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2013
Pacheco, MF, Pereira AI, Branco LC, Parola AJ.  2013.  Varnish removal from paintings using ionic liquids, 2013. Journal of Materials Chemistry A. 1:7016-7018. AbstractWebsite

The possibility of replacing volatile and toxic organic solvents by ionic liquids (ILs) could contribute to safer procedures for conservation and restoration. This study introduces the use of ILs in varnish removal from paintings. The efficacy of this new procedure was assessed by applying different types of ILs in mock-ups of several painting materials and varnishes. The removal of IL residues from the surface of paintings was assessed mainly by FTIR-ATR. The application of ILs to a real painting is illustrated.

Pimentel, A, Gamboa H, Cunha S, Correia A.  2013.  Algorithm for testing behavioural phenotypes in a Zebrafish model of Parkinson's Disease. Proceedings of Biosignals - 6th International Conference on Bio-Inspired and Signal Processing (BIOSIGNALS 2013). , Barcelona, Spain
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
Silva, TF, Smolenski P, Martins LMDRS, da Silva MFG, Fernandes AR, Luis D, Silva A, Santos S, Borralho PM, Rodrigues CMP, Pombeiro AJL.  2013.  Cobalt and Zinc Compounds Bearing 1,10-Phenanthroline-5,6-dione or 1,3,5-Triaza-7-phosphaadamantane Derivatives - Synthesis, Characterization, Cytotoxicity, and Cell Selectivity Studies. Eur J Inorg Chem. 2013(21):3651-3658.13silvaejic.pdf
Ruivo, A, Almeida T, Quintas F, Wiley R, Troeira M, Paulino N, Laia CAT, Queiroz CA, de Matos PA.  2013.  Colours of Luminescent Glasses for Artworks. Proceedings of 12th International AIC Colour Congress. :885-888., Newcastle Gateshead, UK
Thapper, A, Rizzi AC, Brondino CD, Wedd AG, Pais RJ, Maiti BK, Moura I, Pauleta SR, Moura JJG.  2013.  Copper-substituted forms of the wild type and C42A variant of rubredoxin. J Inorg Biochem. 127:232-237.
Nandy, Suman, Gonçalves G, Pinto, Joana, Busani, Tito, Figueiredo, V., Pereira, Paiva Martins RF, Fortunato E.  2013.  Current transport mechanism at metal-semiconductor nanoscale interfaces based on ultrahigh density arrays of p-type NiO nano-pillars. Nanoscale. 5:11699-11709.
Amado, M, Amado A, Poggi F, Correia de Freitas J.  2013.  Efficiency Based Model for Solar Urban Planning. International Journal of Civil, Architectural Science and Engineering. Vol. 7(Nº 12):1-5.
Poggi, F, Amado MP.  2013.  ENERGIA SOLAR: FATOR NO PROCESSO DE PLANEAMENTO DA CIDADE Solar Energy: Factor in the Process of Planning City. 2º Congresso Internacional da habitação no Espaço Lusófono. :240-241., Lisboa, PT: LNEC
Schmolka, N, Serre K, Grosso AR, Rei M, Pennington DJ, Gomes AQ, Silva-santos B.  2013.  Epigenetic and transcriptional signatures of stable versus plastic differentiation of proinflammatory γδT cell subsets.. Nature immunology. 14:1093–1100., Number 10: Nature Publishing Group AbstractWebsite

Two distinct subsets of γδ T cells that produce interleukin 17 (IL-17) (CD27(-) γδ T cells) or interferon-γ (IFN-γ) (CD27(+) γδ T cells) develop in the mouse thymus, but the molecular determinants of their functional potential in the periphery remain unknown. Here we conducted a genome-wide characterization of the methylation patterns of histone H3, along with analysis of mRNA encoding transcription factors, to identify the regulatory networks of peripheral IFN-γ-producing or IL-17-producing γδ T cell subsets in vivo. We found that CD27(+) γδ T cells were committed to the expression of Ifng but not Il17, whereas CD27(-) γδ T cells displayed permissive chromatin configurations at loci encoding both cytokines and their regulatory transcription factors and differentiated into cells that produced both IL-17 and IFN-γ in a tumor microenvironment.

Alves R.D., L.C. R, J.R. A, Fernandes M., Pinto J.V., L. P, Pawlicka A., R. M, Fortunato E., Bermudez V.D., M.M. S.  2013.  GelatinnZn(CF3SO3)2 Polymer Electrolytes for Electrochromic Devices. Electroanalysis. 25(6):1483-1490.
Franco, R, Pereira E.  2013.  Gold Nanoparticles and Proteins, Interactions. Encyclopedia of Metalloproteins. (Kretsinger, R.H., Uversky, V.N., Permyakov, E.A., Eds.).:908-915., New York: Springer Science+Business Media
Cerff, M, Scholz A, Franzreb M, Batalha IL, Roque ACA, Posten C.  2013.  In situ magnetic separation of antibody fragments from Escherichia coli in complex media. BMC biotechnology. 13(1):44. AbstractWebsite

Background
In situ magnetic separation (ISMS) has emerged as a powerful tool to overcome process constraints such as product degradation or inhibition of target production. In the present work, an integrated ISMS process was established for the production of his-tagged single chain fragment variable (scFv) D1.3 antibodies (?D1.3?) produced by E. coli in complex media. This study investigates the impact of ISMS on the overall product yield as well as its biocompatibility with the bioprocess when metal-chelate and triazine-functionalized magnetic beads were used.

Results
Both particle systems are well suited for separation of D1.3 during cultivation. While the triazine beads did not negatively impact the bioprocess, the application of metal-chelate particles caused leakage of divalent copper ions in the medium. After the ISMS step, elevated copper concentrations above 120?mg/L in the medium negatively influenced D1.3 production. Due to the stable nature of the model protein scFv D1.3 in the biosuspension, the application of ISMS could not increase the overall D1.3 yield as was shown by simulation and experiments.

Conclusions
We could demonstrate that triazine-functionalized beads are a suitable low-cost alternative to selectively adsorb D1.3 fragments, and measured maximum loads of 0.08?g D1.3 per g of beads. Although copper-loaded metal-chelate beads did adsorb his-tagged D1.3 well during cultivation, this particle system must be optimized by minimizing metal leakage from the beads in order to avoid negative inhibitory effects on growth of the microorganisms and target production. Hereby, other types of metal chelate complexes should be tested to demonstrate biocompatibility. Such optimized particle systems can be regarded as ISMS platform technology, especially for the production of antibodies and their fragments with low stability in the medium. The proposed model can be applied to design future ISMS experiments in order to maximize the overall product yield while the amount of particles being used is minimized as well as the number of required ISMS steps.

Coelho, C, Marangon J, Rodrigues D, Moura JJG, Romão MJ, Paes de Sousa PM, Correia dos Santos MM.  2013.  Induced peroxidase activity of haem containing nitrate reductases revealed by protein film electrochemistry. J Electroanal Chem. 693:105-113.
Paes de Sousa, PM, Grazina R, Barbosa ADS, de Castro B, Moura JJG, Cunha-Silva L, Salete S.  2013.  Insights into the electrochemical behaviour of composite materials: Monovacant polyoxometalates porous metal-organic framework. Electrochim Acta. 87:853-859.
Grazina, R, Pauleta S, Moura JJG, Moura I.  2013.  Iron-sulfur centers: New roles for ancient metal sites. Comprehensive Inorganic Chemistry II, Vol. 3: Bioinorganic Fundamentals and Applications: Metals in Natural Living Systems and Metals in Toxicology and Medicine. :103-148., Oxford: Elsevier
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
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
Pauleta, SR, Dell’Acqua S, Moura I.  2013.  Nitrous Oxide Reductase. Coord Chem Rev. 257:332-249.
Dell’Acqua, S, Pauleta SR, Moura I, Moura JG.  2013.  Nitrous Oxide Reductase. Encyclopedia of Metalloproteins - Copper. : Springer
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.

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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