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- Ranked adjusted randPublication . Pinto, Francisco Rodrigues; Carriço, João A.; Ramirez, Mário; Almeida, Jonas S.; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); BioMed Central (BMC)Background: Biological information is commonly used to cluster or classify entities of interest such as genes, conditions, species or samples. However, different sources of data can be used to classify the same set of entities and methods allowing the comparison of the performance of two data sources or the determination of how well a given classification agrees with another are frequently needed, especially in the absence of a universally accepted "gold standard" classification. Results: Here, we describe a novel measure - the Ranked Adjusted Rand (RAR) index. RAR differs from existing methods by evaluating the extent of agreement between any two groupings, taking into account the intercluster distances. This characteristic is relevant to evaluate cases of pairs of entities grouped in the same cluster by one method and separated by another. The latter method may assign them to close neighbour clusters or, on the contrary, to clusters that are far apart from each other. RAR is applicable even when intercluster distance information is absent for both or one of the groupings. In the first case, RAR is equal to its predecessor, Adjusted Rand (HA) index. Artificially designed clusterings were used to demonstrate situations in which only RAR was able to detect differences in the grouping patterns. A study with larger simulated clusterings ensured that in realistic conditions, RAR is effectively integrating distance and partition information. The new method was applied to biological examples to compare 1) two microbial typing methods, 2) two gene regulatory network distances and 3) microarray gene expression data with pathway information. In the first application, one of the methods does not provide intercluster distances while the other originated a hierarchical clustering. RAR proved to be more sensitive than HA in the choice of a threshold for defining clusters in the hierarchical method that maximizes agreement between the results of both methods. Conclusion: RAR has its major advantage in combining cluster distance and partition information, while the previously available methods used only the latter. RAR should be used in the research problems were HA was previously used, because in the absence of inter cluster distance effects it is an equally effective measure, and in the presence of distance effects it is a more complete one.
- A European Laboratory network for sequence-based typing of methicillin-resistant Staphylococcus aureus (MRSA) as a communication platform between human and veterinary medicinePublication . Friedrich, Alexander W.; Witte, Wolfgang; Lencastre, Hermínia de; Hryniewicz, Waleria; Scheres, Jacques M. J. C.; Westh, Henrik Torkil; Seqnet.Org Participants; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); European Centre for Disease Prevention and ControlSeqNet.org is currently an initiative of 44 laboratories from 25 European countries and one laboratory from Lebanon (Table 1), founded in 2004, in collaboration with the Robert Koch Instituteat the University of Münster, Germany (http://www.SeqNet.org). Since then, its main objective is to establish a European network of excellence for sequence-based typing of microbial pathogens,having its main focus on Staphylococcus aureus [1]. SeqNet.org comprises a large number of national reference laboratories as well as university laboratories. The principle goal of SeqNet.org is to generate unambiguous, easily comparable typing data in electronic, portable form to be used by infection control at a local level as well as national and European surveillance of sentinel microorganisms, such as methicillin-resistant Staphylococcus aureus (MRSA). spa-typing has been shown to be a useful tool in molecular hospital epidemiology [2,3]. Veterinary laboratories have recently joined the SeqNet.org initiative as MRSA has become an emerging problem in veterinary medicine [4,5]. spa-typing data from human and veterinary medicine can be compared using the spa server database [6].
- Corrigendum to “Circular agriculture designPublication . Gontard, Nathalie; Shi, Aimin; Angellier-Coussy, Hélène; Aouf, Chahinez; Bolzonella, David; Broeze, Jan; Dedieu, Isabelle; Ganigue, Ramon; Housmans, Joëlle A. J.; Hu, Hui; Pereira, Cristina Silva; Reis, Maria; Tassoni, Annalisa; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); Elsevier BV
- High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA familiesPublication . Szittya, Gyorgy; Moxon, Simon; Santos, Dulce M.; Jing, Runchun; Fevereiro, Manuel Pedro S.; Moulton, Vincent; Dalmay, Tamas; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); BioMed Central (BMC)Background: High-throughput sequencing technology is capable to identify novel short RNAs in plant species. We used Solexa sequencing to find new microRNAs in one of the model legume species, barrel medic (Medicago truncatula). Results: 3,948,871 reads were obtained from two separate short RNA libraries generated from total RNA extracted from M. truncatula leaves, representing 1,563,959 distinct sequences. 2,168,937 reads were mapped to the available M. truncatula genome corresponding to 619,175 distinct sequences. 174,504 reads representing 25 conserved miRNA families showed perfect matches to known miRNAs. We also identified 26 novel miRNA candidates that were potentially generated from 32 loci. Nine of these loci produced eight distinct sequences, for which the miRNA* sequences were also sequenced. These sequences were not described in other plant species and accumulation of these eight novel miRNAs was confirmed by Northern blot analysis. Potential target genes were predicted for most conserved and novel miRNAs. Conclusion: Deep sequencing of short RNAs from M. truncatula leaves identified eight new miRNAs indicating that specific miRNAs exist in legume species.
- The ubiquitin/proteasome pathway from Lemna minor subjected to heat shockPublication . Caeiro, Ana S.; Ramos, Paula C.; Teixeira, Artur R.; Ferreira, Ricardo Boavida; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); Springer Science Business MediaExposure of Lemna minor L. to high temperatures leads to an initial decrease in the ubiquitin (Ub) monomer pool size and the accumulation of high molecular mass Ub-protein conjugates, possibly reflecting an increment in the supply of protein substrates to the Ub/proteasome pathway. Alternative explanations include, for example, changes in the transcription rates of one or more pathway components. To measure the effect of heat shock on the simultaneous rates of transcription of selected genes encoding five Ub pathway components (Ub, E1, E2, β subunit and ATPase subunit of the 26S proteasome), a semi-quantitative RT-PCR method was developed using cDNA normalized against the housekeeping gene encoding the 18S ribosomal RNA. Whilst Ub transcription is abruptly increased, there is a moderate increment in the transcription of E1 and the β subunit, a moderate reduction in the transcription of the ATPase subunit and a marked reduction in the case of E2, indicating a differential transcription pattern of the various components of the Ub/proteasome pathway in L. minor subjected to high temperatures. These observations suggest that the increment in the Ub/proteasome pathway intermediates is due to an augmented supply of substrates derived from the stress-induced damage imposed on the cellular proteins. The initial build up of intermediates occurs not only at the expense of the pre-existing pool of free Ub, but also as a result of the prompt increase in Ub expression.
- Improved in vitro rooting of Prunus dulcis Mill. cultivarsPublication . Tereso, Susana; Miguel, Célia M.; Mascarenhas, Miguel; Roque, A.; Trindade, Helena; Maroco, J.; Oliveira, Maria Margarida; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); Springer Science Business MediaA highly reproducible system was developed for efficient rooting of cultivars Boa Casta (BC) and Peneda and a BC seedling-derived clone (BC VII) of almond (Prunus dulcis Mill.). Twenty-four accessions derived from the clone BC VII and subjected to various in vitro culture treatments were screened. The long induction pre-treatment (LIP, 5 d), the brief induction pre-treatment (BIP, 16 h) and the hormonal shock by short dipping in hormone solution (1 min), were tested. BIP was the only that allowed rooting of cultivars. In BC VII, it induced high rooting frequencies (47-100 %) when using a solution of 0.4 mM indole-3-butyric acid solidified with 2 g dm-3 gellam gum for 16-h. The response to the auxin type was variable depending on the cultivar and the root induction pre-treatment used. Root number was significantly different between the two cultivars and BC VII. Root length was significantly higher when using 0.005 mM IBA in LIP but this concentration induced apical necrosis. The improved acclimatization procedure for up to 4 weeks increased the survival to 45 %. The initiation and development of adventitious roots were proved to be asynchronous.
- Prodrugs for aminesPublication . Simplício, Ana L.; Clancy, John M.; Gilmer, John F.; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); MDPI - Multidisciplinary Digital Publishing InstituteThe purpose of this work is to review the published strategies for the production of prodrugs of amines. The review is divided in two main groups of approaches: those that rely on enzymatic activation and those that take advantage of physiological chemical conditions for release of the drugs. A compilation of the most important approaches is presented in the form of a table, where the main advantages and disadvantages of each strategy are also referred.
- Chitosan-based films with beetroot pulp and banana pseudostem extracts for active food packagingPublication . Nascimento, Rosa E. A.; Sales, Joana; Alves, Vitor D.; Crespo, João G.; Neves, Luísa A.; DQ - Departamento de Química; LAQV@REQUIMTE; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); ElsevierThe increasing demand for sustainable alternatives to petroleum-based food packaging materials has driven the development of biodegradable and functional films. This study explores the formulation and characterization of chitosan (Ch)-based films incorporating enzymatically recovered extracts from beetroot pulp (BP) and banana plant pseudostem (PS), for active food packaging applications. The incorporation of these plant-based by-products significantly influenced the films’ physicochemical and functional properties. Fourier transform infrared spectroscopy (FTIR) confirmed the successful integration of BP and PS extracts into the Ch matrix. Optical characterization revealed increased opacity, especially in Ch+BP films, which might offer potential for light-sensitive food protection. Morphological analysis showed homogeneous, dense structures, indicating good compatibility between Ch and the incorporated extracts. The films hydrophilicity, full water solubility within 24 h, and low water vapor barrier, envisage their applicability in single-use short shelf-life packages of low moisture content products, as ready-to-drink instant coffee sachets or protein powder single-serve sachets. The antioxidant performance of the films was markedly enhanced, with 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities of 9.92 ± 1.30 and 7.00 ± 0.37 µmol Trolox/g film for Ch+BP and Ch+PS films, respectively, reinforcing their potential as active packaging materials. This is the first report on Ch films incorporating enzymatic BP and PS extracts, presenting an innovative, circular economy driven strategy for agro-industrial waste valorisation through sustainable, active food packaging solutions.
- Linking NrfD/PsrC-like architecture to energy conservationPublication . Manteigas, Gonçalo; Catarino, Teresa; Vicente, João B.; Duarte, Américo G.; Pereira, Inês A.C.; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); DQ - Departamento de Química; Wiley-BlackwellThe QrcABCD quinone reductase complex is an electrogenic complex present in sulfate-reducing bacteria of the Desulfobacterota phylum. It operates as a cytochrome c3:menaquinone oxidoreductase involved in electron transfer from periplasmic hydrogen or formate oxidation to the menaquinone (MK) pool. Two proteins in this complex, QrcC and QrcD, form a redox dimer (QrcCD) responsible for MK reduction coupled to proton uptake from the cytoplasm. QrcD belongs to the NrfD/PsrC family, and homologs are found in many bacterial redox complexes in different bioenergetic contexts. In this work a homologous overexpression system for QrcABCD was established in Nitratidesulfovibrio vulgaris Hildenborough and used to produce variants with changes in key amino acids proposed to be involved in energy conservation. Growth studies of the modified strains combined with activity assays with isolated protein variants reconstituted in proteoliposomes revealed the essential role of key amino acids involved in the MK-binding site on the P-side of the membrane, and as part of a proposed proton uptake channel from the cytoplasm to the MK-binding site. The results support the proposed model for energy conservation where, upon formate or hydrogen oxidation, QrcABCD is involved in a redox-loop mechanism with another membrane complex, generating pmf by proton and electron uptake from different sides of the membrane, without active proton pumping.
- Deep Eutectic SystemsPublication . Amador, Sandro; Martins, Alice; Matias, Margarida; Pedrosa, Rui; Pinteus, Susete; CENIMAT-i3N - Centro de Investigação de Materiais (Lab. Associado I3N); DCM - Departamento de Ciência dos Materiais; Instituto de Tecnologia Química e Biológica António Xavier (ITQB); MDPI - Multidisciplinary Digital Publishing InstituteThe extraction of bioactive compounds from marine natural products has gained increasing attention due to their diverse applications, such as in pharmaceuticals, nutraceuticals, and cosmetics. Yet, low extraction yields and toxicity associated with common solvents are a major bottleneck. Deep eutectic solvents (DESs) and natural deep eutectic solvents (NADESs) have emerged as promising green alternatives to conventional organic solvents, offering advantages such as biodegradability, greater environmental and economic sustainability, low toxicity, and enhanced extraction selectivity. This review provides a comprehensive analysis of the principles, physicochemical properties, and applications of DESs/NADESs to obtain bioactive compounds from marine organisms. Among the most recent works, it is possible to verify the success of NADESs to extract carrageenan from the seaweed Kappaphycus alvarezii; pigments from Palmaria palmata; and polyphenols and proteins from different brown seaweeds. NADESs have also shown high potential to extract other valuable compounds from marine by-products, such as chitin from crabs and shrimp shells, and also lipids and proteins from different fish species and protein rich extracts from tilapia viscera. The challenges for DESs/NADESs use at industrial scale are also discussed, and success cases are revealed, highlighting their potential as game changers for extracting bioactive compounds from marine organisms and driving the development of innovative biotechnological products.