Folgosa, F, Cordas CM, Santos JA, Pereira AS, Moura JJ, Tavares P, Moura I.
2011.
New spectroscopic and electrochemical insights on a class I superoxide reductase: evidence for an intramolecular electron-transfer pathway, Sep 15. Biochem J. 438:485-94., Number 3
AbstractSORs (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 iron-centre-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 M(1) . s(1) and 1.3 x 10 M(1) . s(1) for SORFe(IIII)-Fe(II) and for SORFe(IIII)-Fe(III) forms respectively, and 3.2 x 10 M(1) . s(1) for the SORZn(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.
Branquinho, R, Veigas B, {Vaz Pinto} J, de Martins {RFP}, Fortunato {EMC}, Baptista {PMRV}.
2011.
Real-time monitoring of PCR amplification of proto-oncogene c-MYC using a Ta₂O₅ electrolyte-insulator-semiconductor sensor, nov. Biosensors & Bioelectronics. 28:44–49., Number 1: Elsevier
AbstractWe present a new approach for real-time monitoring of PCR amplification of a specific sequence from the human c-MYC proto-oncogene using a Ta(2)O(5) electrolyte-insulator-semiconductor (EIS) sensor. The response of the fabricated EIS sensor to cycle DNA amplification was evaluated and compared to standard SYBR-green fluorescence incorporation, showing it was possible to detect DNA concentration variations with 30 mV/μM sensitivity. The sensor's response was then optimized to follow in real-time the PCR amplification of c-MYC sequence from a genomic DNA sample attaining an amplification profile comparable to that of a standard real-time PCR. Owing to the small size, ease of fabrication and low-cost, the developed Ta(2)O(5) sensor may be incorporated onto a microfluidic device and then used for real-time PCR. Our approach may circumvent the practical and economical obstacles posed by current platforms that require an external fluorescence detector difficult to miniaturize and incorporate into a lab-on-chip system.
Pessanha, V, Dias RJ, Lourenço JM, Farchi E, Sousa D.
2011.
Practical verification of high-level dataraces in transactional memory programs, July. Proceedings of 9th the Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging. :26–34., New York, NY, USA: ACM
AbstractIn this paper we present MoTh, a tool that uses static analysis to enable the automatic verification of concurrency anomalies in Transactional Memory Java programs. Currently MoTh detects high-level dataraces and stale-value errors, but it is extendable by plugging-in sensors, each sensor implementing an anomaly detecting algorithm. We validate and benchmark MoTh by applying it to a set of well known concurrent buggy programs and by close comparison of the results with other similar tools. The results achieved so far are very promising, yielding good accuracy while triggering only a very limited number of false warnings.
Fievet, A, My L, Cascales E, Ansaldi M, Pauleta SR, Moura I, Dermoun Z, Bernard CS, Dolla A, Aubert C.
2011.
The Anaerobe-Specific Orange Protein Complex of Desulfovibrio vulgaris Hildenborough Is Encoded by Two Divergent Operons Coregulated by sigma(54) and a Cognate Transcriptional Regulator, Jul. Journal of Bacteriology. 193:3207-3219., Number 13
AbstractAnalysis of sequenced bacterial genomes revealed that the genomes encode more than 30% hypothetical and conserved hypothetical proteins of unknown function. Among proteins of unknown function that are conserved in anaerobes, some might be determinants of the anaerobic way of life. This study focuses on two divergent clusters specifically found in anaerobic microorganisms and mainly composed of genes encoding conserved hypothetical proteins. We show that the two gene clusters DVU2103-DVU2104-DVU2105 (orp2) and DVU2107-DVU2108-DVU2109 (orp1) form two divergent operons transcribed by the sigma(54)-RNA polymerase. We further demonstrate that the sigma(54)-dependent transcriptional regulator DVU2106, located between orp1 and orp2, collaborates with sigma(54)-RNA polymerase to orchestrate the simultaneous expression of the divergent orp operons. DVU2106, whose structural gene is transcribed by the sigma(70)-RNA polymerase, negatively retrocontrols its own expression. By using an endogenous pulldown strategy, we identify a physiological complex composed of DVU2103, DVU2104, DVU2105, DVU2108, and DVU2109. Interestingly, inactivation of DVU2106, which is required for orp operon transcription, induces morphological defects that are likely linked to the absence of the ORP complex. A putative role of the ORP proteins in positioning the septum during cell division is discussed.
Silva, {LB}, Veigas B, c}alo Doria G{\c, Costa P, Inácio J, Martins R, Fortunato E, Baptista {PV}.
2011.
Portable optoelectronic biosensing platform for identification of mycobacteria from the Mycobacterium tuberculosis complex, jan. Biosensors & Bioelectronics. 26:2012–2017., Number 5: Elsevier
AbstractIn this paper we report on the fabrication and performance of a portable and low cost optoelectronic platform integrating a double color tuned light emitting diode as light source, an amorphous/nanocrystalline silicon photodetector with a flat spectral response in the wavelength range from 520. nm to 630. nm and integrated electronic for signal acquisition and conditioning constituted by current to voltage converter, a filter and an amplification stage, followed by an analog to digital converter, with appropriate software for full automation to minimize human error. Incorporation of the double color tuned light emitting diode provides for a simple yet innovative solution to signal acquisition independently from the light intensity and/or solution concentration, while considerably decreasing production costs. Detection based on Au-nanoprobes constitutes the biorecognition step and allowed identification of specific sequences of Mycobacterium tuberculosis complex, namely Mycobacterium bovis and M. tuberculosis in biological samples.
Barbosa, DJ, Capela JP, Oliveira JMA, Ferreira L, Branco P, Fernandes E, Bastos ML, Carvalho F.
2011.
Pro-oxidant effects of ``ecstasy{''} and its metabolites in mouse brain synaptosomes, AUG 28. TOXICOLOGY LETTERS. 205:S113., Number 1: European Soc Toxicol
Abstractn/a
Seixas, J, Simões S, Kanudia A, Gargiulo M, Dias L, Gouveia JP, Fortes P.
2011.
Electric Vehicles in the European Union: Conditions for Success, Impacts on the Power System and on CO2 Emissions, 6-8 July. IEW - International Energy Workshop 2011,. , Standford, USA.
Oliveira, J, Petrov V, Parola AJ, Pina F, Azevedo J, Teixeira N, Bras NF, Fernandes PA, Mateus N, Ramos MJ, de Freitas V.
2011.
Chemical Behavior of Methylpyranomalvidin-3-O-glucoside in Aqueous Solution Studied by NMR and UV-Visible Spectroscopy, 2011. Journal of Physical Chemistry B. 115:1538-1545.
AbstractIn the present work, the proton-transfer reactions of the methylpyranomalvidin-3-O-glucoside pigment in water with different pH values was studied by NMR and UV-visible spectroscopies. The results showed four equilibrium forms: the methylpyranomalvidin-3-O-glucoside cation, the neutral quinoidal base, the respective anionic quinoidal base, and a dianionic base unprotonated at the methyl group. According to the NMR data, it seems that for methylpyranomalvidin-3-O-glucoside besides the acid base equilibrium between the pyranoflavylium cation and the neutral quinoidal base, a new species is formed at pD 4.88-6.10. This is corroborated by the appearance of a new set of signals in the NMR spectrum that may be assigned to the formation of hemiketal/cis-chalcone species to a small extent. The two ionization constants (pK(a1) and pK(a2)) obtained by both methods (NMR and UV-visible) for methylpyranomalvidin-3-O-glucoside are in agreement (pK(a1) = 5.17 +/- 0.03; pK(a2) = 8.85 +/- 0.08; and pK(a1) = 4.57 +/- 0.07; pK(a2) = 8.23 +/- 0.04 obtained by NMR and UV-visible spectroscopies, respectively). Moreover, the fully dianionic unprotonated form (at the methyl group) of the methylpyranomalvidin-3-O-glucoside is converted slowly into a new structure that displays a yellow color at basic pH. On the basis of the results obtained through LC-MS and NMR, the proposed structure was found to correspond to the flavonol syringetin-3-glucoside.
Borges, JP, Godinho MH, Figueirinhas JL, de Pinho MN, Belgacem MN.
2011.
All-cellulosic based composites. Cellulose Fibers: Bio-and Nano-Polymer Composites. (
Susheel Kalia, B. S. Kaith, Inderjeet Kaur, Eds.).:399–421.: Springer Berlin Heidelberg
AbstractThe use of cellulosic fibers as load bearing constituents in composite materials has increased over the last decade due to their relative cheapness compared to conventional materials such as glass and aramid fibers, their ability to recycle, and because they compete well in terms of strength per weight of material. All-cellulosic based composites prepared from cellulose derivatives based matrices and microcrystalline cellulosic fibers made by direct coupling between fibers and matrix present interesting mechanical and gas permeation properties, thus being potential candidates for packaging materials. Both the cellulosic matrix and the reinforcing fibers are biocompatible and widely used in the pharmaceutical industry, which is very important for the envisaged application. In addition to their biocompatibility, cellulosic systems have the ability to form both thermotropic and lyotropic chiral nematic phases, and the composites produced from the latter show improved mechanical properties due to fiber orientation induced by the anisotropic matrix. The preparation and characterization (morphological, topographical, mechanical, gas barrier properties) of all-cellulosic based composites are described in this chapter.
Gromicho, M, Dinis J, Magalhaes M, Fernandes AR, Tavares P, Laires A, Rueff J, Rodrigues AS.
2011.
Development of imatinib and dasatinib resistance: dynamics of expression of drug transporters ABCB1, ABCC1, ABCG2, MVP, and SLC22A1. Leuk Lymphoma. 52(10):1980-90.