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2013
Silva, A, Luis D, Santos S, Silva J, Mendo AS, Coito L, Silva TF, da Silva MFG, Martins LM, Pombeiro AJ, Borralho PM, Rodrigues CM, Cabral MG, Videira PA, Monteiro C, Fernandes AR.  2013.  Biological characterization of the antiproliferative potential of Co(II) and Sn(IV) coordination compounds in human cancer cell lines: a comparative proteomic approach. Drug Metabol Drug Interact. 28(3):167-76.13silvadmdi.pdf
Lipinska, ME, Teixeira DMD, Laia CAT, Silva AMG, Rebelo SLH, Freire C.  2013.  beta-Functionalized zinc(II)aminoporphyrins by direct catalytic hydrogenation. Tetrahedron Letters. 54:110-113., Number 1 AbstractWebsite
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Cruz, C, Santos SD, Cabrita EJ, Queiroz JA.  2013.  Binding analysis between l-histidine immobilized and oligonucleotides by SPR and NMR. International Journal of Biological Macromolecules. 56:175-180. Abstract

Saturation transfer difference (STD) NMR technique and surface plasmon resonance (SPR) are used to study amino acid affinity supports–nucleotides interactions with l-histidine amino acid immobilized on a surface as model support. We have immobilized l-histidine ligand on a carboxymethyldextran- modified gold surface intended for surface plasmon resonance and we analyze the binding profiles of synthetic polynucleotides (1–6 base, sugar and backbone) by determining the equilibrium dissociation constant (KD). The SPR binding profile (square-shaped) is identical for all the complexes and the highest binding affinity can be found for polyA6 followed by polyG6 . As expected, the 5′ -mononucleotides have the lowest affinity. To further study the structural aspects of the interaction we investigate the polynucleotide binding preferences to l-histidine chromatography support by STD-NMR spectroscopy. These results revealed that an increase in the number of bases and backbone to 6 units leads to more contacts with the support, where the main driving force for the interaction with polynucleotides are through the base, except for polyC6 , which is mainly through sugar-phosphate backbone. Therefore, the combination of SPR measurements with STD-NMR technique allowed to establish fine details of the molecular recognition process involved in amino acid affinity supports–nucleotides complexes.

2012
Folgosa, F, Timóteo CG, Guilherme M, Penas D, Tavares P, Pereira AS.  2012.  Bacterioferritin from Desulfovibrio vulgaris Hildenborough is a functional DPS-like enzyme, Sep. FEBS JOURNAL. {279}:{465}., Number {1, SI} Abstract
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Bahubalindruni, Ganga, Tavares, Vitor Grade, Barquinha, Duarte, Candido, Martins, Fortunato, de Oliveira PG.  2012.  Basic analog circuits with a-GIZO thin-film transistors: Modeling and simulation. 2012 International Conference on Synthesis, Modeling, Analysis and Simulation Methods and Applications to Circuit Design (SMACD).
Dell'Acqua, S, Pauleta SR, Moura JJ, Moura I.  2012.  Biochemical characterization of the purple form of Marinobacter hydrocarbonoclasticus nitrous oxide reductase. Philos Trans R Soc Lond B Biol Sci. 367(1593):1204-1212.
Barroso, T, Roque ACA, Aguiar-Ricardo A.  2012.  Bioinspired and Sustainable Chitosan Based Monoliths for Antibody Capture and Release. RSC ADV. 2(30):11285-11294. AbstractWebsite

Chitosan-based monoliths activated by plasma technology induced the coupling of a robust biomimetic ligand, previously reported as an artificial Protein A, with high yields while minimizing the environmental impact of the procedure. Due to the high porosity, good mechanical and tunable physicochemical properties of the affinity chitosan-based monoliths, it is possible to achieve high binding capacities (150 ± 10 mg antibody per gram support), and to recover 90 ± 5% of the bound protein with 98% purity directly from cell-culture extracts. Therefore, the chitosan-based monoliths prepared by clean processes exhibit a remarkable performance for the one-step capture and recovery of pure antibodies or other biological molecules with biopharmaceutical relevance.

Velloso, GT.  2012.  Brain-Computer Interface (BCI): a methodological proposal to assess the impacts of medical applications in 2022. Enterprise and Work Innovation Studies. 8:57-81. AbstractWebsite

Technology assessment is essentially an approach, a collective of the systematic methods used to scientifically investigate the conditions for and the consequences of technology and technicising and to denote their societal evaluation. It is an investigation about the technological developments as well as an evaluation of its potential impacts on society. The assessment of emerging technologies, however, requires special attention. Brain-Computer Interface (BCI) is an emerging technology which allows for the direct communication between the brain and an external device. It is a truly direct connection, with no use of the normal output pathways of peripheral nerves and muscles, allowing for the brain to have control over objects and software without intermediates. To address these kinds of technologies at early stages of development, Constructive Technology Assessment (CTA), a member of Technology Assessment approaches, has been considered as one of the most fitting approaches. As an emerging technology, BCI is at its early stages of research and thus many challenges are still ahead. Mainstream adoption is not expected in least 10 years many challenges are yet to be overcome. Therefore, the objective of this article is to discuss and present a methodological approach to assess brain-computer interface technology considering constructive technology assessment and future oriented technology analysis as the main processes to undertake the assessment. The assessment will focus only on the non-invasive type of BCI and for medical applications in three defined areas: Communication & Control, Motor Substitution and Motor Recovery for a time horizon of 10 years, 2022. These areas were chosen based on the capability of BCI to serve as a replacement of normal neuromuscular pathways. That makes it one of the best technologies to help people in activating and controlling assistive technologies which enable communication and control of the environment. However, the real impacts of BCI will depend directly on the development of competing technologies, and also on the improvement in BCI research. Only then, the potential applications and end users could grow dramatically.

Bonifacio, VDB, Correia VG, Pinho MG, Lima JC, Aguiar-Ricardo A.  2012.  Blue emission of carbamic acid oligooxazoline biotags. Materials Letters. 81:205-208. Abstract
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2011
Morgado, L, Paixão VB, Salgueiro CA, Bruix M.  2011.  Backbone, side chain and heme resonance assignments of the triheme cytochrome PpcA from Geobacter sulfurreducens. Biomolecular NMR Assignments. 5(1):113-116. AbstractWebsite

Gene knock-out studies on Geobacter sulfurreducens cells showed that the periplasmic triheme cytochrome PpcA is involved in respiratory pathways leading to the extracellular reduction of Fe(III) and U(VI) oxides. The crucial role of this protein in bridging the electron transfer between the cytoplasm and cell exterior was further supported by proteomics studies. In comparison with non-heme proteins, the presence of numerous proton-containing groups in the heme groups causes additional challenges to the full protein assignment and structure calculation. Here, we report the complete assignment of the heme proton signals together with the 1H and 15N backbone and side chain assignments of the reduced form of PpcA.

Qian, X, Mester T, Morgado L, Arakawa T, Sharma ML, Inoue K, Joseph C, Salgueiro CA, Maroney MJ, Lovley DR.  2011.  Biochemical characterization of purified OmcS, a c-type cytochrome required for insoluble Fe(III) reduction in Geobacter sulfurreducens. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1807(4):404-412. AbstractWebsite

Previous studies with Geobacter sulfurreducens have demonstrated that OmcS, an abundant c-type cytochrome that is only loosely bound to the outer surface, plays an important role in electron transfer to Fe(III) oxides as well as other extracellular electron acceptors. In order to further investigate the function of OmcS, it was purified from a strain that overproduces the protein. Purified OmcS had a molecular mass of 47 015 Da, and six low-spin bis-histidinyl hexacoordinated heme groups. Its midpoint redox potential was −212 mV. A thermal stability analysis showed that the cooperative melting of purified OmcS occurs in the range of 65–82 °C. Far UV circular dichroism spectroscopy indicated that the secondary structure of purified OmcS consists of about 10% α-helix and abundant disordered structures. Dithionite-reduced OmcS was able to transfer electrons to a variety of substrates of environmental importance including insoluble Fe(III) oxide, Mn(IV) oxide and humic substances. Stopped flow analysis revealed that the reaction rate of OmcS oxidation has a hyperbolic dependence on the concentration of the studied substrates. A ten-fold faster reaction rate with anthraquinone-2,6-disulfonate (AQDS) (25.2 s− 1) was observed as compared to that with Fe(III) citrate (2.9 s− 1). The results, coupled with previous localization and gene deletion studies, suggest that OmcS is well-suited to play an important role in extracellular electron transfer.

Cortez, J, Vorobieva E, Gralheira D, Osório I, Soares L, Vale N, Pereira E, Gomes P, Franco R.  2011.  BIONANOCONJUGATES OF TYROSINASE AND PEPTIDE-DERIVATISED GOLD NANOPARTICLES FOR BIOSENSING OF PHENOLIC COMPOUNDS. J. Nanopart. Res.. 13(2):1101–1113.
Viegas, A, Manso J, Corvo MC, Marques MMB, Cabrita EJ.  2011.  Binding of ibuprofen, ketorolac and diclofenac to COX-1 and COX-2 studied by saturation transfer difference NMR. Journal of Medicinal Chemistry. 54:8555-8562. AbstractWebsite

Saturation Transfer Difference-NMR (STD-NMR) spectroscopy has emerged as a powerful screening tool and a straightforward way to study the binding epitopes of active compounds in early stage lead discovery in pharmaceutical research. Here we report the application of STD NMR to characterize the binding of the anti-inflammatory drugs ibuprofen, diclofenac and ketorolac to COX-1 and COX-2. Using well-studied COX inhibitors and by comparing STD signals with crystallographic structures we show that there is a relation between the orientations of ibuprofen and diclofenac in the COX-2 active site and the relative STD responses detected in the NMR experiments. Based on this analysis we propose that ketorolac should bind to the COX-2 active site in similar orientation as that of diclofenac. We also show that the combination of STD NMR with competition experiments constitutes a valuable tool to address the recently proposed behavior of COX-2 as functional heterodimers and complement enzyme activity studies in the effort to rationalize COX inhibition mechanisms.

Viegas, A, Manso J, Corvo M, Marques MM, Cabrita EJ.  2011.  Binding of ibuprofen, ketorolac, and diclofenac to COX-1 and COX-2 studied by saturation transfer difference NMR. J Med Chem. 54:8555-62., Number 24 AbstractWebsite

Saturation transfer difference NMR (STD-NMR) spectroscopy has emerged as a powerful screening tool and a straightforward way to study the binding epitopes of active compounds in early stage lead discovery in pharmaceutical research. Here we report the application of STD-NMR to characterize the binding of the anti-inflammatory drugs ibuprofen, diclofenac, and ketorolac to COX-1 and COX-2. Using well-studied COX inhibitors and by comparing STD signals with crystallographic structures, we show that there is a relation between the orientations of ibuprofen and diclofenac in the COX-2 active site and the relative STD responses detected in the NMR experiments. On the basis of this analysis, we propose that ketorolac should bind to the COX-2 active site in an orientation similar to that of diclofenac. We also show that the combination of STD-NMR with competition experiments constitutes a valuable tool to address the recently proposed behavior of COX-2 as functional heterodimers and complements enzyme activity studies in the effort to rationalize COX inhibition mechanisms.

Viegas, A, Manso J, Corvo MC, Marques MMB, Cabrita EJ.  2011.  Binding of ibuprofen, ketorolac, and diclofenac to COX-1 and COX-2 studied by saturation transfer difference NMR. Journal of medicinal chemistry. 54:8555–8562., Number 24: ACS Publications Abstract
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Dias, AMGC, Hussain A, Marcos AS, Roque ACA.  2011.  A biotechnological perspective on the application of iron oxide magnetic colloids modified with polysaccharides. Biotechnology Advances. 29:142–155., Number 1 AbstractWebsite

Iron oxide magnetic nanoparticles {(MNPs)} alone are suitable for a broad spectrum of applications, but the low stability and heterogeneous size distribution in aqueous medium represent major setbacks. These setbacks can however be reduced or diminished through the coating of {MNPs} with various polymers, especially biopolymers such as polysaccharides. Polysaccharides are biocompatible, non-toxic and renewable; in addition, they possess chemical groups that permit further functionalization of the {MNPs.} Multifunctional entities can be created through decoration with specific molecules e.g. proteins, peptides, drugs, antibodies, biomimetic ligands, transfection agents, cells, and other ligands. This development opens a whole range of applications for iron oxide nanoparticles. In this review the properties of magnetic structures composed of {MNPs} and several polysaccharides {(Agarose}, Alginate, Carrageenan, Chitosan, Dextran, Heparin, Gum Arabic, Pullulan and Starch) will be discussed, in view of their recent and future biomedical and biotechnological applications.

2010
Lehmann, M, Kohn C, Figueirinhas JL, Feio G, Cruz C, Dong RY.  2010.  Biaxial nematic mesophases from shape-persistent mesogens with a fluorenone bending unit. Chemistry. 16:8275-9., Number 28 AbstractWebsite
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Bazzicalupi, C, Biagini S, Bianchi A, Faggi E, Gratteri P, Mariani P, Pina F, Valtancoli B.  2010.  Binding of H+ and Zn(II) ions with a new fluorescent macrocyclic phenanthrolinophane. Dalton Transactions. 39:10128-10136., Number 42 AbstractWebsite
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Melo, MJ, Claro A.  2010.  Bright Light: Microspectrofluorimetry for the Characterization of Lake Pigments and Dyes in Works of Art. Accounts of Chemical Research. 43:857-866., Number 6 AbstractWebsite
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2009
Hussain, A, Pina AS, Roque ACA.  2009.  Bio-recognition and detection using liquid crystals. Biosensors and Bioelectronics. 25:1–8., Number 1 AbstractWebsite

Liquid crystals {(LCs)} are used extensively by the electronics industry as display devices. Advances in the understanding of the liquid crystalline phase and the chemistry therein lead to the development of {LC} exhibiting faster switching speed with greater twist angle. This in turn lead to the emergence of liquid crystal displays, rendering dial-and-needle based displays (such as those used in various meters) and cathode ray tubes obsolete. In this article, we review the history of {LC} and their emergence as an invaluable material for display devices and the more recent discovery of their use as sensing elements in biosensors. This new application of {LC} as tools in the development of fast and simple biosensors is envisaged to gain more importance in the foreseeable future.

Roque, ACA, Bicho A, Batalha IL, Cardoso AS, Hussain A.  2009.  Biocompatible and bioactive gum Arabic coated iron oxide magnetic nanoparticles. Journal of Biotechnology. 144:313–320., Number 4 AbstractWebsite

The surface modification of iron oxide magnetic nanoparticles {(MNPs)} with gum Arabic {(GA)} via adsorption and covalent coupling was studied. The adsorption of {GA} was assessed during {MNP} chemical synthesis by the co-precipitation method {(MNP\_GA)}, and after {MNP} synthesis on both bare magnetite and {MNP\_GA.} The covalent immobilization of {GA} at the surface of aldehyde-activated {(MNP\_GAAPTES)} or aminated {MNPs} {(MNP\_GAEDC)} was achieved through free terminal amino and carboxylate groups from {GA.} The presence of {GA} at the surface of the {MNPs} was confirmed by {FTIR} and by the quantification of {GA} by the bicinchoninic acid test. Results indicated that the maximum of {GA} coating was obtained for the covalent coupling of {GA} through its free carboxylate groups {(MNP\_GAEDC)}, yielding a maximum of 1.8&\#xa0;g of {GA} bound/g of dried particles. The hydrodynamic diameter of {MNPs} modified with {GA} after synthesis resulted in the lowest values, in opposition to the {MNPs} co-precipitated with {GA} which presented the tendency to form larger aggregates of up to 1&\#xa0;μm. The zeta potentials indicate the existence of negatively charged surfaces before and after {GA} coating. The potential of the {GA} coated {MNPs} for further biomolecule attachment was assessed through anchorage of a model antibody to aldehyde-functionalized {MNP\_GA} and its subsequent detection with an {FITC} labeled anti-antibody.

2008
Correia, C, Besson S, Brondino CD, Gonzalez PJ, Fauque G, Lampreia J, Moura I, Moura JJ.  2008.  Biochemical and spectroscopic characterization of the membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617, Nov. J Biol Inorg Chem. 13:1321-33., Number 8 AbstractWebsite

Membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617 can be solubilized in either of two ways that will ultimately determine the presence or absence of the small (Iota) subunit. The enzyme complex (NarGHI) is composed of three subunits with molecular masses of 130, 65, and 20 kDa. This enzyme contains approximately 14 Fe, 0.8 Mo, and 1.3 molybdopterin guanine dinucleotides per enzyme molecule. Curiously, one heme b and 0.4 heme c per enzyme molecule have been detected. These hemes were potentiometrically characterized by optical spectroscopy at pH 7.6 and two noninteracting species were identified with respective midpoint potentials at Em=+197 mV (heme c) and -4.5 mV (heme b). Variable-temperature (4-120 K) X-band electron paramagnetic resonance (EPR) studies performed on both as-isolated and dithionite-reduced nitrate reductase showed, respectively, an EPR signal characteristic of a [3Fe-4S]+ cluster and overlapping signals associated with at least three types of [4Fe-4S]+ centers. EPR of the as-isolated enzyme shows two distinct pH-dependent Mo(V) signals with hyperfine coupling to a solvent-exchangeable proton. These signals, called "low-pH" and "high-pH," changed to a pH-independent Mo(V) signal upon nitrate or nitrite addition. Nitrate addition to dithionite-reduced samples at pH 6 and 7.6 yields some of the EPR signals described above and a new rhombic signal that has no hyperfine structure. The relationship between the distinct EPR-active Mo(V) species and their plausible structures is discussed on the basis of the structural information available to date for closely related membrane-bound nitrate reductases.

Paes de Sousa, PM, Pauleta SR, Rodrigues D, Simoes Goncalves ML, Pettigrew GW, Moura I, Moura JJ, Correia dos Santos MM.  2008.  Benefits of membrane electrodes in the electrochemistry of metalloproteins: mediated catalysis of Paracoccus pantotrophus cytochrome c peroxidase by horse cytochrome c: a case study, Jun. J Biol Inorg Chem. 13:779-87., Number 5 AbstractWebsite

A comparative study of direct and mediated electrochemistry of metalloproteins in bulk and membrane-entrapped solutions is presented. This work reports the first electrochemical study of the electron transfer between a bacterial cytochrome c peroxidase and horse heart cytochrome c. The mediated catalysis of the peroxidase was analysed both using the membrane electrode configuration and with all proteins in solution. An apparent Michaelis constant of 66 +/- 4 and 42 +/- 5 microM was determined at pH 7.0 and 0 M NaCl for membrane and bulk solutions, respectively. The data revealed that maximum activity occurs at 50 mM NaCl, pH 7.0, with intermolecular rate constants of (4.4 +/- 0.5) x 10(6) and (1.0 +/- 0.5) x 10(6) M(-1) s(-1) for membrane-entrapped and bulk solutions, respectively. The influence of parameters such as pH or ionic strength on the mediated catalytic activity was analysed using this approach, drawing attention to the fact that careful analysis of the results is needed to ensure that no artefacts are introduced by the use of the membrane configuration and/or promoters, and therefore the dependence truly reflects the influence of these parameters on the (mediated) catalysis. From the pH dependence, a pK of 7.5 was estimated for the mediated enzymatic catalysis.

Cruz, C, Figueirinhas JL, Filip D, Feio G, Ribeiro AC, Frere Y, Meyer T, Mehl GH.  2008.  Biaxial nematic order and phase behavior studies in an organosiloxane tetrapode using complementary deuterium NMR experiments. Phys Rev E Stat Nonlin Soft Matter Phys. 78:051702., Number 5 Pt 1 AbstractWebsite

The biaxial nematic phase was recently observed in different thermotropic liquid crystals, namely bent-core compounds, side-chain polymers, bent-core dimers, and organosiloxane tetrapodes. In this work, a series of experiments with a nematic organosiloxane tetrapode where nuclear magnetic resonance (NMR) spectra are collected while the sample is continuously rotating around an axis perpendicular to the magnetic field, are discussed in conjunction with the analysis of a deuterium NMR experiment on the same system reported earlier. The sample used is a mixture of a deuterated probe with the tetrapode. The mixture exhibits a nematic range between -40 degrees C and 37 degrees C. The results of the two independent, but complementary deuterium NMR experiments confirm the existence of a biaxial nematic phase for temperatures below 0 degrees C with high values of the asymmetry parameter at low temperatures. The presence of slow movements of the tetrapode mesogenic units in the low-temperature regime could also be detected through the analysis of the NMR spectra. Simulations indicate that these movements are mainly slow molecular reorientations of the mesogenic units associated with the presence of collective modes in the nematic phases of this compound. In the case of tetrapodes, recent investigations attribute the origin of biaxiality to the hindering of reorientations of the laterally attached mesogenic units which constitute the tetrapode. This study relates the molecular movements with the nematic biaxial ordering of the system.

Chaves, S, Gil M, Canario S, Jelic R, Romao MJ, Trincao J, Herdtweck E, Sousa J, Diniz C, Fresco P, Santos AM.  2008.  Biologically relevant O,S-donor compounds. Synthesis, molybdenum complexation and xanthine oxidase inhibition. Dalton Transactions. :1773-1782., Number 13 AbstractWebsite
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