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2015
Gouveia, JP, Seixas J, Shiming L, Bilo N, Valentim A.  2015.  Understanding electricity consumption patterns in households through data fusion of smart meters and door-to-door surveys, 1–6 June. eceee 2015 Summer Study on energy efficiency. , Club Belambra Les Criques, Presqu’île de Giens. Toulon/Hyères, France: ECEEE
Gouveia, JP, Seixas J, Mendes L, Shiming L.  2015.  Looking Deeper into Residential Electricity Consumption Profiles: The Case of Évora, 19-22 May. EEM15. 12th International Conference on the European Energy market. , Lisbon
Correia, H, Marangon J, Brondino CD, Moura JJG, Romao MJ, Gonzalez PJ, Santos-Silva T.  2015.  Aromatic aldehydes at the active site of aldehyde oxidoreductase from Desulfovibrio gigas: reactivity and molecular details of the enzyme-substrate and enzyme-product interaction. J Biol Inorg Chem. 20:219-229.
Seixas, J, Simões S, Dias L, Kanudia A, Fortes P, Gargiulo M.  2015.  Assessing the cost-effectiveness of electric vehicles in European countries using integrated modeling. Energy Policy. 80(May 2015):165-176. AbstractWebsite

Electric vehicles (EVs) are considered alternatives to internal combustion engines due to their energy efficiency and contribution to CO2 mitigation. The adoption of EVs depends on consumer preferences, including cost, social status and driving habits, although it is agreed that current and expected costs play a major role. We use a partial equilibrium model that minimizes total energy system costs to assess whether EVs can be a cost-effective option for the consumers of each EU27 member state up to 2050, focusing on the impact of different vehicle investment costs and CO2 mitigation targets. We found that for an EU-wide greenhouse gas emission reduction cap of 40% and 70% by 2050 vis-à-vis 1990 emissions, battery electric vehicles (BEVs) are cost-effective in the EU only by 2030 and only if their costs are 30% lower than currently expected. At the EU level, vehicle costs and the capability to deliver both short- and long-distance mobility are the main drivers of BEV deployment. Other drivers include each state’s national mobility patterns and the cost-effectiveness of alternative mitigation options, both in the transport sector, such as plug-in hybrid electric vehicles (PHEVs) or biofuels, and in other sectors, such as renewable electricity.

Fernandes, CSM, Gonçalves B, Sousa M, Martins DL, Barroso T, Pina AS, Peixoto C, Aguiar-Ricardo A, Roque ACA.  2015.  Biobased Monoliths for Adenovirus Purification. ACS Applied Materials & Interfaces. 7(12):6605-6612., Number 12 AbstractWebsite

Adenoviruses are important platforms for vaccine development and vectors for gene therapy, increasing the demand for high titers of purified viral preparations. Monoliths are macroporous supports regarded as ideal for the purification of macromolecular complexes, including viral particles. Although common monoliths are based on synthetic polymers as methacrylates, we explored the potential of biopolymers processed by clean technologies to produce monoliths for adenovirus purification. Such an approach enables the development of disposable and biodegradable matrices for bioprocessing. A total of 20 monoliths were produced from different biopolymers (chitosan, agarose, and dextran), employing two distinct temperatures during the freezing process (−20 °C and −80 °C). The morphological and physical properties of the structures were thoroughly characterized. The monoliths presenting higher robustness and permeability rates were further analyzed for the nonspecific binding of Adenovirus serotype 5 (Ad5) preparations. The matrices presenting lower nonspecific Ad5 binding were further functionalized with quaternary amine anion-exchange ligand glycidyltrimethylammonium chloride hydrochloride by two distinct methods, and their performance toward Ad5 purification was assessed. The monolith composed of chitosan and poly(vinyl) alcohol (50:50) prepared at −80 °C allowed 100% recovery of Ad5 particles bound to the support. This is the first report of the successful purification of adenovirus using monoliths obtained from biopolymers processed by clean technologies.

Echeverria, C, Aguirre LE, Merino EG, Almeida PL, Godinho MH.  2015.  Carbon Nanotubes as Reinforcement of Cellulose Liquid Crystalline Responsive Networks. ACS Appl Mater Interfaces. 7:21005-9., Number 38 AbstractWebsite

The incorporation of small amount of highly anisotropic nanoparticles into liquid crystalline hydroxypropylcellulose (LC-HPC) matrix improves its response when is exposed to humidity gradients due to an anisotropic increment of order in the structure. Dispersed nanoparticles give rise to faster order/disorder transitions when exposed to moisture as it is qualitatively observed and quantified by stress-time measurements. The presence of carbon nanotubes derives in a improvement of the mechanical properties of LC-HPC thin films.

Echeverria, C, Almeida PL, Feio G, Figueirinhas JL, Godinho MH.  2015.  A cellulosic liquid crystal pool for cellulose nanocrystals: Structure and molecular dynamics at high shear rates. European Polymer Journal. 72:72-81. AbstractWebsite

Cellulose and its derivatives, such as hydroxypropylcellulose (HPC) have been studied for a long time but they are still not well understood particularly in liquid crystalline solutions. These systems can be at the origin of networks with properties similar to liquid crystalline (LC) elastomers. The films produced from LC solutions can be manipulated by the action of moisture allowing for instance the development of a soft motor (Geng et al., 2013) driven by humidity. Cellulose nanocrystals (CNC), which combine cellulose properties with the specific characteristics of nanoscale materials, have been mainly studied for their potential as a reinforcing agent. Suspensions of CNC can also self-order originating a liquid-crystalline chiral nematic phases. Considering the liquid crystalline features that both LC-HPC and CNC can acquire, we prepared LC-HPC/CNC solutions with different CNC contents (1,2 and 5 wt.%). The effect of the CNC into the LC-HPC matrix was determined by coupling rheology and NMR spectroscopy - Rheo-NMR a technique tailored to analyse orientational order in sheared systems. (C) 2015 Elsevier Ltd. All rights reserved.

Monteiro, T, Rodrigues PR, Gonçalves AL, Moura JJG, Anorga L, Jubete E, Piknova B, Schechter AN, Silveira CM, Almeida MG.  2015.  Construction of effective disposable biosensors for point-of-care testing of nitrite. Talanta. 142:246-251.
Carvalho, A, Domingues I, Goncalves MC.  2015.  Core-shell superparamagnetic nanoparticles with interesting properties as contrast agents for MRI. Materials Chemistry and Physics. 168:42-49. AbstractWebsite

Core shell nanoparticles (NPs) formed by superparamagnetic iron oxide NPs (SPIONs) coated with inorganic or organically modified (ORMOSIL) sol gel silica exhibited promising properties as negative contrast agents (CA) for MRI applications. The potentiality of these new core shell NPs as negative CA for MRI is demonstrated and quantified. The longitudinal and transverse relaxivities of NPs with three different coating compositions were studied at a 7 T magnetic field: silica (TEOS), (3-aminopropyl) triethoxysilane (APTES) and (3-glycidoxypropyl) methyldiethoxysilane (GPTMS). Clearly, it was found that the core shell NPs efficiency as CA was strongly depend on the SPIONs coating. All the three core shell NPs studied presented a very small effect on the longitudinal relaxation time but a pronounced one on the transverse relaxation time, leading to a very high transverse longitudinal relaxivities ratio, decisive for their efficiency as negative CA for MRI The effect of the core shell NPs on the MRI contrast enhancement is obtained and quantified in a set of MRI of agar phantoms obtained at 7 T magnetic field and with a imaging gradient field of 1.6 T/m. The core shell NPs were tested in Zebra-fish (Danio rerio) animal model. Zebra-fish MRI were obtained with animals injected with the three core shell NPs and the contrast enhancement validated. (C) 2015 Elsevier B.V. All rights reserved.

Maiti, BK, Maia LB, Silveira C, Todorovic S, Carreira C, Carepo M, Grazina R, Moura I, Moura JJG.  2015.  Incorporation of molybdenum in rubredoxin: Models for mononuclear molybdenum enzymes. J Biol Inorg Chem. 20:821-829.
Carvalho, F, Atilano ML, Pombinho R, Covas G, Gallo RL, Filipe SR, Sousa S, Cabanes D.  2015.  L-Rhamnosylation of Listeria monocytogenes wall teichoic acids promotes resistance to antimicrobial peptides by delaying interaction with the membrane. PLoS Pathogens. 11:e1004919.
Nojima, T, Gomes T, Grosso AR, Kimura H, Dye M J, Dhir S, Carmo-fonseca M, Proudfoot N J.  2015.  Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing. Cell. 161:526–540., Number 3 AbstractWebsite

Transcription is a highly dynamic process. Consequently, we have developed native elongating transcript sequencing technology for mammalian chromatin (mNET-seq), which generates single-nucleotide resolution, nascent transcription profiles. Nascent RNA was detected in the active site of RNA polymerase II (Pol II) along with associated RNA processing intermediates. In particular, we detected 5'splice site cleavage by the spliceosome, showing that cleaved upstream exon transcripts are associated with Pol II CTD phosphorylated on the serine 5 position (S5P), which is accumulated over downstream exons. Also, depletion of termination factors substantially reduces Pol II pausing at gene ends, leading to termination defects. Notably, termination factors play an additional promoter role by restricting non-productive RNA synthesis in a Pol II CTD S2P-specific manner. Our results suggest that CTD phosphorylation patterns established for yeast transcription are significantly different in mammals. Taken together, mNET-seq provides dynamic and detailed snapshots of the complex events underlying transcription in mammals.

Moura, JJG, Bernhardt PV, Maia LB, Gonzalez PJ.  2015.  Molybdenum and tungsten enzymes: from biology to chemistry and back. J Biol Inorg Chem. 20:181-182.
Marques, AC, Santos L, Costa MN, Dantas JM, Duarte P, Gonçalves A, Martins R, Salgueiro CA, Fortunato E.  2015.  Office Paper Platform for Bioelectrochromic Detection of Electrochemically Active Bacteria using Tungsten Trioxide Nanoprobes. Sci. Rep. 5(9910) AbstractWebsite

Electrochemically active bacteria (EAB) have the capability to transfer electrons to cell exterior, a feature that is currently explored for important applications in bioremediation and biotechnology fields. However, the number of isolated and characterized EAB species is still very limited regarding their abundance in nature. Colorimetric detection has emerged recently as an attractive mean for fast identification and characterization of analytes based on the use of electrochromic materials. In this work, WO3 nanoparticles were synthesized by microwave assisted hydrothermal synthesis and used to impregnate non-treated regular office paper substrates. This allowed the production of a paper-based colorimetric sensor able to detect EAB in a simple, rapid, reliable, inexpensive and eco-friendly method. The developed platform was then tested with Geobacter sulfurreducens, as a proof of concept. G. sulfurreducens cells were detected at latent phase with an RGB ratio of 1.10 ± 0.04, and a response time of two hours.

Veigas, B, Pedrosa P, Carlos FF, Mancio-Silva L, Grosso AR, Fortunato E, Mota MM, Baptista PV.  2015.  One nanoprobe, two pathogens: gold nanoprobes multiplexing for point-of-care. Journal of Nanobiotechnology. 13:48., Number 1: BioMed Central AbstractWebsite

BACKGROUND:
Gold nanoparticles have been widely employed for biosensing purposes with remarkable efficacy for DNA detection. Amongst the proposed systems, colorimetric strategies based on the remarkable optical properties have provided for simple yet effective sequence discrimination with potential for molecular diagnostics at point of need. These systems may also been used for parallel detection of several targets to provide additional information on diagnostics of pathogens.
RESULTS:
For the first time, we demonstrate that a single Au-nanoprobe may provide for detection of two distinct targets (pathogens) allowing colorimetric multi-target detection. We demonstrate this concept by using one single gold-nanoprobe capable to detect members of the Mycobacterium tuberculosis complex and Plasmodium sp., the etiologic agents of tuberculosis and malaria, respectively. Following characterisation, the developed gold-nanoprobe allowed detection of either target in individual samples or in samples containing both DNA species with the same efficacy.
CONCLUSIONS:
Using one single probe via the non-cross-linking colorimetric methodology it is possible to identify multiple targets in one sample in one reaction. This proof-of-concept approach may easily be integrated into sensing platforms allowing for fast and simple multiplexing of Au-nanoprobe based detection at point-of-need.

Greene, NG, Narciso AR, Filipe SR, Camilli A.  2015.  Peptidoglycan branched stem peptides contribute to Streptococcus pneumoniae virulence by inhibiting pneumolysin release. PLoS Pathogens. 11:e1004996.
Cerqueira, N, Gonzalez PJ, Fernandes PA, Moura JJG, Ramos MJ.  2015.  Periplasmic nitrate reductase and formate dehydrogenase: similar molecular architectures with very different enzymatic activities. Acc Chem Res. 48:2875−2884.
Grosso, AR, Leite AP, Carvalho S, Matos MR, Martins FB, Vítor AC, Desterro JM, Carmo-fonseca M, de Almeida SF.  2015.  Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma. eLife. 4:e09214. AbstractWebsite

Aberrant expression of cancer genes and non-canonical RNA species is a hallmark of cancer. However, the mechanisms driving such atypical gene expression programs are incompletely understood. Here, our transcriptional profiling of a cohort of 50 primary clear cell renal cell carcinoma (ccRCC) samples from The Cancer Genome Atlas (TCGA) reveals that transcription read-through beyond the termination site is a source of transcriptome diversity in cancer cells. Amongst the genes most frequently mutated in ccRCC, we identified SETD2 inactivation as a potent enhancer of transcription read-through. We further show that invasion of neighbouring genes and generation of RNA chimeras are functional outcomes of transcription read-through. We identified the BCL2 oncogene as one of such invaded genes and detected a novel chimera, the CTSC-RAB38, in 20% of ccRCC samples. Collectively, our data highlight a novel link between transcription read-through and aberrant expression of oncogenes and chimeric transcripts that is prevalent in cancer.

Cavique, M, Flores J, Amado MP, Gonçalves-Coelho A, Mourão A.  2015.  A preliminary check of the refurbishing large office buildings to a zero energy condition. Procedia CIRP. 34(DOI: 10.1016/j.procir.2015.07.054):193-198.
Contreras, J, Tornero J, Ferreira I, Martins R, Gomes L, Fortunato E.  2015.  Simulated and Real Sheet-of-Light 3D Object Scanning Using a-Si:H Thin Film PSD Arrays. Sensors. 15(12):29938-29949. Abstract

A MATLAB/SIMULINK software simulation model (structure and component blocks) has been constructed in order to view and analyze the potential of the PSD (Position Sensitive Detector) array concept technology before it is further expanded or developed. This simulation allows changing most of its parameters, such as the number of elements in the PSD array, the direction of vision, the viewing/scanning angle, the object rotation, translation, sample/scan/simulation time, etc. In addition, results show for the first time the possibility of scanning an object in 3D when using an a-Si:H thin film 128 PSD array sensor and hardware/software system. Moreover, this sensor technology is able to perform these scans and render 3D objects at high speeds and high resolutions when using a sheet-of-light laser within a triangulation platform. As shown by the simulation, a substantial enhancement in 3D object profile image quality and realism can be achieved by increasing the number of elements of the PSD array sensor as well as by achieving an optimal position response from the sensor since clearly the definition of the 3D object profile depends on the correct and accurate position response of each detector as well as on the size of the PSD array.

Gonçalves, L, Santos Z, Amado MP, Craveiro I, Cabral J, Lapão L, Alves D, Simões R.  2015.  Urban Planning and Health Inequities: looking in a small-scale in a City of Cape Verde. PlosOne Journal. (DOI: 10.1371/journal.pone.0142955): DOI: 10.1371/journal.pone.0142955
Correia, HD, Marangon J, Brondino CD, Moura JJG, Romao MJ, Gonzalez PJ, Santos-Silva T.  2015.  Aromatic aldehydes at the active site of aldehyde oxidoreductase from Desulfovibrio gigas: reactivity and molecular details of the enzyme-substrate and enzyme-product interaction. Journal of Biological Inorganic Chemistry. 20:219-229., Number 2 AbstractWebsite

Desulfovibrio gigas aldehyde oxidoreductase (DgAOR) is a mononuclear molybdenum-containing enzyme from the xanthine oxidase (XO) family, a group of enzymes capable of catalyzing the oxidative hydroxylation of aldehydes and heterocyclic compounds. The kinetic studies reported in this work showed that DgAOR catalyzes the oxidative hydroxylation of aromatic aldehydes, but not heterocyclic compounds. NMR spectroscopy studies using C-13-labeled benzaldehyde confirmed that DgAOR catalyzes the conversion of aldehydes to the respective carboxylic acids. Steady-state kinetics in solution showed that high concentrations of the aromatic aldehydes produce substrate inhibition and in the case of 3-phenyl propionaldehyde a suicide substrate behavior. Hydroxyl-substituted aromatic aldehydes present none of these behaviors but the kinetic parameters are largely affected by the position of the OH group. High-resolution crystallographic structures obtained from single crystals of active-DgAOR soaked with benzaldehyde showed that the side chains of Phe(425) and Tyr(535) are important for the stabilization of the substrate in the active site. On the other hand, the X-ray data of DgAOR soaked with trans-cinnamaldehyde showed a cinnamic acid molecule in the substrate channel. The X-ray data of DgAOR soaked with 3-phenyl propionaldehyde showed clearly how high substrate concentrations inactivate the enzyme by binding covalently at the surface of the enzyme and blocking the substrate channel. The different reactivity of DgAOR versus aldehyde oxidase and XO towards aromatic aldehydes and N-heterocyclic compounds is explained on the basis of the present kinetic and structural data.

Seixas, JD, Santos MFA, Mukhopadhyay A, Coelho AC, Reis PM, Veiros LF, Marques AR, Penacho N, Goncalves AML, Romao MJ, Bernardes GJL, Santos-Silva T, Romao CC.  2015.  A contribution to the rational design of Ru(CO)(3)Cl2L complexes for in vivo delivery of CO. Dalton Transactions. 44:5058-5075., Number 11 AbstractWebsite

A few ruthenium based metal carbonyl complexes, e.g. CORM-2 and CORM-3, have therapeutic activity attributed to their ability to deliver CO to biological targets. In this work, a series of related complexes with the formula [Ru(CO)(3)Cl2L] (L = DMSO (3), L-H3CSO(CH2)(2)CH(NH2)CO2H) (6a); D,L-H3CSO(CH2)(2)CH-(NH2)CO2H (6b); 3-NC5H4(CH2)(2)SO3.Na (7); 4-NC5H4(CH2)(2)SO3Na (8); PTA (9); DAPTA (10); H3CS-(CH2)(2)CH(OH) CO2H (11); CNCMe2CO2Me (12); CNCMeEtCO2Me (13); CN(c-C3H4)CO2Et) (14)) were designed, synthesized and studied. The effects of L on their stability, CO release profile, cytotoxicity and anti-inflammatory properties are described. The stability in aqueous solution depends on the nature of L as shown using HPLC and LC-MS studies. The isocyanide derivatives are the least stable complexes, and the S-bound methionine oxide derivative is the more stable one. The complexes do not release CO gas to the headspace, but release CO2 instead. X-ray diffraction of crystals of the model protein Hen Egg White Lysozyme soaked with 6b (4UWN) and 8 (4UWV) shows the addition of Ru-II(CO)(H2O)(4) at the His15 binding site. Soakings with 7 (4UWU) produced the metallacarboxylate [Ru(COOH)(CO)(H2O)(3)](+) bound to the His15 site. The aqueous chemistry of these complexes is governed by the water-gas shift reaction initiated with the nucleophilic attack of HO- on coordinated CO. DFT calculations show this addition to be essentially barrierless. The complexes have low cytotoxicity and low hemolytic indices. Following i.v. administration of CORM-3, the in vivo bio-distribution of CO differs from that obtained with CO inhalation or with heme oxygenase stimulation. A mechanism for CO transport and delivery from these complexes is proposed.

Glynn, J, Fortes P, Krook-Riekkola A, Labriet M, Vielle M, Kypreos S, Lehtilä A, Mischke P, Dai H, Gargiulo M, Helgesen PI, Kober T, Summerton P, Merven B, Selosse S, Karlsson K, Strachan N, ÓGallachóir B.  2015.  Economic Impacts of Future Changes in the Energy System—Global Perspectives. Informing Energy and Climate Policies Using Energy Systems Models. 30(George Giannakidis, Labriet, Maryse, Brian ÓGallachóir, GianCarlo Tosato, Eds.).:333-358.: Springer International Publishing Abstract
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