Distribution of trace organic contaminants and total mercury in sediments from the Bilbao and Urdaibai Estuaries (Bay of Biscay).
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Data Collection↗
Biomedical subjects
L A Fernández
Publications and source records attributed to L A Fernández.
Critical behavior of the specific heat in glass formers.
We show numeric evidence that, at low enough temperatures, the potential energy density of a glass-forming liquid fluctuates over length scales much larger than the interaction range. We focus on the behavior of translationally invariant quantities. The growing correlation length is unveiled by studying the finite-size effects. In the thermodynamic limit, the specific heat and the relaxation time diverge as a power law. Both features point towards the existence of a critical point in the metastable supercooled liquid phase.
Journal Article↗
Simultaneous microwave-assisted extraction of polycyclic aromatic hydrocarbons, polychlorinated biphenyls, phthalate esters and nonylphenols in sediments.
A new method was developed for the simultaneous extraction of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), phthalate esters (PEs), nonylphenols (NPs) and nonylphenol mono- and diethoxylates (NP1EOs and NP2EOs, respectively) in sediment samples by means of a closed microwave system. The extractions were carried out at 21 psi and 80% of microwave power and 15 ml of acetone were used as the common extraction solvent. The filtered extract was further fractionated in two groups using Florisil cartridges: PAHs and PCBs were eluted with n-hexane:toluene (4:1) and the PEs, NPs and ethoxylates were eluted with ethyl acetate. All the compounds were analysed by gas chromatography-mass spectrometry (GC-MS). In case of PAHs and PCBs, the developed method was validated by comparison of the results obtained for the certified reference material NIST 1944 with the certified values. In the absence of a reference material for phthalate esters and nonylphenols, one sediment sample was extracted twice under the optimal conditions in order to check than an exhaustive extraction of the analytes occurred. This method is currently used in the study of the distribution of those organic contaminants in the estuaries of the Bay of Biscay (Spain).
Acetone↗
On-line FT-Raman and dispersive Raman spectra database of artists' materials (e-VISART database).
Raman spectroscopy has been widely applied in the analysis of different types of artwork. This technique is sensitive, reliable, non-destructive and can be used in situ. However, there are few references in the literature regarding specific Raman spectra libraries for the field of artwork analysis. In this paper, the development of two on-line databases with Fourier transform Raman (FT-Raman; 1064 nm) and dispersive Raman (785 nm) spectra of materials used in fine art is presented; both are implemented in the e-vibrational spectroscopic databases of artists' materials database (e-VISART). The database provides not only spectra, but also information about each pigment. It must be highlighted that for each pigment or material several spectra are available from different dealers. Some of the FT-Raman spectra available in the e-VISART database have not been published until now. Some examples in which the e-VISART database has been successfully used are presented.
Journal Article↗
MultiSimplex optimisation of the solid-phase microextraction-gas chromatographic-mass spectrometric determination of polycyclic aromatic hydrocarbons, polychlorinated biphenyls and phthalates from water samples.
Solid-phase microextraction coupled to GC-MS was optimised for the determination of polycyclic aromatic hydrocarbons (PAHs), phthalate esters and polychlorinated biphenyls (PCBs) in water samples. A 30-microm polydimethylsiloxane fiber was immersed in a 30-ml water sample that contained the analytes of interest (PAHs, PCBs and phthalate esters) and the variables studied were extraction time (15-60 min), extraction temperature (30-90 degrees C), desorption time (1-5 min), desorption temperature (220-270 degrees C) and the addition of sodium chloride (0-9 g). The MultiSimplex programme based on the simplex algorithm was used to establish the optimal conditions. MultiSimplex allowed the simultaneous study of the variables mentioned above and considered the answers of all types of compounds studied in this work. Thus, the optimal conditions obtained allowed the simultaneous determination of PAHs, phthalate esters and PCBs. Furthermore, the accuracy and repeatability of the developed method were calculated from water samples spiked at known concentrations of the analytes. Finally, the optimised method was used to analyse water samples from different sampling points of the Urdaibai and Nerbioi-Ibaizabal estuaries (Biscay, Spain).
Gas Chromatography-Mass Spectrometry↗
Automation of a procedure to find the polynomial which best fits (kappa, c1, c2, T) data of electrolyte solutions by non-linear regression analysis using MATHEMATICA software.
A MATHEMATICA package, 'CONDU.M', has been developed to find the polynomial in concentration and temperature which best fits conductimetric data of the type (kappa, c, T) or (kappa, c1, c2, T) of electrolyte solutions (kappa: specific conductivity; ci: concentration of component i; T: temperature). In addition, an interface, 'TKONDU', has been written in the TCL/Tk language to facilitate the use of CONDU.M by an operator not familiarised with MATHEMATICA. All this software is available on line (UPV/EHU, 2001). 'CONDU.M' has been programmed to: (i) select the optimum grade in c1 and/or c2; (ii) compare models with linear or quadratic terms in temperature; (iii) calculate the set of adjustable parameters which best fits data; (iv) simplify the model by elimination of 'a priori' included adjustable parameters which after the regression analysis result in low statistical significance; (v) facilitate the location of outlier data by graphical analysis of the residuals; and (vi) provide quantitative statistical information on the quality of the fit, allowing a critical comparison among different models. Due to the multiple options offered the software allows testing different conductivity models in a short time, even if a large set of conductivity data is being considered simultaneously. Then, the user can choose the best model making use of the graphical and statistical information provided in the output file. Although the program has been initially designed to treat conductimetric data, it can be also applied for processing data with similar structure, e.g. (P, c, T) or (P, c1, c2, T), being P any appropriate transport, physical or thermodynamic property.
Journal Article↗
Formation of disulphide bonds during secretion of proteins through the periplasmic-independent type I pathway.
In this work, we have investigated whether the bacterial type I secretion pathway, which does not have a periplasmic intermediate of the secreted protein, allows the formation of disulphide bridges. To this end, the formation of disulphide bonds has been studied in an antibody single-chain Fv (scFv) fragment secreted by the Escherichia coli haemolysin (Hly) transporter (a paradigm of type I secretion). The scFv antibody fragment was used as a disulphide bond and protein-folding reporter, as it contains two disulphide bridges that are required for its correct folding (i.e. to preserve its antigen-binding activity). We show that an scFv-HlyA hybrid secreted by Hly type I transporter (TolC, HlyB, HlyD) is accumulated in the extracellular medium with the disulphide bonds correctly formed. Neither periplasmic and inner membrane-bound Dsb enzymes (e.g. DsbC, DsbG, DsbB and DsbD) nor cytoplasmic thioredoxins (TrxA and TrxC) were required for scFv-HlyA oxidation. However, a mutation of the thioredoxin reductase gene (trxB), which leads to the cytoplasmic accumulation of the oxidized forms of thioredoxins, had a specific inhibitory effect on the Hly-dependent secretion of disulphide-containing proteins. These data suggest that premature cytoplasmic oxidation of the substrate may interfere with the secretion process. Taken together, these results indicate not only that the type I system tolerates secretion of disulphide-containing proteins, but also that disulphide bonds are specifically formed during the passage of the polypeptide through the export conduit.
Bacterial Proteins↗
Monitoring intracellular levels of XylR in Pseudomonas putida with a single-chain antibody specific for aromatic-responsive enhancer-binding proteins.
We have isolated a recombinant phage antibody (Phab) that binds a distinct epitope of the subclass of the sigma(54)-dependent prokaryotic enhancer-binding proteins that respond directly to aromatic effectors, e.g., those that activate biodegradative operons of Pseudomonas spp. The DNA segments encoding the variable (V) domains of the immunoglobulins expressed by mice immunized with the C-terminal half of TouR (TouRDeltaA) of Pseudomonas stutzeri OX1 were amplified and rearranged in vitro as single-chain Fv (scFv) genes. An scFv library was thereby constructed, expressed in an M13 display system, and subjected to a panning procedure with TouR. One clone (named B7) was selected with high affinity for TouR and XylR (the regulator of the upper TOL operon of the pWW0 plasmid). The epitope recognized by this Phab was mapped to the peptide TPRAQATLLRVL, which seems to be characteristic of the group of enhancer-binding proteins to which TouR and XylR belong and which is located adjacent to the Walker B motif of the proteins. The Phab B7 was instrumental in measuring directly the intracellular levels of XylR expressed from its natural promoter in monocopy gene dosage in Pseudomonas putida under various conditions. Growth stage, the physical form of the protein produced (XylR or XylRDeltaA), and the presence or absence of aromatic inducers in the medium influenced the intracellular pool of these molecules. XylR oscillated from a minimum of approximately 30 molecules (monomers) per cell during exponential phase to approximately140 molecules per cell at stationary phase. Activation of XylR by aromatic inducers decreased the intracellular concentration of the regulator. The levels of the constitutively active variant of XylR named XylRDeltaA were higher, fluctuating between approximately 90 and approximately 570 molecules per cell, depending on the growth stage. These results are compatible with the present model of transcriptional autoregulation of XylR and suggest the existence of mechanisms controlling the stability of XylR protein in vivo.
Amino Acid Sequence↗
Multiple regulatory mechanisms act on the 5' untranslated region of the S-layer gene from Thermus thermophilus HB8.
The role of the 5' untranslated region (5'UTR) of the S-layer gene from Thermus thermophilus was analyzed through the isolation of Delta 5'UTR mutants. In these mutants the half-life of splA mRNA was strongly reduced and slpA transcription was no longer subjected to growth phase-dependent repression. Overproduction and detachment of the external envelopes of the mutants were observed in stationary phase.
5' Untranslated Regions↗
Matrix attachment region-dependent function of the immunoglobulin mu enhancer involves histone acetylation at a distance without changes in enhancer occupancy.
Nuclear matrix attachment regions (MARs), which flank the immunoglobulin mu heavy-chain enhancer on either side, are required for the activation of the distal variable-region (V(H)) promoter in transgenic mice. Previously, we have shown that the MARs extend a local domain of chromatin accessibility at the mu enhancer to more distal sites. In this report, we examine the influence of MARs on the formation of a nucleoprotein complex at the enhancer and on the acetylation of histones, which have both been implicated in contributing to chromatin accessibility. By in vivo footprint analysis of transgenic mu gene constructs, we show that the occupancy of factor-binding sites at the mu enhancer is similar in transcriptionally active wild-type and transcriptionally inactive DeltaMAR genes. Chromatin immunoprecipitation experiments indicate, however, that the acetylation of histones at enhancer-distal nucleosomes is enhanced 10-fold in the presence of MARs, whereas the levels of histone acetylation at enhancer-proximal nucleosomes are similar for wild-type and DeltaMAR genes. Taken together, these data indicate that the function of MARs in mediating long-range chromatin accessibility and transcriptional activation of the V(H) promoter involves the generation of an extended domain of histone acetylation, independent of changes in the occupancy of the mu enhancer.
Acetylation↗
Optimization and comparison of MAE, ASE and Soxhlet extraction for the determination of HCH isomers in soil samples.
The microwave-assisted extraction (MAE), accelerated solvent extraction (ASE) and Soxhlet extraction of two isomers of hexachlorocyclohexane, alpha-HCH and gamma-HCH, from a polluted landfill soil have been optimized following different experimental designs. In the case of microwave-assisted extraction, the following variables were considered: pressure, extraction time, microwave power, percentage of acetone in n-hexane mixture and solvent volume. When ASE extraction was studied the variables were pressure, temperature and extraction time. Finally, the percentage of acetone in n-hexane mixture and the extraction time were the only variables studied for Soxhlet extraction. The concentrations obtained by the three extraction techniques were, within their experimental uncertainties, in good agreement. This fact assures the possibility of using both ASE and MAE techniques in the routine determination of lindane in polluted soils and sediments.
Journal Article↗
Engineering a mouse metallothionein on the cell surface of Ralstonia eutropha CH34 for immobilization of heavy metals in soil.
Here we describe targeting of the mouse metallothionein I (MT) protein to the cell surface of the heavy metal-tolerant Ralstonia eutropha (formerly Alcaligenes eutrophus) CH34 strain, which is adapted to thrive in soils highly polluted with metal ions. DNA sequences encoding MT were fused to the autotransporter beta-domain of the IgA protease of Neisseria gonorrhoeae, which targeted the hybrid protein toward the bacterial outer membrane. The translocation, surface display, and functionality of the chimeric MTbeta protein was initially demonstrated in Escherichia coli before the transfer of its encoding gene (mtb) to R. eutropha. The resulting bacterial strain, named R. eutropha MTB, was found to have an enhanced ability for immobilizing Cd2+ ions from the external media. Furthermore, the inoculation of Cd2+-polluted soil with R. eutropha MTB decreased significantly the toxic effects of the heavy metal on the growth of tobacco plants (Nicotiana bentamiana).
Animals↗
Secretion and assembly of regular surface structures in Gram-negative bacteria.
Bacteria synthesize large-sized surface structures through the ordered polymerization of protein subunits. This results in planar or tubular regular structures that have evolved to accomplish specific functions related to the particular environment in which these bacteria are found. Tubular assemblies known as flagella are the most complex structures known in bacteria and consist of a helical rigid filament, a torsion adapter or hook and a proton-fueled rotator known as the basal body. Pili or fimbriae are less complicated helical filaments, which consist of a major subunit and 3-5 minor subunits or pilins, whose main function is the attachment to specific surfaces. Planar structures known as S-layers are the simplest of these regular assemblies and are generally made up of a single subunit packed as a bidimensional crystal around the whole cell surface. Most of the components of these structures have to be secreted through the inner membrane (IM), the periplasm and the outer membrane (OM) before reaching their final destination. The so called general secretory pathway (GSP), or type II secretion system, appears to be implicated in this process to varying degrees, depending on the structure considered. A few S-layers and pili require GSP components but also need specific terminal branches, such as the well known chaperone-usher pathway. On the other hand, only two of the nearly 40 proteins involved in flagellar assembly are dependent on the GSP, while the external components are secreted through a specific pathway similar to the type III systems identified in some pathogens. Moreover, secretion of subunits of S-layers using dedicated type I machinery, without the involvement of any GSP component, has also been observed.
Amino Acid Sequence↗
Specific secretion of active single-chain Fv antibodies into the supernatants of Escherichia coli cultures by use of the hemolysin system.
A simple method for the nontoxic, specific, and efficient secretion of active single-chain Fv antibodies (scFvs) into the supernatants of Escherichia coli cultures is reported. The method is based on the well-characterized hemolysin transport system (Hly) of E. coli that specifically secretes the target protein from the bacterial cytoplasm into the extracellular medium without a periplasmic intermediate. The culture media that accumulate these Hly-secreted scFv's can be used in a variety of immunoassays without purification. In addition, these culture supernatants are stable over long periods of time and can be handled basically as immune sera.
Bacterial Proteins↗
Sources of influence on medical practice.
OBJECTIVES: To explore the opinion of general practitioners on the importance and legitimacy of sources of influence on medical practice. METHODS: General practitioners (n=723) assigned to Primary Care Teams (PCTs) in two Spanish regions were randomly selected to participate in this study. A self administered questionnaire was sent by mail and collected by hand. The dependent variable collected the opinion on different sources that exert influence on medical practice. Importance was measured with a 9 item scale while legitimacy was evaluated with 16 items measured with a 1 to 7 point Likert scale. RESULTS: The most important and legitimate sources of influence according to general practitioners were: training courses and scientific articles, designing self developed protocols and discussing with colleagues. The worst evaluated were: financial incentives and the role played by the pharmaceutical industry. CONCLUSIONS: The development of medical practice is determined by many factors, grouped around three big areas: organisational setting, professional system and social setting. The medical professional system is the one considered as being the most important and legitimate by general practitioners. Other strategies of influence, considered to be very important by the predominant management culture (financial incentives), are not considered to be so by general practitioners. These results, however, are not completely reliable as regards the real network of influences existing in medical practice, which reflect instead different "value systems".
Clinical Protocols↗
Nuclear matrix attachment regions antagonize methylation-dependent repression of long-range enhancer-promoter interactions.
The immunoglobulin intragenic mu enhancer region acts as a locus control region that mediates transcriptional activation over large distances in germ line transformation assays. In transgenic mice, but not in transfected tissue culture cells, the activation of a variable region (V(H)) promoter by the mu enhancer is dependent on flanking nuclear matrix attachment regions (MARs). Here, we examine the effects of DNA methylation, which occurs in early mouse development, on the function of the mu enhancer and the MARs. We find that methylation of rearranged mu genes in vitro, before transfection, represses the ability of the mu enhancer to activate the V(H) promoter over the distance of 1.2 kb. However, methylation does not affect enhancer-mediated promoter activation over a distance of 150 bp. In methylated DNA templates, the mu enhancer alone induces only local chromatin remodeling, whereas in combination with MARs, the mu enhancer generates an extended domain of histone acetylation. These observations provide evidence that DNA methylation impairs the distance independence of enhancer function and thereby imposes a requirement for additional regulatory elements, such as MARs, which facilitate long-range chromatin remodeling.
Acetylation↗
Probing secretion and translocation of a beta-autotransporter using a reporter single-chain Fv as a cognate passenger domain.
The mechanism of protein secretion mediated by the beta-domain of the Neisseria gonorrhoeae IgA protease, a paradigm of a family of secreted polypeptides of Gram-negative bacteria called autotransporters, has been examined using a single-chain antibody (scFv) as a reporter passenger domain to monitor the translocation process. Fusion of a scFv to the beta-module of the IgA protease allowed us to investigate the passage of the chimeric protein through the periplasm, its insertion into the outer membrane and the movement of the N-terminal moiety towards the cell surface. As the binding activity of the scFv to its target antigen is entirely dependent on the formation of disulphide bonds, the relationship between secretion, folding and formation of S-S bridges could be analysed in detail. In contrast to the current notion that only an unfolded N-passenger domain can be translocated through the beta-domain, our results show that the scFv is able to pass through the outer membrane, albeit at a threefold reduced level, in an active conformation with its disulphide bonds preformed in the periplasm through the action of the DsbA product. These data call for a re-evaluation of the prevailing model for secretion of the N-domain of autotransporters.
Animals↗
Nuclear matrix attachment regions confer long-range function upon the immunoglobulin mu enhancer.
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Animals↗