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Soares R.,ITQB UNL | Franco C.,ITQB UNL | Pires E.,ITQB UNL | Ventosa M.,ITQB UNL | And 5 more authors.
Journal of Proteomics | Year: 2012

Proteomic approaches are gaining increasing importance in the context of all fields of animal and veterinary sciences, including physiology, productive characterization, and disease/parasite tolerance, among others. Proteomic studies mainly aim the proteome characterization of a certain organ, tissue, cell type or organism, either in a specific condition or comparing protein differential expression within two or more selected situations. Due to the high complexity of samples, usually total protein extracts, proteomics relies heavily on separation procedures, being 2D-electrophoresis and HPLC the most common, as well as on protein identification using mass spectrometry (MS) based methodologies. Despite the increasing importance of MS in the context of animal and veterinary science studies, the usefulness of such tools is still poorly perceived by the animal science community. This is primarily due to the limited knowledge on mass spectrometry by animal scientists. Additionally, confidence and success in protein identification is hindered by the lack of information in public databases for most of farm animal species and their pathogens, with the exception of cattle (Bos taurus), pig (Sus scrofa) and chicken (Gallus gallus). In this article, we will briefly summarize the main methodologies available for protein identification using mass spectrometry providing a case study of specific applications in the field of animal science. We will also address the difficulties inherent to protein identification using MS, with particular reference to experiments using animal species poorly described in public databases. Additionally, we will suggest strategies to increase the rate of successful identifications when working with farm animal species. This article is part of a Special Issue entitled: Farm animal proteomics. © 2012 Elsevier B.V.

Vicari C.,University of Naples Federico II | Saraiva I.H.,ITQB UNL | Maglio O.,University of Naples Federico II | Maglio O.,CNR Institute of Biostructure and Bioimaging | And 4 more authors.
Chemical Communications | Year: 2014

An empirical equation, describing the relationship between the porphyrin methyl hyperfine shifts and the position of the axial ligand(s), has been applied to an artificial heme-protein in order to obtain insight into the active site properties of heme-protein models. This journal is © the Partner Organisations 2014.

Utesch T.,TU Berlin | Sezer M.,ITQB UNL | Weidinger I.M.,TU Berlin | Mroginski M.A.,TU Berlin
Langmuir | Year: 2012

Sulfite oxidase (SO) is an enzyme catalyzing the terminal step of the metabolism of sulfur-containing amino acids that is essential for almost all living organisms. The catalytic activity of SO in vertebrates strongly depends on the efficiency of the intramolecular electron transfer (IET) between the catalytic Moco domain and the cytochrome b5 (cyt b5) domain. The IET process is assumed to be mediated by large domain motions of the cyt b5 domains within the enzyme. Thus, the interaction of SO with charged surfaces may affect the mobility of the cyt b5 domain required for IET and consequently hinder SO activation. In this study, we present a molecular dynamics approach to investigating the ionic strength dependence of the initial surface adsorption of SO in two different conformations - the crystallographic structure and the model structure for an activated SO - onto mixed amino- and hydroxyl-terminated SAMs. The results show for both conformations at low ionic strengths a strong adsorption of the cyt b5 units onto the SAM, which inhibits the domain motion event required for IET. Under higher ion concentrations, however, the interaction with the surface is weakened by the negatively charged ions acting as a buffer and competing in adsorption with the cathodic cyt b5 domains. This competition prevents the immobilization of the cytochrome b5 units onto the surface, allowing the intramolecular domain motions favoring IET. Our predictions support the interpretation of recent experimental spectroelectrochemical studies on SO. © 2012 American Chemical Society.

Costa R.S.,Institute Engineering Of Sistemas E Computadores | Hartmann A.,Institute Engineering Of Sistemas E Computadores | Gaspar P.,ITQB UNL | Neves A.R.,ITQB UNL | And 2 more authors.
Molecular BioSystems | Year: 2014

Biomedical research and biotechnological production are greatly benefiting from the results provided by the development of dynamic models of microbial metabolism. Although several kinetic models of Lactococcus lactis (a Lactic Acid Bacterium (LAB) commonly used in the dairy industry) have been developed so far, most of them are simplified and focus only on specific metabolic pathways. Therefore, the application of mathematical models in the design of an engineering strategy for the production of industrially important products by L. lactis has been very limited. In this work, we extend the existing kinetic model of L. lactis central metabolism to include industrially relevant production pathways such as mannitol and 2,3-butanediol. In this way, we expect to study the dynamics of metabolite production and make predictive simulations in L. lactis. We used a system of ordinary differential equations (ODEs) with approximate Michaelis-Menten-like kinetics for each reaction, where the parameters were estimated from multivariate time-series metabolite concentrations obtained by our team through in vivo Nuclear Magnetic Resonance (NMR). The results show that the model captures observed transient dynamics when validated under a wide range of experimental conditions. Furthermore, we analyzed the model using global perturbations, which corroborate experimental evidence about metabolic responses upon enzymatic changes. These include that mannitol production is very sensitive to lactate dehydrogenase (LDH) in the wild type (W.T.) strain, and to mannitol phosphoenolpyruvate: a phosphotransferase system (PTSMtl) in a LDH mutant strain. LDH reduction has also a positive control on 2,3-butanediol levels. Furthermore, it was found that overproduction of mannitol-1-phosphate dehydrogenase (MPD) in a LDH/PTS Mtl deficient strain can increase the mannitol levels. The results show that this model has prediction capability over new experimental conditions and offers promising possibilities to elucidate the effect of alterations in the main metabolism of L. lactis, with application in strain optimization. © 2014 The Royal Society of Chemistry.

Silva A.C.,ITQB UNL | Carrondo M.J.T.,ITQB UNL | Carrondo M.J.T.,New University of Lisbon | Alves P.M.,ITQB UNL
Vaccine | Year: 2011

The main focus of this work was the improvement of the stability of the current PPRV vaccine. First, new formulations based on the Tris buffer were tested, with and without the addition of sucrose and trehalose and compared with the formulation normally used to stabilize the vaccine, the Weybridge medium. The results show a virus half-life of 21h at 37°C and 1 month at 4°C for the Tris/trehalose liquid formulation and, in the lyophilized form, the formulation was able to maintain the viral titer above the 1×104 TCID50/mL (>10 doses/mL) for at least 21 months at 4°C (0.6log lost), 144h at 37°C (0.6log lost) and 120h at 45°C (1log lost).Secondly, a strategy based on culture medium composition manipulation aiming at improving the intrinsic PPRV vaccine stability was also evaluated. The addition of 25. mM fructose resulted in a higher virus production (1. log increase) with higher stability (2.6-fold increase compared to glucose 25. mM) at 37 °C. Increased concentrations of NaCl, improved virus release, reducing the cell-associated fraction of the virus produced. Moreover this harvesting strategy is scalable and more suitable for a larger scale production than the freeze/thaw cycles normally used. The information gathered in this work showed that it is possible for the PPRV vaccine to have adequate short-term stability at non-freezing temperatures to support manufacturing, short-term shipping and storage. The identification of a more stable formulation should significantly enhance the utility of the vaccine in the control of a PPRV outbreak. © 2011 Elsevier Ltd.

Cal P.M.S.D.,University of Lisbon | Vicente J.B.,University of Lisbon | Pires E.,ITQB UNL | Coelho A.V.,ITQB UNL | And 3 more authors.
Journal of the American Chemical Society | Year: 2012

Protein modification has entered the limelight of chemical and biological sciences, since, by appending small molecules into proteins surfaces, fundamental biological and biophysical processes may be studied and even modulated in a physiological context. Herein we present a new strategy to modify the lysines η-amino group and the proteins N-terminal, based on the formation of stable iminoboronates in aqueous media. This functionality enables the stable and complete modification of these amine groups, which can be reversible upon the addition of fructose, dopamine, or glutathione. A detailed DFT study is also presented to rationalize the observed stability toward hydrolysis of the iminoboronate constructs. © 2012 American Chemical Society.

Torres V.M.,ITQB UNL | Torres V.M.,National Institute of Health Dr Ricardo Jorge | Posa M.,ITQB UNL | Srdjenovic B.,ITQB UNL | Simplicio A.L.,University of Novi Sad
Colloids and Surfaces B: Biointerfaces | Year: 2011

Fullerene (C60), the third carbon allotrope, is a classical engineered material with the potential application in biomedicine. However, extremely high hydrophobicity of fullerene hampers its direct biomedical evaluation and application. In this work, we investigated the solubilization of fullerene using 9 different solubility enhancers: Tween 20, Tween 60, Tween 80, Triton X-100, PVP, polyoxyethylene (10) lauryl ether, n-dodecyl trimethylammonium chloride, myristyl trimethylammonium bromide and sodium dodecyl sulphate and evaluated its antioxidant activity in biorelevant media. The presence of C60 entrapped in surfactant micelles was confirmed by UV/VIS spectrometry. The efficacy of each modifier was evaluated by chemometric analysis using experimental data for investigating the relationship between solubilization and particle size distribution. Hierarchical clustering and principal component analysis was applied and showed that non-ionic surfactants provide better solubilization efficacy (>85%). A correlation was established (r=0.975) between the degree of solubilization and the surfactant structure. This correlation may be used for prediction of C60 solubilization with non-tested solubility modifiers. Since the main potential biomedical applications of fullerene are based on its free radical quenching ability, we tested the antioxidant potential of fullerene micellar solutions. Lipid peroxidation tests showed that the micellar solutions of fullerene with Triton and polyoxyethylene lauryl ether kept high radical scavenging activity, comparable to that of aqueous suspension of fullerene and BHT. The results of this work provide a platform for further solubilization and testing of pristine fullerene and its hydrophobic derivatives in a biological benign environment. © 2010 Elsevier B.V.

Tostoes R.M.,ITQB UNL | Leite S.B.,ITQB UNL | Serra M.,ITQB UNL | Jensen J.,Cellartis | And 4 more authors.
Hepatology | Year: 2012

Primary cultures of human hepatocyte spheroids are a promising in vitro model for long-term studies of hepatic metabolism and cytotoxicity. The lack of robust methodologies to culture cell spheroids, as well as a poor characterization of human hepatocyte spheroid architecture and liver-specific functionality, have hampered a widespread adoption of this three-dimensional culture format. In this work, an automated perfusion bioreactor was used to obtain and maintain human hepatocyte spheroids. These spheroids were cultured for 3-4 weeks in serum-free conditions, sustaining their phase I enzyme expression and permitting repeated induction during long culture times; rate of albumin and urea synthesis, as well as phase I and II drug-metabolizing enzyme gene expression and activity of spheroid hepatocyte cultures, presented reproducible profiles, despite basal interdonor variability (n = 3 donors). Immunofluorescence microscopy of human hepatocyte spheroids after 3-4 weeks of long-term culture confirmed the presence of the liver-specific markers, hepatocyte nuclear factor 4α, albumin, cytokeratin 18, and cytochrome P450 3A. Moreover, immunostaining of the atypical protein kinase C apical marker, as well as the excretion of a fluorescent dye, evidenced that these spheroids spontaneously assemble a functional bile canaliculi network, extending from the surface to the interior of the spheroids, after 3-4 weeks of culture. Conclusion: Perfusion bioreactor cultures of primary human hepatocyte spheroids maintain a liver-specific activity and architecture and are thus suitable for drug testing in a long-term, repeated-dose format. © 2011 American Association for the Study of Liver Diseases.

Paquete C.M.,ITQB UNL | Louro R.O.,ITQB UNL
Dalton Transactions | Year: 2010

Shewanella are facultative anaerobic bacteria of remarkable respiratory versatility that includes the dissimilatory reduction of metal ores. They contain a large number of multiheme c-type cytochromes that play a significant role in various anaerobic respiratory processes. Of all the cytochromes found in Shewanella, only the two most abundant periplasmic cytochromes, the small tetraheme cytochrome (STC) and flavocytochrome c3 (Fcc3) have been structurally characterized. For these two proteins the molecular bases for their redox properties were determined using spectroscopic methods based on paramagnetic NMR, that allow the contribution of specific hemes to be discriminated. In this perspective these results are reviewed in the context of the continuing effort to understand the molecular mechanisms of electron transfer in the respiratory chains of these organisms. © 2010 The Royal Society of Chemistry.

Vinga S.,Institute Engineering Of Sistemas E Computadores Investigacao E Desenvolvimento Inesc Id | Vinga S.,New University of Lisbon | Neves A.R.,ITQB UNL | Santos H.,ITQB UNL | And 2 more authors.
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2010

The dynamic modelling of metabolic networks aims to describe the temporal evolution of metabolite concentrations in cells. This area has attracted increasing attention in recent years owing to the availability of high-throughput data and the general development of systems biology as a promising approach to study living organisms. Biochemical Systems Theory (BST) provides an accurate formalism to describe biological dynamic phenomena. However, knowledge about the molecular organization level, used in these models, is not enough to explain phenomena such as the driving forces of these metabolic networks. Dynamic Energy Budget (DEB) theory captures the quantitative aspects of the organization of metabolism at the organism level in a way that is nonspecies- specific. This imposes constraints on the sub-organismal organization that are not present in the bottom-up approach of systems biology. We use in vivo data of lactic acid bacteria under various conditions to compare some aspects of BST and DEB approaches. Due to the large number of parameters to be estimated in the BST model, we applied powerful parameter identification techniques. Both models fitted equally well, but the BST model employs more parameters. The DEB model uses similarities of processes under growth and no-growth conditions and under aerobic and anaerobic conditions, which reduce the number of parameters. This paper discusses some future directions for the integration of knowledge from these two rich and promising areas, working top-down and bottom-up simultaneously. This middle-out approach is expected to bring new ideas and insights to both areas in terms of describing how living organisms operate. © 2010 The Royal Society.

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