara Isabel Cruz
Resumo: The unique features of extreme habitats, particularly the high temperature and salinity, make them promising reservoirs for the bioprospection and discovery of novel and interesting bioactive molecules. In fact, the microorganisms inhabiting this type of environments have adopted survival strategies to thrive under hostile conditions, synthesizing several biochemical compounds valuable for many biotechnological applications. Culture-independent techniques, namely metagenomics, have emerged as powerful tools to access and explore the genetic and metabolic diversity of the microbial communities present in extreme and complex ecosystems. Two different metagenomic approaches can be applied, namely, sequence- and function-based metagenomics. The sequence-based studies allow finding new gene sequences that reveal similarities with the annotated genomes available in the databases.
In this study, thermophilic composting samples were collected from two Portuguese composting units (Terra Fértil and Lipor), which handle different types of wastes. The metagenomic DNA was extracted from the composting samples and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to characterize the taxonomic and functional profiles of the metagenomes using both reads and metagenome-assembled genomes (MAGs) as input. Their microbiome was dominated by Bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria and Balneolia stood out for their higher abundance. These data confirm the richness of the composting habitats in bacterial strains known to survive and play an important role in harsh conditions, namely extreme saline environments. Furthermore, the combined analysis of functional annotation against KEGG and COG databases revealed a clear dominance of the contigs associated with the metabolism of carbohydrates, energy, amino acids and xenobiotics biodegradation and metabolism. This work represents the first comparative study on the taxonomic and functional profiles of Portuguese composting samples.
<b>Tipo</b>: conferenceAbstract2024-02-28T15:22:05ZCurrent status and topical issues on the use of eDNA-based targeted detection of rare animal speciesDuarte, Sofia Alexandra FerreiraSimões, Luara AparecidaCosta, Filipe O.https://hdl.handle.net/1822/877042023-12-28T20:45:32ZTítulo: Current status and topical issues on the use of eDNA-based targeted detection of rare animal species
Autor: Duarte, Sofia Alexandra Ferreira; Simões, Luara Aparecida; Costa, Filipe O.
Resumo: Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, key to devising tools to efficiently single out a targeted species from an environmental sample. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 549 publications (2008–2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (74 %), and to a less extent marine (14 %) and terrestrial systems (10 %). Vertebrates, in particular, fish (38 %), and endangered species, have been the focus of most of these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (21 %), in particular, to target invasive species, and COI the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (75 %), while eDNA metabarcoding has been rarely used to target single or few species (approx. 6 %). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data and vouchered tissue or DNA samples from closely related species to assess both marker and primers' specificity. In addition, eDNA-based assays developed for a particular species may have to be refined for use in a new geographic area taking into account site-specific populations, as well as any intraspecific variation.
<b>Tipo</b>: articleThe curious and intricate case of the European Hediste diversicolor (Annelida, Nereididae) species complex, with description of two new speciesTeixeira, Marcos André Machado LimaBakken, TorkildVieira, Pedro Emanuel Ferreira ReisLangeneck, JoachimSampieri, Bruno R.Kasapidis, PanagiotisRavara, AscensãoNygren, ArneCosta, Filipe O.https://hdl.handle.net/1822/875652023-12-18T09:07:11ZTítulo: The curious and intricate case of the European Hediste diversicolor (Annelida, Nereididae) species complex, with description of two new species
Autor: Teixeira, Marcos André Machado Lima; Bakken, Torkild; Vieira, Pedro Emanuel Ferreira Reis; Langeneck, Joachim; Sampieri, Bruno R.; Kasapidis, Panagiotis; Ravara, Ascensão; Nygren, Arne; Costa, Filipe O.
Resumo: Past molecular studies using mtDNA sequences and alloenzymes signalled the existence of at least two cryptic species within the Hediste diversicolor morphotype, in European coasts. However, to this day, no new species descriptions have been made. In this study, we identified five completely sorted lineages using a multi-locus approach, including the mitochondrial DNA cytochrome oxidase I gene (COI-5P) and the nuclear markers ITS2 rRNA and 28S rRNA. The molecular data were complemented with morphometric measurements examined through multivariate statistical analysis and the incorporation of statistical dissimilarities. Apart from the Baltic Sea, where three of the lineages occur in sympatry, Hediste diversicolor comprises four deeply divergent allopatric lineages in the rest of Europe. They group populations from the NE Atlantic and part of the Western Mediterranean Sea; from the Tyrrhenian Sea; from the Adriatic and Ionian Sea; and, lastly, from the Caspian, Black and the northern Aegean Seas. The lineage from the Ionian Sea revealed low genetic distances compared with the one from the Adriatic Sea and lacked enough specimens for the morphometric analysis, preventing further conclusions about its independent status. Three independent morphometric clusters were identified mainly based on worm size, the distance between the anterior and posterior eyes, parapodia proportions and the length of several prostomial appendages. Two sympatric lineages present in the Baltic Sea, showed evidence of possible hybridization and lacked significant PCA morphometric variation between them. The two remaining lineages were formally described as new species, namely Hediste pontii sp. nov. (Adriatic Sea) and Hediste astae sp. nov. (northern Aegean, Caspian and Black Seas). These new species can now be formally recognized and used in biomonitoring or other relevant ecological studies. Finally, a neotype is defined for H. diversicolor, whose usage is restricted to the NE Atlantic lineage.
<b>Tipo</b>: articleCandida albicans chitinase 3 with potential as a vaccine antigen: production, purification, and characterisationBarbosa, Augusto Alexandre CostaFerreira, DiogoPacheco, Maria InêsCasal, MargaridaDuarte, Henrique OliveiraGomes, CatarinaBarbosa, Ana Margarida MartinsTorrado, EgídioSampaio, PaulaCollins, Tonyhttps://hdl.handle.net/1822/872352024-02-23T17:55:36Z2023-11-14T13:19:42ZTítulo: Candida albicans chitinase 3 with potential as a vaccine antigen: production, purification, and characterisation
Autor: Barbosa, Augusto Alexandre Costa; Ferreira, Diogo; Pacheco, Maria Inês; Casal, Margarida; Duarte, Henrique Oliveira; Gomes, Catarina; Barbosa, Ana Margarida Martins; Torrado, Egídio; Sampaio, Paula; Collins, Tony
Resumo: Chitinases are widely studied enzymes that have already found widespread application. Their continued development and valorisation will be driven by the identification of new and improved variants and/or novel applications bringing benefits to industry and society. We previously identified a novel application for chitinases wherein the Candida albicans cell wall surface chitinase 3 (Cht3) was shown to have potential in vaccine applications as a subunit antigen against fungal infections. In the present study, this enzyme was investigated further, developing production and purification protocols, enriching our understanding of its properties, and advancing its application potential. Cht3 was heterologously expressed in Pichia pastoris and a 4-step purification protocol developed and optimised: this involves activated carbon treatment, hydrophobic interaction chromatography, ammonium sulphate precipitation, and gel filtration chromatography. The recombinant enzyme was shown to be mainly O-glycosylated and to retain the epitopes of the native protein. Functional studies showed it to be highly specific, displaying activity on chitin, chitosan, and chito-oligosaccharides larger than chitotriose only. Furthermore, it was shown to be a stable enzyme, exhibiting activity, and stability over broad pH and temperature ranges. This study represents an important step forward in our understanding of Cht3 and contributes to its development for application.
<b>Tipo</b>: article2023-11-14T13:19:42Z