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2011
Ferraz, R, Branco LC, Prudencio C, Noronha JP, Petrovski Z.  2011.  Ionic Liquids as Active Pharmaceutical Ingredients. Chemmedchem. 6:975-985., Number 6 AbstractWebsite
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Timoteo, CG, Pereira AS, Martins CE, Naik SG, Duarte AG, Moura JJG, Tavares P, Huynh BH, Moura I.  2011.  Low-Spin Heme b(3) in the Catalytic Center of Nitric Oxide Reductase from Pseudomonas nautica. Biochemistry. {50}:{4251-4262}., Number {20} Abstract

Respiratory nitric oxide reductase (NOR) was purified from membrane extract of Pseudomonas (Ps.) nautica cells to homogeneity as judged by polyacrylamide gel electrophoresis. The purified protein is a heterodimer with subunits of molecular masses of 54 and 18 kDa. The gene encoding both subunits was cloned and sequenced. The amino acid sequence shows strong homology with enzymes of the cNOR class. Iron/heme determinations show that one heme c is present in the small subunit (NORC) and that approximately two heme b and one non-heme iron are associated with the large subunit (NORB), in agreement with the available data for enzymes of the cNOR class. Mossbauer characterization of the as-purified, ascorbate-reduced, and dithionite-reduced enzyme confirms the presence of three heme groups (the catalytic heme b(3) and the electron transfer heme b and heme c) and one redox-active non-heme Fe (Fe-B). Consistent with results obtained for other cNORs, heme c and heme b in Ps. nautica cNOR were found to be low-spin while FeB was found to be high-spin. Unexpectedly, as opposed to the presumed high-spin state for heme b(3), the Mossbauer data demonstrate unambiguously that heme b(3) is, in fact, low-spin in both ferric and ferrous states, suggesting that heme b(3) is six-coordinated regardless of its oxidation state. EPR spectroscopic measurements of the as-purified enzyme show resonances at the g similar to 6 and g similar to 2-3 regions very similar to those reported previously for other cNORs. The signals at g = 3.60, 2.99, 2.26, and 1.43 are attributed to the two charge-transfer low-spin ferric heme c and heme b. Previously, resonances at the g similar to 6 region were assigned to a small quantity of uncoupled high-spin Fe-III heme b(3). This assignment is now questionable because heme b(3) is low-spin. On the basis of our spectroscopic data, we argue that the g = 6.34 signal is likely arising from a spin spin coupled binuclear center comprising the low-spin Fe-III heme b(3) and the high-spin Fe-B(III). Activity assays performed under various reducing conditions indicate that heme b(3) has to be reduced for the enzyme to be active. But, from an energetic point of view, the formation of a ferrous heme-NO as an initial reaction intermediate for NO reduction is disfavored because heme [FeNO](7) is a stable product. We suspect that the presence of a sixth ligand in the Fe-II-heme b(3) may weaken its affinity for NO and thus promotes, in the first catalytic step, binding of NO at the Fe-B(II) site. The function of heme b(3) would then be to orient the Fe-B-bound NO molecules for the formation of the N-N bond and to provide reducing equivalents for NO reduction.

Garcia-Alvarez, B, Melero R, Dias FMV, Prates JAM, Fontes CMGA, Smith SP, Romao MJ, Carvalho AL, Llorca O.  2011.  Molecular Architecture and Structural Transitions of a Clostridium thermocellum Mini-Cellulosome. Journal of Molecular Biology. 407:571-580., Number 4 AbstractWebsite
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Baptista, {PV}, c}alo Dória G{\c, Quaresma P, Cavadas M, Neves {CS }, Gomes I, Eaton P, Pereira E, Franco R.  2011.  Nanoparticles in molecular diagnostics. Nanoparticles in Translational Science and Medicine. (Antonio Villaverde, Ed.).:427–488., Netherlands: Elsevier Abstract

The aim of this chapter is to provide an overview of the available and emerging molecular diagnostic methods that take advantage of the unique nanoscale properties of nanoparticles (NPs) to increase the sensitivity, detection capabilities, ease of operation, and portability of the biodetection assemblies. The focus will be on noble metal NPs, especially gold NPs, fluorescent NPs, especially quantum dots, and magnetic NPs, the three main players in the development of probes for biological sensing. The chapter is divided into four sections: a first section covering the unique physicochemical properties of NPs of relevance for their utilization in molecular diagnostics; the second section dedicated to applications of NPs in molecular diagnostics by nucleic acid detection; and the third section with major applications of NPs in the area of immunoassays. Finally, a concluding section highlights the most promising advances in the area and presents future perspectives.

Folgosa, F, Cordas CM, Santos JA, Pereira AS, Moura JJG, Tavares P, Moura I.  2011.  New spectroscopic and electrochemical insights on a class I superoxide reductase: evidence for an intramolecular electron-transfer pathway. BIOCHEMICAL JOURNAL. {438}:{485-494}., Number {3} Abstract

SORs (superoxide reductases) are enzymes involved in bacterial resistance to reactive oxygen species, catalysing the reduction of superoxide anions to hydrogen peroxide. So far three structural classes have been identified. Class I enzymes have two ironcentre-containing domains. Most studies have focused on the catalytic iron site (centre II), yet the role of centre I is poorly understood. The possible roles of this iron site were approached by an integrated study using both classical and fast kinetic measurements, as well as direct electrochemistry. A new heterometallic form of the protein with a zinc-substituted centre I, maintaining the iron active-site centre II, was obtained, resulting in a stable derivative useful for comparison with the native all-iron from. Second-order rate constants for the electron transfer between reduced rubredoxin and the different SOR forms were determined to be 2.8 x 10(7) M(-1) . s(-1) and 1.3 x 10(6) M(-1) . s(-1) for SOR(Fe(IIII)-Fe(II)) and for SOR(Fe(IIII)-Fe(III)) forms respectively, and 3.2 x 10(6) M(-1) s(-1) for the SOR(Zn(II)-Fe(III)) form. The results obtained seem to indicate that centre I transfers electrons from the putative physiological donor rubredoxin to the catalytic active iron site (intramolecular process). In addition, electrochemical results show that conformational changes are associated with the redox state of centre I, which may enable a faster catalytic response towards superoxide anion. The apparent rate constants calculated for the SOR-mediated electron transfer also support this observation.

Magin, R, Ortigueira MD, Podlubny I, Trujillo J.  2011.  On the fractional signals and systems. Signal Processing. 91:350–371., Number 3: Elsevier AbstractWebsite

A look into fractional calculus and its applications from the signal processing point of view is done in this paper. A coherent approach to the fractional derivative is presented, leading to notions that are not only compatible with the classic but also constitute a true generalization. This means that the classic are recovered when the fractional domain is left. This happens in particular with the impulse response and transfer function. An interesting feature of the systems is the causality that the fractional derivative imposes. The main properties of the derivatives and their representations are presented. A brief and general study of the fractional linear systems is done, by showing how to compute the impulse, step and frequency responses, how to test the stability and how to insert the initial conditions. The practical realization problem is focussed and it is shown how to perform the input?ouput computations. Some biomedical applications are described.

Luis, AS, Alves VD, Romao MJ, Prates JAM, Fontes CMGA, Najmudin S.  2011.  Overproduction, purification, crystallization and preliminary X-ray characterization of a novel carbohydrate-binding module of endoglucanase Cel5A from Eubacterium cellulosolvens. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 67:491-493. AbstractWebsite
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Gago, S, Bruno SM, Queiros DC, Valente AA, Goncalves IS, Pillinger M.  2011.  Oxidation of Ethylbenzene in the Presence of an MCM-41-Supported or Ionic Liquid-Standing Bischlorocopper(II) Complex. Catalysis Letters. 141:1009-1017., Number 7 AbstractWebsite
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Gavara, R, Petrov V, Lopez V, Pina F.  2011.  Photochromism of naphthoflavylium. On the role of 4-OH hemiketal in flavylium network. Journal of Photochemistry and Photobiology a-Chemistry. 220:4-10., Number 1 AbstractWebsite
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Rodriguez, L, Lima JC, Pina F, Cacciapaglia R, Di Stefano S, Ruggi A.  2011.  Photophysical Study of Naphthalenophanes: Evidence of Adduct Formation with Molecular Oxygen. Journal of Physical Chemistry a. 115:123-127., Number 2 Abstract
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Bras, JLA, Correia MAS, Romao MJ, Prates JAM, Fontes CMGA, Najmudin S.  2011.  Purification, crystallization and preliminary X-ray characterization of the pentamodular arabinoxylanase CtXyl5A from Clostridium thermocellum. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 67:833-836. AbstractWebsite
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Palma, LB, Coito FV, Gil PS.  2011.  Real-time detection of oscillations in control loops. Power Engineering, Energy and Electrical Drives (POWERENG), 2011 International Conference on. :1–6.: IEEE Abstract

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Pereira, P, Helena Fino M, Coito F, Ventim-Neves M.  2011.  RF integrated inductor modeling and its application to optimization-based design. Analog Integrated Circuits and Signal Processing. :1–9.: Springer Abstract

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Bras, JLA, Cartmell A, Carvalho ALM, Verze G, Bayer EA, Vazana Y, Correia MAS, Prates JAM, Ratnaparkhe S, Boraston AB, Romao MJ, Fontes CMGA, Gilbert HJ.  2011.  Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis. Proceedings of the National Academy of Sciences of the United States of America. 108:5237-5242., Number 13 AbstractWebsite
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Costa, F, Coito F, Palma L.  2011.  Switched Unfalsified Multicontroller. Technological Innovation for Sustainability. :393–401.: Springer Abstract

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Neves, P, Gago S, Balula SS, Lopes AD, Valente AA, Cunha-Silva L, Almeida Paz FA, Pillinger M, Rocha J, Silva CM, Goncalves IS.  2011.  Synthesis and Catalytic Properties of Molybdenum(VI) Complexes with Tris(3,5-dimethyl-1-pyrazolyl)methane. Inorganic Chemistry. 50:3490-3500., Number 8 AbstractWebsite
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Gawande, MB, Branco PS, Parghi K, Shrikhande JJ, Pandey RK, Ghumman CAA, Bundaleski N, Teodoro OMND, Jayaram RV.  2011.  Synthesis and characterization of versatile MgO-ZrO2 mixed metal oxide nanoparticles and their applications. CATALYSIS SCIENCE & TECHNOLOGY. 1:1653-1664., Number 9 Abstract
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Palma, LB, Coito FV.  2011.  Tuning PCA controllers based on manual control data. Emerging Technologies & Factory Automation (ETFA), 2011 IEEE 16th Conference on. :1–4.: IEEE Abstract

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Coito, F, Palma LB.  2011.  Unfalsification based Fault Tolerant Controller. Emerging Technologies & Factory Automation (ETFA), 2011 IEEE 16th Conference on. :1–4.: IEEE Abstract

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Martins, R, Brás B, Ferreira I, Pereira L, Barquinha P, Correia N, Costa R, Busani T, Gonçalves A, Pimentel A, Fortunato E.  2011.  {Away from silicon era: the paper electronics}. 7940(Teherani, Ferechteh H., Look, David C., Rogers, David J., Eds.).:79400P\{$\backslash$textendash\}79400P\{$\backslash$textendash\}10. Abstract

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Martins, R, Brás B, Ferreira I, Pereira L, Barquinha P, Correia N, Costa R, Busani T, Gonçalves A, Pimentel A, Fortunato E.  2011.  {Away from silicon era: the paper electronics}. Proc. SPIE. 7940(Teherani, Ferechteh H., Look, David C., Rogers, David J., Eds.).:79400P–79400P–10. Abstract

Today there is a strong interest in the scientific and industrial community concerning the use of biopolymers for electronic applications, mainly driven by low-cost and disposable applications. Adding to this interest, we must recognize the importance of the wireless auto sustained and low energy consumption electronics dream. This dream can be fulfilled by cellulose paper, the lightest and the cheapest known substrate material, as well as the Earth's major biopolymer and of tremendous global economic importance. The recent developments of oxide thin film transistors and in particular the production of paper transistors at room temperature had contributed, as a first step, for the development of disposable, low cost and flexible electronic devices. To fulfil the wireless demand, it is necessary to prove the concept of self powered devices. In the case of paper electronics, this implies demonstrating the idea of self regenerated thin film paper batteries and its integration with other electronic components. Here we demonstrate this possibility by actuating the gate of paper transistors by paper batteries. We found that when a sheet of cellulose paper is covered in both faces with thin layers of opposite electrochemical potential materials, a voltage appears between both electrodes -paper battery, which is also self-regenerated. The value of the potential depends upon the materials used for anode and cathode. An open circuit voltage of 0.5V and a short-circuit current density of 1$μ$A/cm2 were obtained in the simplest structure produced (Cu/paper/Al). For actuating the gate of the paper transistor, seven paper batteries were integrated in the same substrate in series, supplying a voltage of 3.4V. This allows proper ON/OFF control of the paper transistor. Apart from that transparent conductive oxides can be also used as cathode/anode materials allowing so the production of thin film batteries with transparent electrodes compatible with flexible, invisible, self powered and wireless electronics.

Martins, R, Nathan A, Barros R, Pereira L\'ıs, Barquinha P, Correia N, Costa R, Ahnood A, Ferreira I, Fortunato E.  2011.  {Complementary metal oxide semiconductor technology with and on paper.}. Advanced materials (Deerfield Beach, Fla.). 23:4491–6., Number 39 AbstractWebsite
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2010
Veigas, B, Machado D, Perdigão J, Portugal I, Couto I, Viveiros M, Baptista {PV}.  2010.  Au-nanoprobes for detection of SNPs associated with antibiotic resistance in Mycobacterium tuberculosis, oct. Nanotechnology. 21, Number 41: IOP Publishing Abstract

Tuberculosis (TB) is one of the leading causes of infection in humans, causing high morbility and mortality all over the world. The rate of new cases of multidrug resistant tuberculosis (MDRTB) continues to increase, and since these infections are very difficult to manage, they constitute a serious health problem. In most cases, drug resistance in Mycobacterium tuberculosis has been related to mutations in several loci within the pathogen's genome. The development of fast, cheap and simple screening methodologies would be of paramount relevance for the early detection of these mutations, essential for the timely and effective diagnosis and management of MDRTB patients. The use of gold nanoparticles derivatized with thiol-modified oligonucleotides (Au-nanoprobes) has led to new approaches in molecular diagnostics. Based on the differential non-cross-linking aggregation of Au-nanoprobes, we were able to develop a colorimetric method for the detection of specific sequences and to apply this approach to pathogen identification and single base mutations/single nucleotide polymorphisms (SNP) discrimination. Here we report on the development of Au-nanoprobes for the specific identification of SNPs within the beta subunit of the RNA polymerase (rpoB locus), responsible for resistance to rifampicin in over 95% of rifampicin resistant M. tuberculosis strains.

da Silva, DG, de Pinho PG, Pontes H, Ferreira L, Branco P, Remiao F, Carvalho F, Bastos LM, Carmo H.  2010.  Gas chromatography-ion trap mass spectrometry method for the simultaneous measurement of MDMA (ecstasy) and its metabolites, MDA, HMA, and HMMA in plasma and urine, MAR 15. JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES. 878:815-822., Number 9-10 Abstract

The investigation of 3,4-methylenedioxymethamphetamine (MDMA: ecstasy) abuse requires very robust methods with high sensitivity and wide linearity ranges for the quantification of this drug of abuse and its main metabolites in body fluids. An optimized gas chromatography-ion trap mass spectrometry (GC-IT/MS) methodology with electron impact ionization addressing these issues is presented. The sample preparation involves an enzymatic hydrolysis of urine and plasma for conjugate cleavage, a SPE extraction, and a derivatization process. The method was fully validated in rat plasma and urine. Linearity for a wide concentration range was achieved for MDMA, and the metabolites 3,4-methylenedioxyamphetamine (MDA), 4-hydroxy-3-methoxyamphetamine (HMA) and 4-hydroxy-3-methoxymethamphetamine (HMMA). Limits of quantification were 2 ng/mL in plasma and 3.5 ng/mL in urine using a Selected Ion Monitoring detection mode. Selectivity, accuracy, precision, and recovery met the required criteria for the method validation. This GC-IT/MS method provides high sensitivity and adequate performance characteristics for the simultaneous quantification of MDMA, MDA, HMA and HMMA in the studied matrices. (C) 2010 Elsevier B.V. All rights reserved.

Najmudin, S, Pauleta SR, Moura I, Romao MJ.  2010.  The 1.4 angstrom resolution structure of Paracoccus pantotrophus pseudoazurin, Jun. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 66:627-635. AbstractWebsite

Pseudoazurins are small type 1 copper proteins that are involved in the flow of electrons between various electron donors and acceptors in the bacterial periplasm, mostly under denitrifying conditions. The previously determined structure of Paracoccus pantotrophus pseudoazurin in the oxidized form was improved to a nominal resolution of 1.4 angstrom, with R and R(free) values of 0.188 and 0.206, respectively. This high-resolution structure makes it possible to analyze the interactions between the monomers and the solvent structure in detail. Analysis of the high-resolution structure revealed the structural regions that are responsible for monomer-monomer recognition during dimer formation and for protein-protein interaction and that are important for partner recognition. The pseudoazurin structure was compared with other structures of various type 1 copper proteins and these were grouped into families according to similarities in their secondary structure; this may be useful in the annotation of copper proteins in newly sequenced genomes and in the identification of novel copper proteins.

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