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2009
Kladova, AV, Gavel YO, Mukhopaadhyay A, Boer DR, Teixeira S, Shnyrov VL, Moura I, Moura JJG, Romao MJ, Trincao J, Bursakov SA.  2009.  Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacterium Desulfovibrio gigas: purification, crystallization and preliminary X-ray diffraction analysis. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 65:926-929. AbstractWebsite
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Antunes, R, Coito FV.  2009.  A Cognitive Model for Frequency Signal Classification. International Journal of Mathematical, Physical and Engineering Sciences. 3:240–245., Number 4: Citeseer Abstract

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Figueirinhas, JL, Cruz C, Feio G, Mehl GH.  2009.  Collective Modes and Biaxial Ordering Observed by Deuterium NMR in the Nematic Phases of an Organosiloxane Tetrapode. Molecular Crystals and Liquid Crystals. 510:158-174. AbstractWebsite

Calculations of deuterium NMR spectra were performed using a model of slow motions based on the collective modes present in liquid crystalline systems and evaluated within the Landau de Gennes free energy expansion on the order parameter tensor. Simulations obtained with this model are applied to the case of deuterium NMR spectra collected in static and rotating samples of organosiloxane tetrapodes exhibiting uniaxial and biaxial nematic phases. The analysis of the slow motions influence on deuterium NMR spectra shows that molecular motions within a time-scale of the order of magnitude of NMR observation times are particularly effective on modulating the NMR line-shape in the case of the liquid crystalline system investigated.

Ortigueira, M.  2009.  Comments on ?Modeling fractional stochastic systems as non-random fractional dynamics driven Brownian motions? Applied Mathematical Modelling. 33:2534–2537., Number 5: Elsevier Inc. AbstractWebsite

Some results presented in the paper ?Modeling fractional stochastic systems as non-random fractional dynamics driven Brownian motions? ?I. Podlubny, Fractional Differential Equations, Academic Press, San Diego, 1999? are discussed in this paper. The slightly modified Grünwald-Letnikov derivative proposed there is used to deduce some interesting results that are in contradiction with those proposed in the referred paper.

Ortigueira, MD.  2009.  Comments on ?Modeling fractional stochastic systems as non-random fractional dynamics driven Brownian motions? Applied Mathematical Modelling. 33:2534–2537., Number 5 AbstractWebsite

Some results presented in the paper ?Modeling fractional stochastic systems as non-random fractional dynamics driven Brownian motions? ?I. Podlubny, Fractional Differential Equations, Academic Press, San Diego, 1999? are discussed in this paper. The slightly modified Grünwald-Letnikov derivative proposed there is used to deduce some interesting results that are in contradiction with those proposed in the referred paper. Keywords: Fractional calculus; Grünwald-Letnikov derivative; Fractional Brownian motion

Monteiro, B, Balula SS, Gago S, Grosso C, Figueiredo S, Lopes AD, Valente AA, Pillinger M, Lourenco JP, Goncalves IS.  2009.  Comparison of liquid-phase olefin epoxidation catalysed by dichlorobis-(dimethylformamide)dioxomolybdenum(VI) in homogeneous phase and grafted onto MCM-41. Journal of Molecular Catalysis a-Chemical. 297:110-117., Number 2 AbstractWebsite
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Najmudin, S, Bonifacio C, Duarte AG, Pualeta SR, Moura I, Moura JJG, Romao MJ.  2009.  Crystallization and crystallographic analysis of the apo form of the orange protein (ORP) from Desulfovibrio gigas. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 65:730-732. AbstractWebsite
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Najmudin, S, Bonifacio C, Duarte AG, Pauleta SR, Moura I, Moura JJG, Romao MJ.  2009.  Crystallization and crystallographic analysis of the apo form of the orange protein (ORP) from Desulfovibrio gigas. (vol F65, pg 730, 2009). Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 65:856-856. AbstractWebsite
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2008
Costa, VM, Ferreira LM, Branco PS, Carvalho F, Bastos ML, Carvalho RA, Carvalho M, Remiao F.  2008.  Characterization of adrenaline and adrenaline-GSH adduct transport in freshly isolated rat cardiomyocytes, OCT 5. TOXICOLOGY LETTERS. 180:S99., Number 1: European Soc Toxicol Abstract
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Tavares, {JRRF}, Baptista {PMRV}, Doria {GMRPDF}, Flores {AODL}.  2008.  Colorimetric method and kit for the detection of specific nucleic acid sequences using metal nanoparticles functionalized with modified oligonucleotides, nov. Abstract

The present invention relates to a colorimetric method for the detection of specific nucleic acids sequences, including mutations or single nucleotide polymorphisms within nucleic acid sequences, through the aggregation of nanoparticles functionalized with modified oligonucleotides, induced by an increase of the medium's ionic strength. Another aspect of the present invention relates with the development of a kit based on the method of the present invention, allowing for a quick and easy detection of specific nucleic acids sequences, including mutations or single nucleotide polymorphisms within nucleic acid sequences.

Silva, {LB }, Baptista P, Raniero L, c}alo Doria G{\c, de Martins {RFP}, Fortunato {EMC}.  2008.  Characterization of optoelectronic platform using an amorphous/nanocrystalline silicon biosensor for the specific identification of nucleic acid sequences based on gold nanoparticle probes, jun. Sensors and Actuators B: Chemical. 132:508–511., Number 2: Elsevier Abstract
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Abrantes, P, Dimopoulos G, Grosso AR, do Rosário VE, Silveira H.  2008.  Chloroquine mediated modulation of Anopheles gambiae gene expression. PloS one. 3:e2587., Number 7 AbstractWebsite

BACKGROUND:
Plasmodium development in the mosquito is crucial for malaria transmission and depends on the parasite's interaction with a variety of cell types and specific mosquito factors that have both positive and negative effects on infection. Whereas the defensive response of the mosquito contributes to a decrease in parasite numbers during these stages, some components of the blood meal are known to favor infection, potentiating the risk of increased transmission. The presence of the antimalarial drug chloroquine in the mosquito's blood meal has been associated with an increase in Plasmodium infectivity for the mosquito, which is possibly caused by chloroquine interfering with the capacity of the mosquito to defend against the infection.
METHODOLOGY/PRINCIPAL FINDINGS:
In this study, we report a detailed survey of the Anopheles gambiae genes that are differentially regulated by the presence of chloroquine in the blood meal, using an A. gambiae cDNA microarray. The effect of chloroquine on transcript abundance was evaluated separately for non-infected and Plasmodium berghei-infected mosquitoes. Chloroquine was found to affect the abundance of transcripts that encode proteins involved in a variety of processes, including immunity, apoptosis, cytoskeleton and the response to oxidative stress. This pattern of differential gene expression may explain the weakened mosquito defense response which accounts for the increased infectivity observed in chloroquine-treated mosquitoes.
CONCLUSIONS/SIGNIFICANCE:
The results of the present study suggest that chloroquine can interfere with several putative mosquito mechanisms of defense against Plasmodium at the level of gene expression and highlight the need for a better understanding of the impacts of antimalarial agents on parasite transmission.

Brás, AR, Dionísio M, Schoenhals A.  2008.  Confinement and Surface Effects on the Molecular Dynamics of a Nematic Mixture Investigated by Dielectric Relaxation Spectroscop. The Journal of Physical Chemistry B. 112:8227–8235.Website
Simões, S, Cleto J, Fortes P, Seixas J, Huppes G.  2008.  Cost of energy and environmental policy in Portuguese CO2 abatement—scenario analysis to 2020. Energy Policy. 36:3598–3611., Number 9 AbstractWebsite

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Kulkarni, PS, Branco LC, Crespo JG, Afonso CAM.  2008.  Capture of Dioxins by ionic liquids. Environmental Science & Technology. 42:2570-2574., Number 7 AbstractWebsite
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Feio, G, Figueirinhas JL, Tajbakhsh AR, Terentjev EM.  2008.  Critical fluctuations and random-anisotropy glass transition in nematic elastomers. Physical Review B. 78, Number 2 AbstractWebsite

We carry out a detailed deuterium nuclear magnetic resonance (NMR) study of local nematic ordering in polydomain nematic elastomers. This system has a close analogy to the random-anisotropy spin glass. We find that, in spite of the quadrupolar nematic symmetry in three dimensions requiring a first-order transition, the order parameter in the quenched "nematic glass" emerges via a continuous phase transition. In addition to this remarkable effect, by a careful analysis of the NMR line shape, we deduce that the local director fluctuations grow in a critical manner around the transition point. This could become an essential experimental evidence for the quenched disorder changing the order of discontinuous transition.

2007
Fisher, K, Lowe DJ, Tavares P, Pereira AS, Huynh BH, Edmondson D, Newton WE.  2007.  Conformations generated during turnover of the Azotobacter vinelandii nitrogenase MoFe protein and their relationship to physiological function, Nov. Journal Of Inorganic Biochemistry. {101}:{1649-1656}., Number {11-12} Abstract

Various S = 3/2 EPR signals elicited from wild-type and variant Azotobacter vinelandii nitrogenase MoFe proteins appear to reflect different conformations assumed by the FeMo-cofactor with different protonation states. To determine whether these presumed changes in protonation and conformation reflect catalytic capacity, the responses (particularly to changes in electron flux) of the alpha H195Q, alpha H195N, and alpha Q191 K variant MoFe proteins (where His at position 195 in the alpha subunit is replaced by Gln/Asn or Gln at position alpha-191 by Lys), which have strikingly different substrate-reduction properties, were studied by stopped-flow or rapid-freeze techniques. Rapid-freeze EPR at low electron flux (at 3-fold molar excess of wild-type Fe protein) elicited two transient FeMo-cofactor-based EPR signals within 1 s of initiating turnover under N-2 with the alpha H195Q and alpha H195N variants, but not with the alpha Q191K variant. No EPR signals attributable to P cluster oxidation were observed for any of the variants under these conditions. Furthermore, during turnover at low electron flux with the wild-type, alpha H195Q or alpha H195N MoFe protein, the longer-time 430-nm absorbance increase, which likely reflects P cluster oxidation, was also not observed (by stopped-flow spectrophotometry); it did, however, occur for all three MoFe proteins under higher electron flux. No 430-nm absorbance increase occurred with the alpha Q191K variant, not even at higher electron flux. This putative lack of involvement of the P cluster in electron transfer at low electron flux was confirmed by rapid-freeze Fe-57 Mossbauer spectroscopy, which clearly showed FeMo-factor reduction without P cluster oxidation. Because the wild-type, alpha H195Q and alpha H195N MoFe proteins can bind N-2, but alpha Q195K cannot, these results suggest that P cluster oxidation occurs only under high electron flux as required for N-2 reduction. (C) 2007 Elsevier Inc. All rights reserved.

Thapper, A, Boer DR, Brondino CD, Moura JJ, Romao MJ.  2007.  Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase, Mar. J Biol Inorg Chem. 12:353-66., Number 3 AbstractWebsite

Two arsenite-inhibited forms of each of the aldehyde oxidoreductases from Desulfovibrio gigas and Desulfovibrio desulfuricans have been studied by X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy. The molybdenum site of these enzymes shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. Arsenite addition to active as-prepared enzyme or to a reduced desulfo form yields two different species called A and B, respectively, which show different Mo(V) EPR signals. Both EPR signals show strong hyperfine and quadrupolar couplings with an arsenic nucleus, which suggests that arsenic interacts with molybdenum through an equatorial ligand. X-ray data of single crystals prepared from EPR-active samples show in both inhibited forms that the arsenic atom interacts with the molybdenum ion through an oxygen atom at the catalytic labile site and that the sulfido ligand is no longer present. EPR and X-ray data indicate that the main difference between both species is an equatorial ligand to molybdenum which was determined to be an oxo ligand in species A and a hydroxyl/water ligand in species B. The conclusion that the sulfido ligand is not essential to determine the EPR properties in both Mo-As complexes is achieved through EPR measurements on a substantial number of randomly oriented chemically reduced crystals immediately followed by X-ray studies on one of those crystals. EPR saturation studies show that the electron transfer pathway, which is essential for catalysis, is not modified upon inhibition.

Santos-Silva, T, Dias JM, Dolla A, Durand M-C, Goncalves LL, Lampreia J, Moura I, Romao MJ.  2007.  Crystal structure of the 16 heme cytochrome from Desulfovibrio gigas: A glycosylated protein in a sulphate-reducing bacterium, Jul 20. Journal of Molecular Biology. 370:659-673., Number 4 AbstractWebsite

Sulphate-reducing bacteria have a wide variety of periplasmic cytochromes involved in electron transfer from the periplasm to the cytoplasm. HmcA is a high molecular mass cytochrome of 550 amino acid residues that harbours 16 c-type heme groups. We report the crystal structure of HmcA isolated from the periplasm of Desulfovibrio gigas. Crystals were grown. using polyethylene glycol 8K and zinc acetate, and diffracted beyond 2.1 angstrom resolution. A multiple-wavelength anomalous dispersion experiment at the iron absorption edge enabled us to obtain good-quality phases for structure solution and model building. DgHmcA has a V-shape architecture, already observed in HmcA isolated from Desulfovibrio vulgaris Hildenborough. The presence of an oligosaccharide molecule covalently bound to an Asn residue was observed in the electron density maps of DgHmcA and confirmed by mass spectrometry. Three modified monosaccharides appear at the highly hydrophobic vertex, possibly acting as an anchor of the protein to the cytoplasmic membrane. (c) 2007 Elsevier Ltd. All rights reserved.

Rial-Otero, R, Gaspar EM, Moura I, Capelo JL.  2007.  Chromatographic-based methods for pesticide determination in honey: An overview, Feb 15. Talanta. 71:503-514., Number 2 AbstractWebsite

Nowadays the control of pesticides in honey is an issue of primary health importance as consequence of the increasing content of these chemicals in the aforementioned matrix. This poisoning has led to the worldwide increasing loss of bees since 1995. From Europe to Canada, scientist, beekeepers and chemical companies disagree about the reasons that have led to colony losses higher than 50% in some areas. This problem has become a public health issue due to the high honey worldwide consumption. The presence of pesticides in honey has been directly related to bees' mortality by some researchers through pesticide presence in (1) pollen, (2) honeycomb walls, (3) own bees and (4) honey. In this work we describe the actual state-of-the-art for pesticides determination in honey along with a review in this subject focused on sample treatments and instrumentation. Finally, future trends are also commented. (c) 2006 Elsevier B.V. All rights reserved.

Jimenez, A, Pinheiro C, Parola AJ, Maestri M, Pina F.  2007.  The chemistry of 6-hydroxyflavylium: zwitterionic base and p-quinoidal chalcones. A multiswitchable system operated by proton, electron and photon inputs, 2007. Photochemical & Photobiological Sciences. 6:372-380. AbstractWebsite

The complex network of chemical reactions of the compound 6-hydroxyflavylium perchlorate was studied by different techniques including UV-vis absorption spectrophotometry, stopped-flow, electrochemistry, and photochemistry. The network is characterized by the formation of a very reactive zwitterionic base as well as by p-quinoidal chalcones. The trans-chalcone is metastable in very acidic solutions and exhibits reversible redox reactions, allowing to introduce for the first time in the flavylium network an electrochemical input.

Moniz, AB.  2007.  The collaborative work concept and the information systems support: perspectives for and from manufacturing industry. Technikfolgenabschätzung – Theorie und Praxis. 16(2):49-57. AbstractWebsite

Most of the discussion and controversy on organisation of work concepts has been referenced to the manufacturing industry along the 20th century: it started with the concept of “scientific management” from Taylor, and continued with the new ideas on the importance of human factors as Mayo pointed out in the 1930s. Immediately after the 2nd World War Friedmann studied the human problems related to new manufacturing technologies and automation. And the late 1950 and 1960s were decades of strong debate on the socio-technics with the research at Tavistock Institute of London and the emergence of national programmes on new forms of work organisation. At the end of the last century the concept of collaborative work was developed together with the definition(s) of information systems and organisational design. However, the interest came from other production activities, like the services. This article analyses the approaches developed on these debates on the collaborative work and information system and its application to the manufacturing industry.

Moniz, A.  2007.  The Collaborative Work Concept and the Information Systems Support: Perspectives for and from Manufacturing Industry. , Number 5627: University Library of Munich, Germany Abstract

Most of the discussion and controversy on organisation of work concepts has been referenced to the manufacturing industry along the 20th century: it started with the concept of “scientific management” from Taylor, and continued with the new ideas on the importance of human factors as Mayo pointed out in the 1930s. Immediately after the 2nd World War Friedmann studied the human problems related to new manufacturing technologies and automation. And the late 1950 and 1960s were decades of strong debate on the socio-technics with the research at Tavistock Institute of London and the emergence of national programmes on new forms of work organisation. At the end of the last century the concept of collaborative work was developed together with the definition(s) of information systems and organisational design. However, the interest came from other production activities, like the services. This article analyses the approaches developed on these debates on the collaborative work and information system and its application to the manufacturing industry.

Kulkarni, PS, Branco LC, Crespo JG, Afonso CAM.  2007.  A comparative study on absorption and selectivity of organic vapors by using ionic liquids based on imidazolium, quaternary ammonium, and guanidinium cations. Chemistry-a European Journal. 13:8470-8477., Number 30 AbstractWebsite
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Kulkarni, PS, Branco LC, Crespo JG, Nunes CM, Raymundo A, Afonso CAM.  2007.  Comparison of physicochemical properties of new ionic liquids based on imidazolium, quaternary ammonium, and guanidinium cations. Chemistry-a European Journal. 13:8478-8488., Number 30 AbstractWebsite
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