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2013
Marangon, J, Correia HD, Brondino CD, Moura JJG, Romao MJ, Gonzalez PJ, Santos-Silva T.  2013.  Kinetic and structural studies of aldehyde oxidoreductase from Desulfovibrio gigas reveal a dithiolene-based chemistry for enzyme activation and inhibition by H2O2. PLoS One. 8:e83234.
Martins, J.  2013.  Lightweight monitoring of transactional memory programs. Universidade Nova de Lisboa. 2013-joao_martins.pdf
Borlido, L, Azevedo AM, Roque ACA, Aires-Barros MR.  2013.  Magnetic separations in biotechnology. Biotechnology Advances. 31(8):1374-1385. AbstractWebsite

Magnetic separations are probably one of the most versatile separation processes in biotechnology as they are able to purify cells, viruses, proteins and nucleic acids directly from crude samples. The fast and gentle process in combination with its easy scale-up and automation provide unique advantages over other separation techniques. In the midst of this process are the magnetic adsorbents tailored for the envisioned target and whose complex synthesis spans over multiple fields of science. In this context, this article reviews both the synthesis and tailoring of magnetic adsorbents for bioseparations as well as their ultimate application.

Pauleta, SR, Ramos S, Pietsch M, Carreira C, Dell'Acqua S, Moura I.  2013.  Marinobacter hydrocarbonoclasticus is an aerobic denitrifier. EuroBIC 11. :49-53., Granada: Medimone, Intern. Proceedings
Marcelo, F, Dias C, Madeira PJ, Jorge T, Florêncio HM, Canada JF, Cabrita EJ, Jiménez-Barbero J, Rauter AP.  2013.  Molecular Recognition of Rosmarinic Acid from Salvia sclareoides Extracts by Acetylcholinesterase: A New Binding Site Detected by NMR Spectroscopy. Chemistry: A European Journal. 19(21):6641–6649. Abstract

Acetylcholinesterase (AChE) inhibition is one of the most currently available therapies for the management of Alzheimer’s disease (AD) symptoms. In this context, NMR spectroscopy binding studies were accomplished to explain the inhibition of AChE activity by Salvia sclareoides extracts. HPLC-MS analyses of the acetone, butanol and water extracts eluted with methanol and acidified water showed that rosmarinic acid is present in all the studied samples and is a major constituent of butanol and water extracts. Moreover, luteolin 4′-O-glucoside, luteolin 3′,7-di-O-glucoside and luteolin 7-O-(6′′-O-acetylglucoside) were identified by MS2 and MS3 data acquired during the LC-MSn runs. Quantification of rosmarinic acid by HPLC with diode-array detection (DAD) showed that the butanol extract is the richest one in this component (134 μg mg−1 extract). Saturation transfer difference (STD) NMR spectroscopy binding experiments of S. sclareoides crude extracts in the presence of AChE in buffer solution determined rosmarinic acid as the only explicit binder for AChE. Furthermore, the binding epitope and the AChE-bound conformation of rosmarinic acid were further elucidated by STD and transferred NOE effect (trNOESY) experiments. As a control, NMR spectroscopy binding experiments were also carried out with pure rosmarinic acid, thus confirming the specific interaction and inhibition of this compound against AChE. The binding site of AChE for rosmarinic acid was also investigated by STD-based competition binding experiments using Donepezil, a drug currently used to treat AD, as a reference. These competition experiments demonstrated that rosmarinic acid does not compete with Donepezil for the same binding site. A 3D model of the molecular complex has been proposed. Therefore, the combination of the NMR spectroscopy based data with molecular modelling has permitted us to detect a new binding site in AChE, which could be used for future drug development.

Baptista, AC, Soares PIP, Ferreira I, Borges JP.  2013.  Nanofibers and nanoparticles in biomedical applications. Bioengineered Nanomaterials. (Tiwari, Atul, Tiwari, Ashutosh, Eds.)., USA: CRC Press (Taylor & Francis Group)
Carja, Gabriela, Dartu, Laura, Okada, Kiyoshi, Fortunato E.  2013.  Nanoparticles of copper oxide on layered double hydroxides and the derived solid solutions as wide spectrum active nano-photocatalysts. Chemical Engineering Journal. 222:60-66.
Fartaria, RPS, Pereira F, Bonifácio VDB, Mata P, Aires-de-Sousa J, Lobo AM.  2013.  NavMol 2.0 – A Molecular Structure Navigator/Editor for Blind and Visually Impaired Users. Eur. J. Org. Chem. 8:1415–1419.Website
Teixiera, SS, Dias CJ, Dionísio M, Costa LC.  2013.  New method to analyze dielectric relaxation processes: a study on polymethacrylate series. Polymer International. 62:1744-1749.Website
C., C, M. R, C.M. S, J.J.G. M, E. O, E. J, M.G. A.  2013.  Nitrite biosensing using cytochrome c nitrite reductase: Towards a disposable strip electrode. Biomedical Engineering Systems and Technologies, Communications in Computer and Information Science. :41-51., DOI:10.1007/978-3-642-38256-7_3: Springer, Heidelberg
Dell’Acqua, S, Pauleta SR, Moura I, Moura JG.  2013.  Nitrous Oxide Reductase. Encyclopedia of Metalloproteins - Copper. : Springer
Pauleta, SR, Dell’Acqua S, Moura I.  2013.  Nitrous Oxide Reductase. Coord Chem Rev. 257:332-249.
Pimenta, J, Viegas A, Sardinha J, Martins IC, Cabrita EJ, Fontes CMGA, Prates JAM, Pereira RMLN.  2013.  NMR Solution Structure and SRP54M predicted interaction of the N-Terminal sequence (1-30) of the ovine Doppel protein. Peptides. 49:32-40. AbstractWebsite

Prion protein (PrPC) biosynthesis involves a multi-step process that includes translation and post-translational modifications. While PrP has been widely investigated, for the homolog Doppel (Dpl), limited knowledge is available. In this study, we focused on a vital step of eukaryotic protein biosynthesis: targeting by the signal recognition particle (SRP). Taking the ovine Dpl (OvDpl(1-30)) peptide as a template, we studied its behavior in two different hydrophobic environments using CD and NMR spectroscopy. In both trifluoroethanol (TFE) and dihexanoyl-sn-glycero-3-phosphatidylcholine (DHPC), the OvDpl(1-30) peptide revealed to fold in an alpha-helical conformation with a well-defined central region extending from residue Cys8 until Ser22. The NMR structure was subsequently included in a computational docking complex with the conserved M-domain of SRP54 protein (SRP54M), and further compared with the N-terminal structures of mouse Dpl and bovine PrPC proteins. This allowed the determination of (i) common predicted N-terminal/SRP54M polar contacts (Asp331, Gln335, Glu365 and Lys432) and (ii) different N–C orientations between prion and Dpl peptides at the SRP54M hydrophobic groove, that are in agreement with each peptide electrostatic potential. Together, these findings provide new insights into the biosynthesis of prion-like proteins. Besides they also show the role of protein conformational switches in signalization toward the endoplasmic membrane, a key event of major significance in the cell cycle. They are thus of general applicability to the study of the biological function of prion-like as well as other proteins.

Vale, TM, Dias RJ, Lourenço JM.  2013.  On the Relevance of Total-Order Broadcast Implementations in Replicated Software Transactional Memories. Multicore Software Engineering, Performance, and Tools. 8063(João M. Lourenço, Farchi, Eitan, Eds.).:49–60.: Springer Berlin Heidelberg Abstract2013-musepat.pdf

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M, E, B.A. S, I.C. V, R.C.C. M, J.P. V, L. G, I. F, R. I.  2013.  Optical and structural characterization of samarium and europium-doped phosphate glasses. Journal of Non-Crystalline Solids. 369:55-60. AbstractWebsite

The work deals with optical and structural properties of aluminophosphate glasses from Li2O–BaO–Al2O3–La2O3–P2O5 system containing Sm3+ and Eu3+ ions. X-ray fluorescence (XRF) has been used to establish the elemental composition of these materials. The influence of Sm3+ and Eu3+ ions on the optical properties of these glasses has been investigated in relation with their structural characteristics. The optical behavior of these materials has been studied by ultra-violet–visible (UV–Vis) spectroscopy, revealing absorption maxima specific to the doping ions. Structural information via vibration modes was provided by Fourier Transform Infrared (FTIR) absorption spectra evidenced as P–O–P symmetrical and asymmetrical stretching vibration modes, P–O–P bend, PO2- symmetrical and asymmetrical stretching vibration modes, P=O stretching vibration mode and P–O–H water absorbance. Raman spectra acquired by 514.5 nm laser excitation disclosed peaks specific to metaphosphate network. Information about the elemental compositional homogeneity of Sm3+ and Eu3+ -containing glasses as well as about the defects of the doped-glasses is revealed by scanning electron microscopy/energy dispersive spectrometry (SEM/EDS). Fluorescence spectroscopy measurements put in evidence important fluorescence peaks found at 596 nm and 643 nm for Sm3 + ions in phosphate matrix and 611 nm and 700 nm in the case of Eu3+ -doped glass.

Figueiredo, V., Pinto, Joana, Deuermeier, J., Barros, R., Alves, C, Martins, Fortunato E.  2013.  p-Type CuxO Thin-Film Transistors Produced by Thermal Oxidation. Journal of Display Technology. 9(9):735-740.
Parthiban, S., Elangovan, E., Nayak, Pradipta K., Gonçalves, G., Nunes, D., Pereira, Barquinha, Busani, Tito, Fortunato, Martins R.  2013.  Performances of Microcrystalline Zinc Tin Oxide Thin-Film Transistors Processed by Spray Pyrolysis. Journal of Display Technology, . 9(10):825-831.
Amado, MP, Poggi F.  2013.  PLANNING FOR SOLAR SMART CITIES. CISBAT 2013. :1017-1022., Lausanne, CH: EPFL, CH
Dias, RJ, Pessanha V, Lourenço JM.  2013.  Precise Detection of Atomicity Violations. Hardware and Software: Verification and Testing. 7857(Biere, Armin, Nahir, Amir, Vos, Tanja, Eds.).:8-23.: Springer Berlin / Heidelberg Abstract2012-hvc.pdf

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Ramos, A.M., Pereira, Cidade, M.T., Pereira, Branquinho, R., Pereira, Martins, Fortunato E.  2013.  Preparation and characterization of cellulose nanocomposite hydrogels as functional electrolytes. Solid State Ionics. 242:26-32.
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