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2006
Possoz*, C, Filipe* SR, Grainge I, Sherratt DJ.  2006.  Tracking of controlled Escherichia coli replication fork stalling and restart at repressor-bound DNA in vivo. EMBO J. 25:2596-2604.
Vilela, M, Ferreira LM, Vieira J.  2006.  Discolouration of architectural photoreproductions - Causes and prevention. RESTAURATOR-INTERNATIONAL JOURNAL FOR THE PRESERVATION OF LIBRARY AND ARCHIVAL MATERIAL. 27:1-8., Number 1 Abstract
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Fortunato, R, Branco LC, Afonso CAM, Benavente J, Crespo JG.  2006.  Electrical impedance spectroscopy characterisation of supported ionic liquid membranes. Journal of Membrane Science. 270:42-49., Number 1-2 AbstractWebsite
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Laia, CAT, Costa SMB, Ferreira VLF.  2006.  Electron-transfer mechanism of the triplet state quenching of aluminium tetrasulfonated phthalocyanine by cytochrome c. Biophysical Chemistry. 122:143-155., Number 2 AbstractWebsite
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Gago, S, Fernandes JA, Abrantes M, Kuhn FE, Ribeiro-Claro P, Pillinger M, Santos TM, Goncalves IS.  2006.  Immobilisation of methyltrioxorhenium on functionalised MCM-41. Microporous and Mesoporous Materials. 89:284-290., Number 1-3 AbstractWebsite
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Trincao, J, Silva MS, Barata L, Bonifacio C, Carvalho S, Tomas AM, Ferreira AEN, Cordeiro C, Freire AP, Romao MJ.  2006.  Purification, crystallization and preliminary X-ray diffraction analysis of the glyoxalase II from Leishmania infantum. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 62:805-807. AbstractWebsite
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Najmudin, S, Guerreiro C, Carvalho AL, Prates JAM, Correia MAS, Alves VD, Ferreira LMA, Romao MJ, Gilbert HJ, Bolam DN, Fontes C.  2006.  Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains. Journal of Biological Chemistry. 281:8815-8828., Number 13 AbstractWebsite
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Fiedeler, U, Krings B.  2006.  {Naturalness and Neuronal Implants – Changes in the perception of human beings}. , Number 8501: University Library of Munich, Germany Abstract

With our contribution we would like to refer to the debate on nanotechnology (NT) and its implications for the public discourse on the relationship of human beings and technologies. Within NT the convergence of some technologies has been considered as a crucial step towards the long term objective of “enhancing human performance”. The discussion was initiated with an US-American workshop in the year 2002, where the innovative character of converging technology (CT) was strongly underlined (Roco 2002). In the final document of the workshop futuristic and far reaching scenarios on technical development based on NT and on CT were presented. First we address the implications of the mentioned document for research policy in general and especially of NT. Based on the example of neural implants we second qualify the normative expectations within the debate without however denying the helpfulness of these innovations especially in the field of medicine. But we third agree on a critical discussion, which consider a new quality of technological penetration into social and human processes.

2005
Baptista, {PMRV}, c}alo Dória G{\c, Henriques D, Pereira E, Franco R.  2005.  Colorimetric detection of eukaryotic gene expression with DNA-derivatized gold nanoparticles, jan. Journal of Biotechnology. 119:111–7., Number 2: Elsevier Abstract

Thiol-linked DNA-gold nanoparticles were used in a novel colorimetric method to detect the presence of specific mRNA from a total RNA extract of yeast cells. The method allowed detection of expression of the FSY1 gene that encodes a specific fructose/H+ symporter in Saccharomyces bayanus PYCC 4565. FSY1 is strongly expressed when the yeast is grown in fructose as the sole carbon source, while cells cultivated in glucose as the sole carbon source repress gene expression. The presence of FSY1 mRNA is detected based on color change of a sample containing total RNA extracted from the organism and gold nanoparticles derivatized with a 15-mer of complementary single stranded DNA upon addition of NaCl. If FSY1 mRNA is present, the solution remains pink, changing to blue-purple in the absence of FSY1 mRNA. Direct detection of specific expression was possible from only 0.3 microg of unamplified total RNA without any further enhancement. This novel method is inexpensive, very easy to perform as no amplification or signal enhancement steps are necessary and takes less than 15 min to develop after total RNA extraction. No temperature control is necessary and color change can be easily detected visually.

Abreu, AR, Costa I, Rosa C, Ferreira LM, Lourenco A, Santos PP.  2005.  New enantioselective method for hydration of alkenes using cyclodextrins as phase transfer catalyst, DEC 12. TETRAHEDRON. 61:11986-11990., Number 50 Abstract
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Salgueiro, CA, Morgado L, Fonseca B, Lamosa P, Catarino T, Turner DL, Louro RO.  2005.  Binding of ligands originates small perturbations on the microscopic thermodynamic properties of a multicentre redox protein. FEBS Journal. 272(9):2251-2260. AbstractWebsite

NMR and visible spectroscopy coupled to redox measurements were used to determine the equilibrium thermodynamic properties of the four haems in cytochrome c3 under conditions in which the protein was bound to ligands, the small anion phosphate and the protein rubredoxin with the iron in the active site replaced by zinc. Comparison of these results with data for the isolated cytochrome shows that binding of ligands causes only small changes in the reduction potentials of the haems and their pairwise interactions, and also that the redox-sensitive acid–base centre responsible for the redox–Bohr effect is essentially unaffected. Although neither of the ligands tested is a physiological partner of cytochrome c3, the small changes observed for the thermodynamic properties of cytochrome c3 bound to these ligands vs. the unbound state, indicate that the thermodynamic properties measured for the isolated protein are relevant for a physiological interpretation of the role of this cytochrome in the bioenergetic metabolism of Desulfovibrio.

Filipe, SR, Tomasz A, Ligoxygakis P.  2005.  Requirements of peptidoglycan structure allowing detection by the Drosophila Toll pathway. EMBO Reports. 6:327-333.
Giestas, L, Folgosa F, Lima JC, Parola AJ, Pina F.  2005.  Bio-inspired multistate networks responsive to light, pH and thermal inputs - An example of a multistate system operating through different algorithms. European Journal of Organic Chemistry. :4187-4200., Number 19 Abstract
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da Silva, PF, Lima JC, Freitas AA, Shimizu K, Macanita AL, Quina FH.  2005.  Charge-transfer complexation as a general phenomenon in the copigmentation of anthocyanins. Journal of Physical Chemistry a. 109:7329-7338., Number 32 Abstract
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Figueirinhas, JL, Cruz C, Filip D, Feio G, Ribeiro AC, Frere Y, Meyer T, Mehl GH.  2005.  Deuterium NMR investigation of the biaxial nematic phase in an organosiloxane tetrapode. Phys Rev Lett. 94:107802., Number 10 AbstractWebsite

Deuterium NMR is used to examine the molecular order exhibited by an organosiloxane tetrapode giving the first experimental evidence, using a bulk sample, for the existence of a biaxial nematic phase in this type of compounds. The temperature dependence of the averaged quadrupolar coupling constant and asymmetry parameter was determined in the compound's nematic phase. Two distinct regimes could be identified, one with a vanishing asymmetry parameter corresponding to a uniaxial nematic phase and another with a significant temperature dependent asymmetry parameter, corresponding to a biaxial nematic phase. The high values obtained for the asymmetry parameter at the lower end of the nematic range are well above experimental error and constitute a definite proof of the biaxial nature of the nematic phase exhibited by the studied compound for those temperatures.

Gago, S, Fernandes JA, Rainho JP, Ferreira RAS, Pillinger M, Valente AA, Santos TM, Carlos LD, Ribeiro-Claro PJA, Goncalves IS.  2005.  Highly luminescent tris(beta-diketonate)europium(III) complexes immobilized in a functionalized mesoporous silica. Chemistry of Materials. 17:5077-5084., Number 20 AbstractWebsite
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Gago, S, Pillinger M, Ferreira RAS, Carlos LD, Santos TM, Goncalves IS.  2005.  Immobilization of lanthanide ions in a pillared layered double hydroxide. Chemistry of Materials. 17:5803-5809., Number 23 AbstractWebsite
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Carvalho, AL, Pires VMR, Gloster TM, Turkenburg JP, Prates JAM, Ferreira LMA, Romao MJ, Davies GJ, Fontes C, Gilbert HJ.  2005.  Insights into the structural determinants of cohesin dockerin specificity revealed by the crystal structure of the type II cohesin from Clostridium thermocellum SdbA. Journal of Molecular Biology. 349:909-915., Number 5 AbstractWebsite
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Boer, DR, Muller A, Fetzner S, Lowe DJ, Romao MJ.  2005.  On the purification and preliminary crystallographic analysis of isoquinoline 1-oxidoreductase from Brevundimonas diminuta 7. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 61:137-140. AbstractWebsite
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Schafer, T, Branco LC, Fortunato R, Izak P, Rodrigues CM, Afonso CAM, Crespo JG.  2005.  Opportunities for membrane separation processes using ionic liquids. Ionic Liquids Iiib: Fundamentals, Progress, Challenges and Opportunities: Transformations and Processes. 902(Rogers, R. D., Seddon, K. R., Eds.).:97-110. Abstract
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Lopez-Cortes, A, Bursakov S, Figueiredo A, Thapper AE, Todorovic S, Moura JJ, Ollivier B, Moura I, Fauque G.  2005.  Purification and preliminary characterization of tetraheme cytochrome c3 and adenylylsulfate reductase from the peptidolytic sulfate-reducing bacterium Desulfovibrio aminophilus DSM 12254. Bioinorg Chem Appl. :81-91. AbstractWebsite

Two proteins were purified and preliminarily characterized from the soluble extract of cells (310 g, wet weight) of the aminolytic and peptidolytic sulfate-reducing bacterium Desulfovibrio (D.) aminophilus DSM 12254. The iron-sulfur flavoenzyme adenylylsulfate (adenosine 5'-phosphosulfate, APS) reductase, a key enzyme in the microbial dissimilatory sulfate reduction, has been purified in three chromatographic steps (DEAE-Biogel A, Source 15, and Superdex 200 columns). It contains two different subunits with molecular masses of 75 and 18 kDa. The fraction after the last purification step had a purity index (A(278nm) / A(388nm)) of 5.34, which was used for further EPR spectroscopic studies. The D. aminophilus APS reductase is very similar to the homologous enzymes isolated from D. gigas and D. desulfuricans ATCC 27774. A tetraheme cytochrome c(3) (His-heme iron-His) has been purified in three chromatographic steps (DEAE- Biogel A, Source 15, and Biogel-HTP columns) and preliminarily characterized. It has a purity index ([A(553nm) - A(570nm)](red) / A(280nm)) of 2.9 and a molecular mass of around 15 kDa, and its spectroscopic characterization (NMR and EPR) has been carried out. This hemoprotein presents similarities with the tetraheme cytochrome c(3) from Desulfomicrobium (Des.) norvegicum (NMR spectra, and N-terminal amino acid sequence).

2004
Brondino, CD, Passeggi MC, Caldeira J, Almendra MJ, Feio MJ, Moura JJ, Moura I.  2004.  Incorporation of either molybdenum or tungsten into formate dehydrogenase from Desulfovibrio alaskensis NCIMB 13491; EPR assignment of the proximal iron-sulfur cluster to the pterin cofactor in formate dehydrogenases from sulfate-reducing bacteria, Mar. J Biol Inorg Chem. 9:145-51., Number 2 AbstractWebsite

We report the characterization of the molecular properties and EPR studies of a new formate dehydrogenase (FDH) from the sulfate-reducing organism Desulfovibrio alaskensis NCIMB 13491. FDHs are enzymes that catalyze the two-electron oxidation of formate to carbon dioxide in several aerobic and anaerobic organisms. D. alaskensis FDH is a heterodimeric protein with a molecular weight of 126+/-2 kDa composed of two subunits, alpha=93+/-3 kDa and beta=32+/-2 kDa, which contains 6+/-1 Fe/molecule, 0.4+/-0.1 Mo/molecule, 0.3+/-0.1 W/molecule, and 1.3+/-0.1 guanine monophosphate nucleotides. The UV-vis absorption spectrum of D. alaskensis FDH is typical of an iron-sulfur protein with a broad band around 400 nm. Variable-temperature EPR studies performed on reduced samples of D. alaskensis FDH showed the presence of signals associated with the different paramagnetic centers of D. alaskensis FDH. Three rhombic signals having g-values and relaxation behavior characteristic of [4Fe-4S] clusters were observed in the 5-40 K temperature range. Two EPR signals with all the g-values less than two, which accounted for less than 0.1 spin/protein, typical of mononuclear Mo(V) and W(V), respectively, were observed. The signal associated with the W(V) ion has a larger deviation from the free electron g-value, as expected for tungsten in a d(1) configuration, albeit with an unusual relaxation behavior. The EPR parameters of the Mo(V) signal are within the range of values typically found for the slow-type signal observed in several Mo-containing proteins belonging to the xanthine oxidase family of enzymes. Mo(V) resonances are split at temperatures below 50 K by magnetic coupling with one of the Fe/S clusters. The analysis of the inter-center magnetic interaction allowed us to assign the EPR-distinguishable iron-sulfur clusters with those seen in the crystal structure of a homologous enzyme.

Bencini, A, Berni E, Bianchi A, Fornasari P, Giorgi C, Lima JC, Lodeiro C, Melo MJ, de Melo JS, Parola AJ, Pina F, Pina J, Valtancoli B.  2004.  A fluorescent chemosensor for Zn(II). Exciplex formation in solution and the solid state, 2004. Dalton Transactions. :2180-2187. AbstractWebsite

The macrocyclic phenanthrolinophane 2,9-[2,5,8-triaza-5-(N-anthracene-9-methylamino) ethyl]-[9]-1,10-henanthrolinophane(L) bearing a pendant arm containing a coordinating amine and an anthracene group forms stable complexes with Zn(II), Cd(II) and Hg(II) in solution. Stability constants of these complexes were determined in 0.10 mol dm(-3) NMe4Cl H2O-MeCN (1:1, v/v) solution at 298.1+/-0.1 K by means of potentiometric (pH metric) titration. The fluorescence emission properties of these complexes were studied in this solvent. For the Zn(II) complex, steady-state and time-resolved fluorescence studies were performed in ethanol solution and in the solid state. In solution, intramolecular pi-stacking interaction between phenanthroline and anthracene in the ground state and exciplex emission in the excited state were observed. From the temperature dependence of the photostationary ratio (I-Exc/I-M), the activation energy for the exciplex formation (E-a) and the binding energy of the exciplex (-DeltaH) were determined. The crystal structure of the [ZnLBr](ClO4).H2O compound was resolved, showing that in the solid state both intra- and inter-molecular pi-stacking interactions are present. Such interactions were also evidenced by UV-vis absorption and emission spectra in the solid state. The absorption spectrum of a thin film of the solid complex is red-shifted compared with the solution spectra, whereas its emission spectrum reveals the unique featureless exciplex band, blue shifted compared with the solution. In conjunction with X-ray data the solid-state data was interpreted as being due to a new exciplex where no pi-stacking (full overlap of the pi-electron cloud of the two chromophores-anthracene and phenanthroline) is observed. L is a fluorescent chemosensor able to signal Zn(II) in presence of Cd(II) and Hg(II), since the last two metal ions do not give rise either to the formation of pi-stacking complexes or to exciplex emission in solution.

Moncada, MC, Fernandez D, Lima JC, Parola AJ, Lodeiro C, Folgosa F, Melo MJ, Pina F.  2004.  Multistate properties of 7-(N,N-diethylamino)-4 '-hydroxyflavylium. An example of an unidirectional reaction cycle driven by pH, 2004. Organic & Biomolecular Chemistry. 2:2802-2808. AbstractWebsite

The synthetic flavylium salt 7-(N,N-diethylamino)-4'-hydroxyflavylium tetrafluoroborate gives rise in aqueous solution to a complex network of chemical reactions driven by pH. The system was studied by H-1 NMR, single crystal X-ray diffraction, steady state and transient UV-Vis spectrophotometry as well as stopped flow. The crystal structure shows a high degree of coplanarity between the pyrylium system and the phenyl group in position 2. Thermodynamic and kinetic constants for the pH dependent network of chemical reactions were obtained. The introduction of an amino group in position 7 allows formation of protonated species leading, in particular, to a tautomeric form of the protonated cis-chalcone, CcH(+), whose absorption spectra is rather red shifted, in comparison with the correspondent protonated trans-chalcone, CtH(+). The CcH(+) species can be rapidly converted into the flavylium cation through a first order process with lifetime of 0.2 s at pH = 2.35. This new reaction channel confers this compound a peculiar behaviour in acidic media, allowing to define an unidirectional pH driven reaction cycle.

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