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2014
Silva, M, Figueiredo AM, Cabrita EJ.  2014.  Epitope mapping of imidazolium cation in ionic liquid-protein interactions unveils the balance between hydrophobicity and electrostatics towards protein destabilisation. Physical Chemistry Chemical Physics. in press Abstract

We investigated imidazolium-based ionic liquid (IL) interactions with human serum albumin (HSA) to discern the level of cation interactions towards protein stability. STD-NMR spectroscopy was used to observe the imidazolium ILs protons involved in direct binding and to identify the interactions responsible for changes in Tm as accessed by differential scanning calorimetry (DSC). Cations influence protein stability less than anions but still significantly. It was found that longer alkyl side chains of imidazolium-based ILs (more hydrophobic) are associated with a higher destabilisation effect on HSA than short-alkyl groups (less hydrophobic). The reason for such destabilisation lies on the increase surface contact area of the cation with the protein, particularly on the hydrophobic contacts promoted by the terminus of the alkyl chain. The relevance of the hydrophobic contacts is clearly demonstrated by the introduction of a polar moiety in the alkyl chain: a methoxy or alcohol group. Such structural modification reduces the degree of hydrophobic contacts with HSA explaining the lesser extent of protein destabilisation when compared to longer alkyl side chain groups: above [C2mim]+. Competition STD-NMR experiments using [C2mim]+, [C4mim]+ and [C2OHmim]+ also validate the importance of the hydrophobic interactions. The combined effect of cation and anion interactions was explored using 35Cl NMR. Such experiments show that the nature of the cation has no influence in the anion-protein contacts, still the nature of the anion modulates the cation-protein interaction. Herein we propose that more destabilising anions are likely to be a result of a partial contribution from the cation as a direct consequence of the different levels of interaction (cation-anion pair and cation-protein).

Dantas, JM, Morgado L, Catarino T, Kokhan O, Pokkuluri PR, Salgueiro CA.  2014.  Evidence for interaction between the triheme cytochrome PpcA from Geobacter sulfurreducens and anthrahydroquinone-2,6-disulfonate, an analog of the redox active components of humic substances. Biochim Biophys Acta. 1837(6):750-760. AbstractWebsite

The bacterium Geobacter sulfurreducens displays an extraordinary respiratory versatility underpinning the diversity of electron donors and acceptors that can be used to sustain anaerobic growth. Remarkably, G. sulfurreducens can also use as electron donors the reduced forms of some acceptors, such as the humic substance analog anthraquinone-2,6-disulfonate (AQDS), a feature that confers environmentally competitive advantages to the organism. Using UV-visible and stopped-flow kinetic measurements we demonstrate that there is electron exchange between the triheme cytochrome PpcA from Gs and AQDS. 2D-(1)H-(15)N HSQC NMR spectra were recorded for (15)N-enriched PpcA samples, in the absence and presence of AQDS. Chemical shift perturbation measurements, at increasing concentration of AQDS, were used to probe the interaction region and to measure the binding affinity of the PpcA-AQDS complex. The perturbations on the NMR signals corresponding to the PpcA backbone NH and heme substituents showed that the region around heme IV interacts with AQDS through the formation of a complex with a definite life time in the NMR time scale. The comparison of the NMR data obtained for PpcA in the presence and absence of AQDS showed that the interaction is reversible. Overall, this study provides for the first time a clear illustration of the formation of an electron transfer complex between AQDS and a G. sulfurreducens triheme cytochrome, shedding light on the electron transfer pathways underlying the microbial oxidation of humics.

Sequeira, SO, Cabrita EJ, Macedo MF.  2014.  Fungal Biodeterioration of Paper: How are Paper and Book Conservators Dealing with it? An International Survey Restaurator. International Journal for the Preservation of Library and Archival Material. 35(2):181–199. Abstract

Paper biodeterioration by fungi has always been a concern in archives, libraries and museums. Several guidelines have been published regarding the prevention of fungal development in paper collections and recovery of affected objects, but what is actually being implemented from the literature by worldwide paper and book conservators? How common is this type of biodeterioration? What needs to be further studied? In order to access this information we conducted an online international questionnaire with participants from 20 different countries. The results show that fungal biodeterioration is highly common in paper collections. All of the respondents already had to deal with paper deteriorated by fungi, and although the vast majority uses active measures to prevent fungal development, most of them have already experienced active fungal infestations. The mainly used preventive measures are the ones concerned with the control of the environmental conditions in storage and display rooms. Drying the affected paper objects and applying 70% ethanol are the most preferred options to stop active fungal growth. The study of non-toxic and safer antifungals is considered here as the most relevant research topic in the area of paper biodeterioration by fungi, meaning that the options currently available are not totally satisfactory.

de Almeida, MP, Pereira E, Baptista P, Gomes I, Figueiredo S, Soares L, Franco R.  2014.  Gold Nanoparticles as (bio)chemical Sensors. Comprehensive Analytical Chemistry; Gold Nanoparticles in Analytical Chemistry . (Valcárcel, M., López-Lorente, A.I., Eds.).:529–567., Amsterdam: Elsevier
Conde, J, Larguinho M, Cordeiro A, Raposo LR, Costa PM, Santos S, Diniz MS, Fernandes AR, Baptista PV.  2014.  Gold-nanobeacons for gene therapy: evaluation of genotoxicity, cell toxicity and proteome profiling analysis. Nanotoxicology. 8(5):521-32.14condenantox.pdf14condenantoxsuppl.pdf
Brás, AR, Fonseca IM, Dionísio M, Schonhals A, Affouard F, Correia NT.  2014.  Influence of Nanoscale Confinement on the Molecular Mobility of Ibuprofen. The Journal of Physical Chemistry C. 118(25):13857–13868.Website
Luis, DV, Silva J, Tomaz AI, de Almeida RF, Larguinho M, Baptista PV, Martins LM, Silva TF, Borralho PM, Rodrigues CM, Rodrigues AS, Pombeiro AJ, Fernandes AR.  2014.  Insights into the mechanisms underlying the antiproliferative potential of a Co(II) coordination compound bearing 1,10-phenanthroline-5,6-dione: DNA and protein interaction studies. J Biol Inorg Chem. 19(6):787-803.14luisjbic.pdf
Gouveia, JP, Bilo N, Gargiulo M, Giannakidis G, Gregório V, Duncan I, Nunes V, Robinson D, Seixas J, Valentim A.  2014.  InSMART - Integrative Smart City Planning - The case of Households in Évora. Urban Futures Squaring Circles: Proceedings, International Conference on Urban Futures Squaring Circles 2050,. , Calouste Gulbenkian Foundation: Institute of Social Sciences of the University of Lisbon and Calouste Gulbenkian Foundation Abstract

European policy has acknowledged the significance of local and regional communities for the
deployment of new low carbon technologies and their potential for sustainable energy production and use.
Several initiatives and programmes (e.g. Covenant of Mayors) have been set up to engage European cities in the
effort towards a low carbon future. At the same time, there is a critical need to improve comprehensive city
planning driven by an integrated approach and focused on cost benefit assessment towards sustainable energy
use. Hence, innovative tools and models to assess and perform in-depth analysis of the alternative measures
towards efficient energy use, will help pave the way to fully capture the potential of each city in the most
efficient (economically, socially and technically) way.
The InSMART concept brings together four European cities: Évora (Portugal), Cesena (Italy), Nottingham (UK)
and Trikala (Greece), and scientific organizations of these countries, to establish a methodology for enhancing
sustainable planning for city needs through an integrative and multidisciplinary planning approach, aiming to
developing detailed sustainable energy action plans. Such an approach will identify the optimum mix of short,
medium and long term projects and investments, addressing the efficiency of energy flows across various city
sectors with regards to economic, environmental and social criteria and will highlight priority actions.
Tools and models, like Geographic Information System, buildings models (CitySim and EnergyPlus) and
transport-based energy and carbon model, as well as a technological partial equilibrium energy model (TIMES),
are used to analyse, all the relevant sectors (buildings, industries, transports, waste and water management).
Furthermore, the cities buildings stocks are being characterized through an extensive 110-question survey
(around 410 door-to-door interviews) and will be modelled through a typology approach. Four hundred 20-
question surveys are also being carried out to evaluate transport and mobility patterns, supported on travel diaries and fulfilling different quotas for several variables (geographic location, days of the week, age and working
status) in order to assure representativeness of the data collected.
The main differences between rural and urban areas results from the building surveys and high-resolution
electricity consumption from smart meters for the Portuguese city of Évora are highlighted.

Fortes, P, Pereira R, Pereira A, Seixas J.  2014.  Integrated technological-economic modeling platform for energy and climate policy analysis. Energy. 73:716–730.: Elsevier Ltd AbstractWebsite

CGE (computable general equilibrium) and bottom-up models each have unique strengths and weakness in evaluating energy and climate policies. This paper describes the development of an integrated technological, economic modeling platform (HYBTEP), built through the soft-link between the bottom-up TIMES (The Integrated MARKAL-EFOM system) and the CGE GEM-E3 models. HYBTEP combines cost minimizing energy technology choices with macroeconomic responses, which is essential for energy-climate policy assessment. HYBTEP advances on other hybrid tools by assuming 'full-form' models, integrating detailed and extensive technology data with disaggregated economic structure, and 'full-link', i.e., covering all economic sectors. Using Portugal as a case study, we examine three scenarios: (i) the current energy-climate policy, (ii) a CO2 tax, and (iii) renewable energy subsidy, with the objective of assessing the advantages of HYBTEP vis-à-vis bottom-up approach. Results show that the economic framework in HYBTEP partially offsets the increase or decrease in energy costs from the policy scenarios, while TIMES is very sensitive to energy services-price elasticities, setting a wide range of results. HYBTEP allows the computation of the economic impacts of policies in a technological detailed environment. The hybrid platform increases transparency of policy analysis by making explicit the mechanisms through which energy demand evolves, resulting in high confidence for decision-making. © 2014 Elsevier Ltd.

Figueiredo, S, Cabral R, Luis D, Fernandes AR, Baptista PV.  2014.  Integration of Gold nanoparticles and liposomes for combined anti-cancer drug delivery. Nanomedicine. (Alexander Seifalian, Achala de Mel, Deepak M. Kalaskar, Eds.)., Manchester: One Central Press (OCP)conjugation_of_gold_nanoparticles_and_liposomes_for_combined_vehicles_of_drug_delivery_in_cancer.pdf
Gouveia, JP, Seixas J, Bilo N, Valentim A, Nunes V, Giannakidis G, Robinson D, Irons D, Gargiulo M.  2014.  Integrative Smart City Planning - Buildings and Mobility in Évora. 4th IAEE European Energy Conference - Sustainable Energy Policy and Strategies for Europe. , LUISS University, Rome, Italy.
Sanguino P, Monteiro T, Marques F, Dias CJ, Igreja R, Franco R.  2014.  INTERDIGITATED CAPACITIVE IMMUNOSENSORS WITH PVDF IMMOBILIZATION LAYERS. IEEE SENSORS JOURNAL. 14(4):1260-1265.
Soares L, Csáki A, Fritzsche W, Orfeu F, Franco R, Pereira E.  2014.  LOCALIZED SURFACE PLASMON RESONANCE (LSPR) BIOSENSING USING GOLD NANOTRIANGLES: DETECTION OF DNA HYBRIDIZATION EVENTS AT ROOM-TEMPERATURE. Analyst. 139:4964-4973.
Costa, Veigas, Bruno, Jacob, Jorge M., Santos, GMC, Santos, GMC, Baptista, Ana Catarina, Martins, Inacio, Joao, Fortunato E.  2014.  A low cost, safe, disposable, rapid and self-sustainable paper-based platform for diagnostic testing: lab-on-paper. Nanotechnology. 25(9):12pp..
Loureiro, J, Santos JR, Nogueira A, Wyczisk F, Divay L, Reparaz S, Alzina F, Torres CMS, Cuffe J, Montemor F, Martins R, Ferreira I.  2014.  Nanostructured p-type Cr/V2O5 thin films with boosted thermoelectric properties. J. Mater. Chem. A. 2(18):6456-6462. AbstractWebsite

The urgent need for non-toxic and abundant thermoelectric materials has become a significant motivation to improve the figures of merit of metal oxides in order to remove the barrier towards their widespread use for thermoelectric applications. Here we show the influence of a Cr layer in boosting the thermoelectric properties of vanadium pentoxide (V2O5) thin films, deposited by thermal evaporation and annealed at 500 °C. The Cr to V2O5 thickness ratio controls the morphological and thermoelectric properties of the thin films produced. The optimized Seebeck coefficient and power factor values at room temperature are +50 μV K−1 and 7.9 × 10−4 W m−1 K−2, respectively. The nanograin structure of the films is responsible for an improvement in the electrical conductivity up to 3 × 105 (Ω m)−1 with a typical thermal conductivity of 1.5 W m−1 K−1. These results combine to yield promising p-type thermoeletric CrV2O5 thin films with a ZT of 0.16 at room temperature.

Silveira, CM, Almeida MG, Moura JJG.  2014.  Nitrite biosensing - Electrochemical biosensors based on cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. , ISBN 978-3-659-10593-7: Lambert Academic Publishing (ISBN 978-3-659-10593-7)
Bird, LJ, Saraiva IH, Park S, Calçada EO, Salgueiro CA, Nitschke W, Louro RO, Newman DK.  2014.  Nonredundant roles for cytochrome c2 and two high-potential iron-sulfur proteins in the photoferrotroph Rhodopseudomonas palustris TIE-1. J Bacteriol. 196(4):850-858. AbstractWebsite

The purple bacterium Rhodopseudomonas palustris TIE-1 expresses multiple small high-potential redox proteins during photoautotrophic growth, including two high-potential iron-sulfur proteins (HiPIPs) (PioC and Rpal_4085) and a cytochrome c2. We evaluated the role of these proteins in TIE-1 through genetic, physiological, and biochemical analyses. Deleting the gene encoding cytochrome c2 resulted in a loss of photosynthetic ability by TIE-1, indicating that this protein cannot be replaced by either HiPIP in cyclic electron flow. PioC was previously implicated in photoferrotrophy, an unusual form of photosynthesis in which reducing power is provided through ferrous iron oxidation. Using cyclic voltammetry (CV), electron paramagnetic resonance (EPR) spectroscopy, and flash-induced spectrometry, we show that PioC has a midpoint potential of 450 mV, contains all the typical features of a HiPIP, and can reduce the reaction centers of membrane suspensions in a light-dependent manner at a much lower rate than cytochrome c2. These data support the hypothesis that PioC linearly transfers electrons from iron, while cytochrome c2 is required for cyclic electron flow. Rpal_4085, despite having spectroscopic characteristics and a reduction potential similar to those of PioC, is unable to reduce the reaction center. Rpal_4085 is upregulated by the divalent metals Fe(II), Ni(II), and Co(II), suggesting that it might play a role in sensing or oxidizing metals in the periplasm. Taken together, our results suggest that these three small electron transfer proteins perform different functions in the cell.

Maiti, BK, Maia LB, Pal K, Pakira B, Aviles T, Moura I, Pauleta SR, Nuñez JL, Rizzi AC, Brondino CD, Sarkar S, Moura JJG.  2014.  One Electron Reduced Square Planar Bis(benzene-1,2-dithiolato) Copper Dianionic Complex and Redox Switch by O2/HO-. Inorg Chem. 53:12799-12808.
Santos, S, Freitas AT, Fernandes AR.  2014.  Overview of HCM genomics and transcriptomics: molecular tools in HCM assessment for application in clinical medicine. Cardiovascular Disease II. , Hong Kong: iConcept Press Ltd.overview_of_hypertrophic_cardiomyopathy.pdf
Sousa, D, Lourenço JM, Ferreira C, Dias RJ.  2014.  Preventing Atomicity Violations with Contracts. , Number UNL-2014: Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Abstract2014-sousa.pdf

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Dantas, JM, Morgado L, Marques AC, Salgueiro CA.  2014.  Probing the effect of ionic strength on the functional robustness of the triheme cytochrome PpcA from Geobacter sulfurreducens: a contribution for optimizing biofuel cell's power density. J Phys Chem B. 118(43):12416-12425. AbstractWebsite

The increase of conductivity of electrolytes favors the current production in microbial fuel cells (MFCs). Adaptation of cell cultures to higher ionic strength is a promising strategy to increase electricity production. The bacterium Geobacter sulfurreducens is considered a leading candidate for MFCs. Therefore, it is important to evaluate the impact of the ionic strength on the functional properties of key periplasmic proteins that warrants electron transfer to cell exterior. The effect of the ionic strength on the functional properties of triheme cytochrome PpcA, the most abundant periplasmic cytochrome in G. sulfurreducens, was investigated by NMR and potentiometric methods. The redox properties of heme IV are the most affected ones. Chemical shift perturbation measurements on the backbone NMR signals, at increasing ionic strength, also showed that the region close to heme IV is the most affected due to the large number of positively charged residues, which confer a highly positive electrostatic surface around this heme. The shielding of these positive charges at high ionic strength explain the observed decrease in the reduction potential of heme IV and shows that PpcA was designed to maintain its functional mechanistic features even at high ionic strength.

Sampaio, JM, Madeira TI, Parente F, Indelicato P.  2014.  Relativistic calculations of M-shell photoionization and X-ray production cross-sections for Hg at 5.96 keV excitation energy. Radiation Physics and Chemistry. AbstractWebsite

In this work we calculate photoionization and X-ray production cross-sections (XPCS) of M-shell vacancies in Hg at incident photon energy of 5.96 keV (low.

Simoes, S, Seixas J, Fortes P, Huppes G.  2014.  The savings of energy saving: Interactions between energy supply and demand-side options-quantification for Portugal. Energy Efficiency. 7:179–201. Abstract

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Teixeira, SS, Graça MPF, Dionísio M, Ilcikova M, Mosnacek J, Spitalsky Z, Krupa I, Costa LC.  2014.  Self-standing elastomeric composites based on lithium ferrites and their dielectric behavior. Journal of Applied Physics. 116:224102(1-8).Website
Fernandes, DM, Granadeiro CM, de M. PSP, Grazina R, Moura JJG, Silva P, Almeida Paz FA, Cunha-Silva L, Balula SS, Freire C.  2014.  SiW11Fe@MIL-101(Cr) composite: A novel and versatile electrocatalyst. ChemElectroChem. 1:1293-1300.