This work examines a recent study that used various forecasting methods and in particular the Delphi method, to understand how the indicators were selected during the development of the prospective study. It can be concluded that the indicators in the study were selected through discussion on existing knowledge (formal and informal) and the broad consensus of the respective community, which established and confirmed the choice of indicators as the most relevant to prospectively examine the matter concerned. The technical support provided to choose certain forecasting methods as well as to choose the methods that could not be used throughout the development of the work, contributed to the strength of the list of indicators.

Analysis of sequenced bacterial genomes revealed that the genomes encode more than 30% hypothetical and conserved hypothetical proteins of unknown function. Among proteins of unknown function that are conserved in anaerobes, some might be determinants of the anaerobic way of life. This study focuses on two divergent clusters specifically found in anaerobic microorganisms and mainly composed of genes encoding conserved hypothetical proteins. We show that the two gene clusters DVU2103-DVU2104-DVU2105 (orp2) and DVU2107-DVU2108-DVU2109 (orp1) form two divergent operons transcribed by the sigma(54)-RNA polymerase. We further demonstrate that the sigma(54)-dependent transcriptional regulator DVU2106, located between orp1 and orp2, collaborates with sigma(54)-RNA polymerase to orchestrate the simultaneous expression of the divergent orp operons. DVU2106, whose structural gene is transcribed by the sigma(70)-RNA polymerase, negatively retrocontrols its own expression. By using an endogenous pulldown strategy, we identify a physiological complex composed of DVU2103, DVU2104, DVU2105, DVU2108, and DVU2109. Interestingly, inactivation of DVU2106, which is required for orp operon transcription, induces morphological defects that are likely linked to the absence of the ORP complex. A putative role of the ORP proteins in positioning the septum during cell division is discussed.

We report a new strategy that combines a Forster Resonance Energy Transfer (FRET) based spectral codification tool with a single base extension (SBE) reaction for rapid and medium-throughput analysis of single nucleotide polymorphisms (SNPs). This strategy is based on the spectral codification - a donor (fluorophore labeled probe complementary to the region adjacent to an SNP) is used to induce specific FRET signatures from an acceptor fluorophore revealing the SNP variant. Using an SBE reaction and differently labeled ddNTPs, we can directly question each donor probe and retrieve information about which allele variant is present at that locus. The potential of the method is demonstrated by application to simultaneous questioning of two loci in the same reaction tube. Following calibration with all possible combinations of FRET pairs, an evaluation algorithm was calibrated so as to optimize base calling and allow unequivocal allele scoring with more than 80% confidence (for two simultaneous loci being questioned, one homo-and one heterozygous). In conclusion, this spectral codification approach may constitute a solution towards increasing throughput capability of single base extension based assays.

Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt, and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions (Zn(2+), Zn-AK; Co(2+), Co-AK; and Fe(2+), Fe-AK) bound in its LID domain have been determined by X-ray crystallography to resolutions 1.8, 2.0, and 3.0 A, respectively. The zinc and iron forms of the enzyme were crystallized in space group I222, whereas the cobalt-form crystals were C2. The presence of the metals was confirmed by calculation of anomalous difference maps and by X-ray fluorescence scans. The work presented here is the first report of a structure of a metal-containing AK from a Gram-negative bacterium. The native enzyme was crystallized, and only zinc was detected in the LID domain. Co-AK and Fe-AK were obtained by overexpressing the protein in Escherichia coli. Zn-AK and Fe-AK crystallized as monomers in the asymmetric unit, whereas Co-AK crystallized as a dimer. Nevertheless, all three crystal structures are very similar to each other, with the same LID domain topology, the only change being the presence of the different metal atoms. In the absence of any substrate, the LID domain of all holoforms of AK was present in a fully open conformational state. Normal mode analysis was performed to predict fluctuations of the LID domain along the catalytic pathway.

Nanotechnology has prompted researchers to develop new and improved materials aimed at biomedical applications with particular emphasis in diagnostics and therapy. Special interest has been directed at providing enhanced biomolecular diagnostics, including SNP detection gene expression profiles and biomarker characterisation. These strategies have focused on the development of nanoscale devices and platforms that can be used for single molecule characterisation of nucleic acid, DNA or RNA, and protein at an increased rate when compared to traditional techniques. Also, several advances have been reported on DNA analysis in real time, at both high resolution and very high throughputs, suitable for biomedical diagnostics. Here, we shall provide a review of available nanotechnology-based platforms for biomolecular recognition, and their application to molecular diagnostics and genome analysis, with emphasis on the use of noble metal nanoparticles for simple and specific analysis systems. Particular focus will be put on those already being translated into clinical settings. This article is part of a Special Issue entitled: Clinical Proteomics.

In this paper we report on the fabrication and performance of a portable and low cost optoelectronic platform integrating a double color tuned light emitting diode as light source, an amorphous/nanocrystalline silicon photodetector with a flat spectral response in the wavelength range from 520. nm to 630. nm and integrated electronic for signal acquisition and conditioning constituted by current to voltage converter, a filter and an amplification stage, followed by an analog to digital converter, with appropriate software for full automation to minimize human error. Incorporation of the double color tuned light emitting diode provides for a simple yet innovative solution to signal acquisition independently from the light intensity and/or solution concentration, while considerably decreasing production costs. Detection based on Au-nanoprobes constitutes the biorecognition step and allowed identification of specific sequences of Mycobacterium tuberculosis complex, namely Mycobacterium bovis and M. tuberculosis in biological samples.

This working paper is based on the development of the Thesis Plan presented for the Units Project II and Project III at the 1st Winter School of PhD programme on Technology Assessment at FCT/UNL. It focuses the methodology analysis and includes empirical information elements, in order to understand how composite indicators of innovation can influence technology policy decisions. In order to test the hypotheses raised in the Thesis Plan, two separate phases were designed. On the first part, the work tests hypotheses 1 and partially 2, identifying the quality, depth and limitations of three famous complex indicator-based systems, namely the Science, Technology and Industry Scoreboard, the European Innovation Scoreboard 2008 and Innovation Union Scoreboard 2010. On the second phase, the remaining hypotheses are tested adding media databases analysis, which will provide complementary information to a set of interviews to policy makers, in order to understand the role of the composite indicators on technology decisions.

Metal-dependent formate dehydrogenases (Fdh) from prokaryotic organisms are members of the dimethyl sulfoxide reductase family of mononuclear molybdenum-containing and tungsten-containing enzymes. Fdhs catalyze the oxidation of the formate anion to carbon dioxide in a redox reaction that involves the transfer of two electrons from the substrate to the active site. The active site in the oxidized state comprises a hexacoordinated molybdenum or tungsten ion in a distorted trigonal prismatic geometry. Using this structural model, we calculated the catalytic mechanism of Fdh through density functional theory tools. The simulated mechanism was correlated with the experimental kinetic properties of three different Fdhs isolated from three different Desulfovibrio species. Our studies indicate that the C-H bond break is an event involved in the rate-limiting step of the catalytic cycle. The role in catalysis of conserved amino acid residues involved in metal coordination and near the metal active site is discussed on the basis of experimental and theoretical results.

The redox behaviour of a ferredoxin (Fd) from Desulfovibrio alaskensis was characterized by electrochemistry. The protein was isolated and purified, and showed to be a tetramer containing one [3Fe-4S] and one [4Fe-4S] centre. This ferredoxin has high homology with FdI from Desulfovibrio vulgaris Miyazaki and Hildenborough and FdIII from Desulfovibrio africanus. From differential pulse voltammetry the following signals were identified: [3Fe-4S](+1/0) (E(0')=-158+/-5mV); [4Fe-4S](+2/+1) (E(0')=-474+/-5mV) and [3Fe-4S](0/-2) (E(0')=-660+/-5mV). The effect of pH on these signals showed that the reduced [3Fe-4S](0) cluster has a pK'(red)(')=5.1+/-0.1, the [4Fe-4S](+2/+1) centre is pH independent, and the [3Fe-4S](0/-2) reduction is accompanied by the binding of two protons. The ability of the [3Fe-4S](0) cluster to be converted into a new [4Fe-4S] cluster was proven. The redox potential of the original [4Fe-4S] centre showed to be dependent on the formation of the new [4Fe-4S] centre, which results in a positive shift (ca. 70mV) of the redox potential of the original centre. Being most [Fe-S] proteins involved in electron transport processes, the electrochemical characterization of their clusters is essential to understand their biological function. Complementary EPR studies were performed.

In the present work, the proton-transfer reactions of the methylpyranomalvidin-3-O-glucoside pigment in water with different pH values was studied by NMR and UV-visible spectroscopies. The results showed four equilibrium forms: the methylpyranomalvidin-3-O-glucoside cation, the neutral quinoidal base, the respective anionic quinoidal base, and a dianionic base unprotonated at the methyl group. According to the NMR data, it seems that for methylpyranomalvidin-3-O-glucoside besides the acid base equilibrium between the pyranoflavylium cation and the neutral quinoidal base, a new species is formed at pD 4.88-6.10. This is corroborated by the appearance of a new set of signals in the NMR spectrum that may be assigned to the formation of hemiketal/cis-chalcone species to a small extent. The two ionization constants (pK(a1) and pK(a2)) obtained by both methods (NMR and UV-visible) for methylpyranomalvidin-3-O-glucoside are in agreement (pK(a1) = 5.17 +/- 0.03; pK(a2) = 8.85 +/- 0.08; and pK(a1) = 4.57 +/- 0.07; pK(a2) = 8.23 +/- 0.04 obtained by NMR and UV-visible spectroscopies, respectively). Moreover, the fully dianionic unprotonated form (at the methyl group) of the methylpyranomalvidin-3-O-glucoside is converted slowly into a new structure that displays a yellow color at basic pH. On the basis of the results obtained through LC-MS and NMR, the proposed structure was found to correspond to the flavonol syringetin-3-glucoside.

The use of cellulosic fibers as load bearing constituents in composite materials has increased over the last decade due to their relative cheapness compared to conventional materials such as glass and aramid fibers, their ability to recycle, and because they compete well in terms of strength per weight of material. All-cellulosic based composites prepared from cellulose derivatives based matrices and microcrystalline cellulosic fibers made by direct coupling between fibers and matrix present interesting mechanical and gas permeation properties, thus being potential candidates for packaging materials. Both the cellulosic matrix and the reinforcing fibers are biocompatible and widely used in the pharmaceutical industry, which is very important for the envisaged application. In addition to their biocompatibility, cellulosic systems have the ability to form both thermotropic and lyotropic chiral nematic phases, and the composites produced from the latter show improved mechanical properties due to fiber orientation induced by the anisotropic matrix. The preparation and characterization (morphological, topographical, mechanical, gas barrier properties) of all-cellulosic based composites are described in this chapter.

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Gene knock-out studies on Geobacter sulfurreducens cells showed that the periplasmic triheme cytochrome PpcA is involved in respiratory pathways leading to the extracellular reduction of Fe(III) and U(VI) oxides. The crucial role of this protein in bridging the electron transfer between the cytoplasm and cell exterior was further supported by proteomics studies. In comparison with non-heme proteins, the presence of numerous proton-containing groups in the heme groups causes additional challenges to the full protein assignment and structure calculation. Here, we report the complete assignment of the heme proton signals together with the 1H and 15N backbone and side chain assignments of the reduced form of PpcA.

The present work deals with the use of innovation indicators in the decision-making process. It intends to contribute to the discussion on the construction, use and analysis of indicator systems and also to evaluate its weight on decision-making in innovation. The goal is to help understand how innovation indicators can influence technology policy and through it, society at large. This work will start by analysing the use of indicators (their problems and consistency) and other sources of information that contribute to build the opinions of innovation decision makers. This will be followed by a survey and interviews with main innovation actors. The results will shed light on the impact of the use of indicators by the innovation community – both in terms of technology policy and in the social sphere. Proposals and implications for the future will be advanced, hopefully adding new contributions to the governance of the science, technology and innovation field.

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