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2008
Wang, L, Gilbert RJC, Atilano ML, Filipe SR, Gay NJ, Ligoxygakis P.  2008.  Peptidoglycan Recognition Protein-SD provides versatility of receptor formation in Drosophila immunity. Proc. Natl. Acad. Sci. USA. 105:11881-11886.
Fernandes, P, Vilarigues M, Alves LC, da Silva RC.  2008.  Stained glass from Monastery of Batalha: non-destructive characterization of glass and paintings. Journal of Cultural Heritage. 9(1):e5-e9.
Memmi, G, Filipe SR, Pinho MG, Fu Z, Cheung A.  2008.  Staphylococcus aureus PBP4 is essential for beta-lactams resistance in community-acquired methicillin resistant strains. Antimicrob Agents Chemother. 52:3955-3966.
Cruz, C, Figueirinhas JL, Filip D, Feio G, Ribeiro AC, Frere Y, Meyer T, Mehl GH.  2008.  Biaxial nematic order and phase behavior studies in an organosiloxane tetrapode using complementary deuterium NMR experiments. Phys Rev E Stat Nonlin Soft Matter Phys. 78:051702., Number 5 Pt 1 AbstractWebsite

The biaxial nematic phase was recently observed in different thermotropic liquid crystals, namely bent-core compounds, side-chain polymers, bent-core dimers, and organosiloxane tetrapodes. In this work, a series of experiments with a nematic organosiloxane tetrapode where nuclear magnetic resonance (NMR) spectra are collected while the sample is continuously rotating around an axis perpendicular to the magnetic field, are discussed in conjunction with the analysis of a deuterium NMR experiment on the same system reported earlier. The sample used is a mixture of a deuterated probe with the tetrapode. The mixture exhibits a nematic range between -40 degrees C and 37 degrees C. The results of the two independent, but complementary deuterium NMR experiments confirm the existence of a biaxial nematic phase for temperatures below 0 degrees C with high values of the asymmetry parameter at low temperatures. The presence of slow movements of the tetrapode mesogenic units in the low-temperature regime could also be detected through the analysis of the NMR spectra. Simulations indicate that these movements are mainly slow molecular reorientations of the mesogenic units associated with the presence of collective modes in the nematic phases of this compound. In the case of tetrapodes, recent investigations attribute the origin of biaxiality to the hindering of reorientations of the laterally attached mesogenic units which constitute the tetrapode. This study relates the molecular movements with the nematic biaxial ordering of the system.

Chaves, S, Gil M, Canario S, Jelic R, Romao MJ, Trincao J, Herdtweck E, Sousa J, Diniz C, Fresco P, Santos AM.  2008.  Biologically relevant O,S-donor compounds. Synthesis, molybdenum complexation and xanthine oxidase inhibition. Dalton Transactions. :1773-1782., Number 13 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.

Cardoso, M, Figueirinhas JL, Cruz C, Van-Quynh A, Ribeiro AC, Feio G, Apreutesei D, Mehl GH.  2008.  Deuterium NMR Investigation of the Influence of Molecular Structure on the Biaxial Ordering of Organosiloxane Tetrapodes Nematic Phase. Molecular Crystals and Liquid Crystals. 495:700-+. AbstractWebsite

In order to contribute to the understanding of the origin of biaxial nematic ordering in tetrapodes, a deuterium NMR study was performed on mixtures of monomers from organosiloxane tetrapodes with a deuterated nematic probe. Contrary to the tetrapode system previously studied, which exhibits a biaxial nematic phase, the results for monomers are compatible, within the experimental error, with uniaxial nematic ordering in the whole nematic range. The data are in agreement with the conjecture that the nematic biaxial behaviour is related to hindering of the mesogenic units' rotational movements, arising from interdigitation and connection to the central silicon core.

Bazzicalupi, C, Bencini A, Bianchi A, Danesi A, Faggi E, Giorgi C, Lodeiro C, Oliveira E, Pina F, Valtancoli B.  2008.  Interaction of polyamine macrocycles with Zn(II) and ATP in aqueous solution. Binary and ternary systems. A potentiometric, NMR and fluorescence emission study. Inorganica Chimica Acta. 361:3410-3419., Number 12-13 AbstractWebsite
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Viegas, A, Bras NF, Cerqueira NMFSA, Fernandes PA, Prates JAM, Fontes CMGA, Bruix M, Romao MJ, Carvalho AL, Ramos MJ, Macedo AL, Cabrita EJ.  2008.  Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach. Febs Journal. 275:2524-2535., Number 10 AbstractWebsite
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Giestas, L, Ferreira GNM, Baptista PV, Lima JC.  2008.  Multiplexed spectral coding for simultaneous detection of DNA hybridization reactions based on FRET. Sensors and Actuators B-Chemical. 134:146-157., Number 1 Abstract
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Najmudin, S, Pinheiro BA, Romao MJ, Prates JAM, Fontes CMGA.  2008.  Purification, crystallization and crystallographic analysis of Clostridium thermocellum endo-1,4-beta-D-xylanase 10B in complex with xylohexaose. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 64:715-718. AbstractWebsite
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Branco, LC, Ferreira FC, Santos JL, Crespo JG, Afonso CAM.  2008.  Sharpless asymmetric dihydroxylation of olefins in water-surfactant media with recycling of the catalytic system by membrane nanofiltration. Advanced Synthesis & Catalysis. 350:2086-2098., Number 13 AbstractWebsite
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Ferrer, M, Gutierrez A, Rodriguez L, Rossell O, Lima JC, Font-Bardia M, Solans X.  2008.  Study of the effect of the phosphane bridging chain nature on the structural and photophysical properties of a series of gold(I) ethynylpyridine complexes. European Journal of Inorganic Chemistry. :2899-2909., Number 18 Abstract
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Fortunato, E, Correia N, Barquinha P, Pereira LÍ, Goncalves G\c{C}alo, Martins R.  2008.  {High-Performance Flexible Hybrid Field-Effect Transistors Based on Cellulose Fiber Paper}. IEEE Electron Device Letters. 29:988–990., Number 9 AbstractWebsite

In this letter, we report for the first time the use of a sheet of cellulose-fiber-based paper as the dielectric layer used in oxide-based semiconductor thin-film field-effect transis- tors (FETs). In this new approach, we are using the cellulose– fiber-based paper in an “interstrate” structure since the device is built on both sides of the cellulose sheet. Such hybrid FETs present excellent operating characteristics such as high channel saturation mobility (> 30 cm2/Vs), drain–source current on/off modulation ratio of approximately 104, near-zero threshold voltage, enhance- ment n-type operation, and subthreshold gate voltage swing of 0.8 V/decade. The cellulose-fiber-based paper FETs’ character- istics have been measured in air ambient conditions and present good stability, after two months of being processed. The obtained results outpace those of amorphous Si thin-film transistors (TFTs) and rival with the same oxide-based TFTs produced on either glass or crystalline silicon substrates. The compatibility of these devices with large-scale/large-area deposition techniques and low– cost substrates as well as their very low operating bias delin- eates this as a promising approach to attain high-performance disposable electronics like paper displays, smart labels, smart packaging, RFID, and point-of-care systems for self-analysis in bioapplications, among others.

Martins, R, Barquinha P, Pereira L, Correia N, Gonçalves G, Ferreira I, Fortunato E.  2008.  {Write-erase and read paper memory transistor}. Applied Physics Letters. 93:203501., Number 20 AbstractWebsite
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2007
Santos, HM, Rial-Otero R, Fernandes L, Vale G, Rivas MG, Moura I, Capelo JL.  2007.  Improving sample treatment for in-solution protein identification by peptide mass fingerprint using matrix-assisted laser desorption/ionization time-of-flight mass Spectrometry, Sep. Journal of Proteome Research. 6:3393-3399., Number 9 AbstractWebsite

Three ultrasonic energy sources were studied to speed up the sample treatment for in-solution protein identification by peptide mass fingerprint using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Protein reduction, alkylation, and enzymatic digestion steps were done in 15 min. Nine proteins, including zinc resistance-associated protein precursor from Desulfovibrio desulfuricans strain G20 and split-soret cytochrome c from D. desulfuricans ATCC27774 were successfully identified with the new protocol.

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.

Capela, JP, Macedo C, Branco PS, Ferreira LM, Lobo AM, Fernandes E, Remiao F, Bastos ML, Dirnagl U, Meisel A, Carvalho F.  2007.  Neurotoxicity mechanisms of thioether ecstasy metabolites, JUN 8. NEUROSCIENCE. 146:1743-1757., Number 4 Abstract
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Ferreira, IMPLV, Pinho O, Mota MV, Tavares P, Pereira A, Goncalves MP, Torres D, Rocha C, Teixeira JA.  2007.  Preparation of ingredients containing an ACE-inhibitory peptide by tryptic hydrolysis of whey protein concentrates, Jun. INTERNATIONAL DAIRY JOURNAL. {17}:{481-487}., Number {5} Abstract

This study describes the characterisation of whey protein hydrolysates obtained from tryptic hydrolysis to assess their application as ingredients with angiotensin-converting-enzyme (ACE) inhibitory action. The levels of a-lactalbumin (alpha-la) and P-lactoglobulin (beta-lg) remaining after hydrolysis were quantified. Peptides were separated by RP-HPLC, and Ala-Leu-Pro-Met-His-Ile-Arg (ALPMHIR), the most potent beta-lg-derived ACE-inhibitory peptide was monitored. A correlation curve was established for the production of this peptide as a function of hydrolysis time. Heat-induced gelation of hydrolysates was studied by small-deformation rheology. The gelation times and the strength of the final gels were highly dependent on the degree of hydrolysis. Smaller peptides liberated by hydrolysis contributed to the inability of whey protein hydrolysates to gel. (c) 2006 Elsevier Ltd. All rights reserved.

Pereira, AS, Tavares P, Folgosa F, Almeida RM, Moura I, Moura JJG.  2007.  Superoxide reductases, Jul. European Journal of Inorganic Chemistry. :{2569-2581}., Number {18} Abstract

Reactive oxygen species (ROS), when in excess, are among the most deleterious species an organism can deal with. The physiological effects of ROS include amino acid chain cleavage, DNA degradation and lipid oxidation, among others. They can be formed in the cytoplasm in a variety of ways, including autooxidation reactions (FMN- and FAD-containing enzymes) and Fenton reactions as a result of the cytoplasmatic pool of iron ions. The superoxide anion (021, despite its short half-life in solution, is particularly pernicious as it can form other reactive ROS (such as the strong oxidant peroxynitrite) or oxidize and/or reduce cellular components. For strict anaerobic or microaerophilic bacteria it is of particular importance to be able to dispose of ROS in a controlled manner, especially if these organisms are temporarily exposed to air. This review aims to describe the structural characteristics of superoxide reductases (SORs) and mechanistic aspects of biological superoxide anion reduction. SORs can be considered the main class of enzymes behind the oxygen detoxification pathway of anaerobic and microaerophilic bacteria. The geometry of the active site (three classes have been described), the possible electron donors in vivo and the current hypothesis for the catalytic mechanism will be discussed. Some phylogenetic considerations are presented, regarding the primary structure of SORs currently available in genome databases. ((c) Wiley-VCH Verlag GmbH \& Co. KGaA, 69451 Weinheim, Germany, 2007).

de Martins, {RFP}, Baptista P, Raniero L, c}alo Doria G{\c, Silva {LB }, Franco R, Fortunato {EMC}.  2007.  Amorphous/nanocrystalline silicon biosensor for the specific identification of unamplified nucleic acid sequences using gold nanoparticle probes, jan. Applied Physics Letters. 90:n/d., Number 2: AIP - American Institute of Physics Abstract

Amorphous/nanocrystalline silicon pi'ii'n devices fabricated on micromachined glass substrates are integrated with oligonucleotide-derivatized gold nanoparticles for a colorimetric detection method. The method enables the specific detection and quantification of unamplified nucleic acid sequences (DNA and RNA) without the need to functionalize the glass surface, allowing for resolution of single nucleotide differences between DNA and RNA sequences-single nucleotide polymorphism and mutation detection. The detector's substrate is glass and the sample is directly applied on the back side of the biosensor, ensuring a direct optical coupling of the assays with a concomitant maximum photon capture and the possibility to reuse the sensor. (c) 2007 American Institute of Physics.

Baptista, {PMRV}, Franco R.  2007.  Imaging gold nanoparticles for DNA sequence recognition in biomedical applications, jan. Ieee Transactions On Nanobioscience. 6:282–288., Number 4: Institute of Electrical and Electronics Engineers (IEEE) Abstract

The hybridization of single-stranded oligonucleotide-derivatized gold nanoparticles (An nanoprobes) with double stranded complementary DNA was directly observed by atomic force microscopy (AFM). This specific interaction is the basis for an An nanoprobe-based homogeneous assay for specific DNA sequence detection, based on salt-induced particle aggregation that is prevented when a complementary target is present. For long DNA targets (linearized plasmid DNA) complicated hybridized target DNA-Au-nanoprobes structures were formed, that were interpreted as the basis for stability of the An nanoprobes against salt-induced aggregation. For shorter DNA targets (PCR amplified fragments) hybridization with the An nanoprobes occurred, in the majority of cases, in the expected location of the DNA target fragment containing the specific sequence. The formation of the observed DNA hybridized structures provides evidence at the molecular level for specific hybridization to the target sequence as the method of binding of the An nanoprobes.

Baptista, {PMRV}, Franco R.  2007.  Nanodiagnostics: fast colorimetric method for single nucleotide polymorphism/mutation detection, jan. Iet Nanobiotechnology. 1:53–57., Number 4: INST ENGINEERING TECHNOLOGY-IET Abstract

Advances in nanosciences are having a significant impact in many areas of research. The impact of new nanotechnologies has been particularly large in biodiagnostics, where a number of nanoparticle-based assays have been introduced for biomolecules detection. To date, applications of nanoparticles have largely focused on DNA-functionalised gold nanoparticles used as the target-specific probes. These gold nanoparticle-based systems can be used for the detection of specific sequences of DNA (pathogen detection, characterisation of mutation and/or single nucleotide polymorphisms) or RNA (without prior retro-transcription and amplification). Here a rapid and inexpensive nanoparticle-based method for single-base mismatch detection (single nucleotide polymorphism/mutation) in DNA samples is reported. Gold nanoparticles derivatised with thiol modified oligonucleotides complementary to DNA targets - Au-nanoprobes - are used to distinguish fully complementary from mismatched sequences, with a single-base mismatch. The authors have successfully applied this strategy to detect common mutations within the beta-globin gene.

Silva, {LB}, Baptista P, Raniero L, c}alo Dória G{\c, Franco R, de Martins {RFP}, Fortunato {EMC}.  2007.  Novel optoelectronic platform using an amorphous/nanocrystalline silicon biosensor for the specific identification of unamplified nucleic acid sequences based on gold nanoparticle probes, jan. Solid-State Sensors, Actuators and Microsystems Conference, 2007. :935–938. Abstract
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Rial-Otero, R, Carreira RJ, Cordeiro FM, Moro AJ, Fernandes L, Moura I, Capelo JL.  2007.  Sonoreactor-based technology for fast high-throughput proteolytic digestion of proteins, Feb. Journal of Proteome Research. 6:909-912., Number 2 AbstractWebsite

Fast (120 s) and high-throughput (more than six samples at once) in-gel trypsin digestion of proteins using sonoreactor technology has been achieved. Successful protein identification was done by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF-MS. Specific identification of the adenylylsulphate reductase alfa subunit from a complex protein mixture from Desulfovibrio desulfuricans ATCC 27774 was done as a proof of the methodology. The new sample treatment is of easy implementation, saves time and money, and can be adapted to online procedures and robotic platforms.

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