Biomedical subjects

J Salgado

Publications and source records attributed to J Salgado.

At least 19 recordsLinked to original sources

PubMed2005

MCNP simulation to optimise in-pile and shielding parts of the Portuguese SANS instrument.

A Small Angle Neutron Scattering instrument is being installed at one end of the tangential beam tube of the Portuguese Research Reactor. The instrument is fed using a neutron scatterer positioned in the middle of the beam tube. The scatterer consists of circulating H2O contained in a hollow disc of Al. The in-pile shielding components and the shielding installed around the neutron selector have been the object of an MCNP simulation study. The quantities calculated were the neutron and gamma-ray fluxes in different positions, the energy deposited in the material by the neutron and gamma-ray fields, the material activation resulting from the neutron field and radiation doses at the exit wall of the shutter and around the shielding. The MCNP results are presented and compared with results of an analytical approach and with experimental data collected after installation.

Computer Simulation↗

PubMed2005

Towards the enhancement of the photon/neutron discrimination of C6D6 detectors in the range from 1 to 10 MeV using liquid scintillator materials doped with high-Z elements.

The study on the behaviour of deuterated benzene detectors in the energy range from 1 to 10 MeV has been carried out. It is shown that the photon-to-neutron discrimination, attained with standard detectors, can be improved by doping the C6D6 liquid scintillator with high-Z elements. The motivation for doping the organic scintillator stems from the fact that they should increase the gamma detection efficiencies with no significant changes in the abilities to detect neutrons. The results obtained using the MCNP and EGS4 codes show that increasing the fraction of high-Z elements: (a) the energy deposited in the medium by photons increases, (b) the energy deposited by neutrons decreases and (c) the rate of detection of photon/neutron is enhanced. Owing to their low sensitivity to neutrons and the enhanced gamma detection efficiency, these detectors could be ideally used to carry out studies in mixed neutron-photon fields in the energy range considered and to assess the gamma backgrounds in noisy neutron environments.

Algorithms↗

PubMed2005

Structure-based assessment of BRCA1 and BRCA2 mutations in a small Spanish population.

Breast cancer is the most frequent cancer type among women in the world. There is abundant evidence, that alterations in the breast cancer susceptibility genes, BRCA1 and BRCA2, are present in a large proportion of families with multiple cases of breast and ovarian cancer. Our aim was to better understand the molecular and structural insights associated with the most frequent alterations, found in the BRCA1 and BRCA2 genes, within our patients. We analyzed 50 breast cancer cases. Of those, 24% were found to carry deleterious mutations, and up to 10 rare variants of unknown significance were detected. The frequency of polymorphic changes was considerably different between genes, BRCA1 (55%) and BRCA2 (19.4%). By looking at the protein level, the changes observed within the BRCA1 and BRCA2 genes could affect not only the nucleic location of the protein but also disrupt the folding and, therefore, the tumor suppressor function.

BRCA1 Protein↗

PubMed2004

Neutron capture cross section measurement of 151Sm at the CERN neutron time of flight facility (n_TOF).

The151Sm(n,gamma)152Sm cross section has been measured at the spallation neutron facility n_TOF at CERN in the energy range from 1 eV to 1 MeV. The new facility combines excellent resolution in neutron time-of-flight, low repetition rates, and an unsurpassed instantaneous luminosity, resulting in rather favorable signal/background ratios. The 151Sm cross section is of importance for characterizing neutron capture nucleosynthesis in asymptotic giant branch stars. At a thermal energy of kT=30 keV the Maxwellian averaged cross section of this unstable isotope (t(1/2)=93 yr) was determined to be 3100+/-160 mb, significantly larger than theoretical predictions.

Journal Article↗

PubMed2004

Epithermal neutron self-shielding factors in foils for collimated beams.

An epithermal neutron self-shielding factor must be introduced to take into account the absorption of a neutron beam crossing a sample. This factor depends on the geometry and dimension of the sample, as well as on the physical and nuclear properties of the nuclides. On the basis of a dimensionless variable, which includes the relevant characteristics of the sample, universal curves for monoenergetic and 1/E collimated neutron beams are proposed, which enable the determination of the self-shielding factor for isolated resonances of high absorber nuclides.

Gold↗

PubMed2002

Field preconcentration of cadmium from seawater by using a minicolumn packed with Amberlite XAD-4/4-(2-pyridylazo) resorcinol and its flow-injection-flame atomic absorption spectrometric determination at the ng L(-1) Level.

A flow injection analysis-flame atomic absorption spectrometric method for the determination of cadmium in seawater was developed with the aim of yielding a sensitive assay with a low detection limit. The method employs a field flow preconcentration technique involving a minicolumn containing Amberlite XAD-4 impregnated with the complexing agent 4-(2-pyridylazo) resorcinol. A Plackett-Burman 2(7)x3/32 design for seven factors (sample pH, sample flow rate, eluent volume, eluent concentration, eluent flow rate, ethanol percentage in the eluent and minicolumn diameter) was carried out in order to find the significant variables affecting the field continuous preconcentration system (FCPS) and the flow injection elution manifold for cadmium determination in seawater samples by flame atomic absorption spectrometry. Cadmium can be preconcentrated with an enrichment factor of 1053 for a sample volume of 200 mL and a preconcentration time of 57 min. In these experimental conditions, the method provides a linear relationship between absorbance and cadmium concentration in the range from 22-1900 ng L(-1), with a detection limit (3SD) of 6 ng L(-1). The precision (expressed as relative standard deviation) for eleven independent determinations reached values of 8.9-0.8% in cadmium solutions of 50-700 ng L(-1). Analysis of certified reference materials (SLEW-3 and NASS-5) showed good agreement with the certified value. This procedure was applied to the determination of cadmium in seawater from Galicia (Spain).

Cadmium↗

PubMed2002

Respiratory oscillations in yeast: clock-driven mitochondrial cycles of energization.

Respiratory oscillations in continuous yeast cultures can be accounted for by cyclic energization of mitochondria, dictated by the demands of a temperature-compensated ultradian clock with a period of 50 min. Inner mitochondrial membranes show both ultrastructural modifications and electrochemical potential changes. Electron transport components (NADH and cytochromes c and c oxidase) show redox state changes as the organisms cycle between their energized and de-energized phases. These regular cycles are transiently perturbed by uncouplers of energy conservation, with amplitudes more affected than period; that the characteristic period is restored after only one prolonged cycle, indicates that mitochondrial energy generation is not part of the clock mechanism itself, but is responding to energetic requirement.

Activity Cycles↗

PubMed2002

Monte Carlo calculation of epithermal neutron resonance self-shielding factors in foils of different materials.

Epithermal neutron resonance self-shielding factors in foils of materials used as activation detectors or as targets for radionuclide production have been calculated using the MCNP code. Two irradiation conditions have been considered: (a) foils immersed into an isotropic neutron flux and (b) foils submitted to a collimated neutron beam. The self-shielding factors, Gres(t), for gold, indium, manganese and cobalt have been compared with available published values. The self-shielding factor depends on various physical and nuclear parameters. However, it is shown that for the isotropic case and for high absorber elements submitted to a collimated beam, a dimensionless variable could be adopted that describes the self-shielding factors of different materials by quasi "universal curves". Gres(t) for the collimated beam are always higher than those for the isotropic case.

Monte Carlo Method↗

PubMed2001

Monte Carlo calculation of epithermal neutron resonance self-shielding factors in wires of different materials.

Epithermal neutron resonance self-shielding factors in wires of materials used as activation detectors or as targets for radionuclide production have been calculated using the MCNP code. The energy dependent self-shielding factor depends on the ratio scattering/capture cross sections. The self-shielding factors for cobalt and gold have been compared with available values. The self-shielding factor depends on various physical and nuclear parameters. However, an adimensional variable can be adopted that describes the self-shielding factors of different materials by a quasi "universal curve".

Journal Article↗

PubMed2001

Membrane-bound structure and alignment of the antimicrobial beta-sheet peptide gramicidin S derived from angular and distance constraints by solid state 19F-NMR.

The antimicrobial properties of the cyclic beta-sheet peptide gramicidin S are attributed to its destabilizing effect on lipid membranes. Here we present the membrane-bound structure and alignment of a derivative of this peptide, based on angular and distance constraints. Solid-state 19F-NMR was used to study a 19F-labelled gramicidin S analogue in dimyristoylphosphatidylcholine bilayers at a lipid:peptide ratio of 80:1 and above. Two equivalent leucine side chains were replaced by the non-natural amino acid 4F-phenylglycine, which serves as a highly sensitive reporter on the structure and dynamics of the peptide backbone. Using a modified CPMG multipulse sequence, the distance between the two 19F-labels was measured from their homonuclear dipolar coupling as 6 A. in good agreement with the known backbone structure of natural gramicidin S in solution. By analyzing the anisotropic chemical shift of the 19F-labels in macroscopically oriented membrane samples, we determined the alignment of the peptide in the bilayer and described its temperature-dependent mobility. In the gel phase, the 19F-labelled gramicidin S is aligned symmetrically with respect to the membrane normal, i.e., with its cyclic beta-sheet backbone lying flat in the plane of the bilayer, which is fully consistent with its amphiphilic character. Upon raising the temperature to the liquid crystalline state, a considerable narrowing of the 19F-NMR chemical shift dispersion is observed, which is attributed the onset of global rotation of the peptide and further wobbling motions. This study demonstrates the potential of the 19F nucleus to describe suitably labelled polypeptides in membranes, requiring only little material and short NMR acquisition times.

Anti-Bacterial Agents↗

PubMed2001

[Acute cholangitis caused by choledocholithiasis: traditional surgery or endoscopic biliary drainage].

BACKGROUND: Endoscopic drainage of the biliary tree for acute cholangitis is a therapeutic modality with a lower mortality and complication rates. AIM: To compare endoscopic drainage with surgical treatment in the emergency management of acute cholangitis. PATIENTS AND METHODS: Between 1995 and 1998, sixty five patients with acute cholangitis were subjected to an endoscopic drainage of the biliary tree. In the same period, 40 patients were treated with traditional surgical procedures. The evolution of both groups of patients were compared. RESULTS: Sixty two patients (95.4%) subjected to endoscopic treatment had a satisfactory evolution, compared with 23 (58%) of those operated (p < 0.001). Five operated patients and no individual subjected to endoscopic drainage died (p < 0.01). Mean postoperative hospital stay of operated patients was 15.5 +/- 19.6 days compared to 5.8 +/- 4.2 days in those subjected to endoscopic drainage (p < 0.001). Definitive resolution of biliary obstruction was achieved in 83% of patients subjected to endoscopic drainage or traditional surgery. CONCLUSIONS: Endoscopic drainage has a lower rate of complications and mortality than traditional surgery, in the treatment of acute cholangitis.

Acute Disease↗

PubMed1999

1H NMR spectroscopy of the binuclear Cu(II) active site of Streptomyces antibioticus tyrosinase.

The 600 MHz 1H NMR spectrum of tyrosinase (31 kDa) of Streptomyces antibioticus in the oxidized, chloride-bound form is reported. The downfield part of the spectrum (15-55 ppm) exhibits a large number of paramagnetically shifted signals. The paramagnetism is ascribed to a thermally populated triplet state. The signals derive from six histidines binding to the metals through their Nepsilon atoms. There is no evidence for endogenous bridges. The exchange coupling, -2J, amounts to 298 cm(-1). In the absence of chloride the peaks broaden. This is ascribed to a slowing down of the electronic relaxation. The exchange coupling decreases to -2J=103 cm(-1).

Binding Sites↗

PubMed1999

Paramagnetic NMR studies of blue and purple copper proteins.

1H- and 13C-NMR spectroscopy is applied to investigate the CU(A) and type 1 active sites of copper proteins in solution. The analysis of hyperfine shifted 1H resonances allows the comparison of the electron spin density delocalization in the CU(A) site of the wild-type soluble domains of various cytochrome c oxidases (Thermus thermophilus, Paracoccus denitrificans, and Paracoccus versutus) and genetically engineered constructs (soluble domain of quinol oxidase from Escherichia coli and Thiobacillus versutus amicyanin). Comparable spin densities are found on the two terminal His ligands for the wild-type constructs as opposed to the engineered proteins where the spin is more unevenly distributed on the two His residues. A reevaluation of the Cys H(beta) chemical shifts that is in agreement with the data published for both the P. denitrificans and the P. versutus Cu(A) soluble domains confirms the thermal accessibility of the 2B(3u) electronic excited state and indicates the existence of slightly different spin densities on the two bridging Cys ligands. The 13C-NMR spectrum of isotopically enriched oxidized azurin from Pseudomonas aeruginosa reveals six fast relaxing signals, which can be partially identified by 1- and 2-dimensional (1-D, 2-D) direct detection techniques combined with 3-D triple resonance experiments. The observed contact shifts suggest the presence of direct spin density transfer and spin polarization mechanisms for the delocalization of the unpaired electron.

Azurin↗

PubMed1999

Paramagnetic NMR investigations of Co(II) and Ni(II) amicyanin.

The paramagnetic 1H NMR spectra of the Co(II) and Ni(II) substituted forms of the type 1 blue copper protein (cupredoxin) amicyanin have been assigned. This is the first such analysis of a cupredoxin, which has a distorted tetrahedral active site with the ligands provided by two histidines, a cysteine and a methionine. The isotropic shifts of the resonances in these spectra are compared with those of Co(II) and Ni(II) azurin. A number of interesting similarities and differences are found. The coordination of the metal by the two equatorial histidine ligands is very similar in both proteins. The interaction between the introduced metal and the thiolate sulfur of the equatorial cysteine ligand is enhanced in the amicyanin derivatives. Resonances belonging to the weak axial methionine ligand exhibit much larger shifts in the amicyanin derivatives, indicative of shorter M(II)-S(Met) distances. The presence of shorter axial M(II)-S(Met) and equatorial M(II)-S(Cys) distances in both Co(II) and Ni(II) amicyanin is ascribed to the absence of a second axially interacting amino acid at the active site of this cupredoxin.

Azurin↗

PubMed1998

Determination of the magnetic axes of cobalt(II) and nickel(II) azurins from 1H NMR data: influence of the metal and axial ligands on the origin of magnetic anisotropy in blue copper proteins.

The orientation and the axial, Deltachiax, and rhombic, Deltachirh, components of the magnetic susceptibility tensor anisotropy for the cobalt(II) and nickel(II) derivatives of azurin from Pseudomonas aeruginosa have been determined from 1H NMR data. For both derivatives, the axial geometry of the system determines the orientation of the chi-tensor, whose z-axis forms an angle of 18.6 and 20.1 degrees with the Cu-OGly45 axial bond in the cobalt(II) and nickel(II) derivatives, respectively. For protons close to this axis, large negative pseudocontact shifts are observed, while those close to the NNS plane of the equatorial ligands experience lower and positive pseudocontact shifts for the same distance. Dipolar shifts are larger in the cobalt derivative, not only because of the larger spin number but also due to its intrinsically higher anisotropy. The contact contribution to the hyperfine shifts for the coordinated residues has been evaluated and analyzed in terms of unpaired spin delocalization mechanisms and geometry considerations. The results are extended to other blue copper proteins whose cobalt derivatives have been studied by 1H NMR. The electronic structure and its implications in the redox properties of the native copper proteins are also commented.

Anisotropy↗

PubMed1998

Understanding the electronic properties of the CuA site from the soluble domain of cytochrome c oxidase through paramagnetic 1H NMR.

The soluble domain of the subunit II of cytochrome c oxidase from Paracoccus versutus was cloned, expressed, and studied by 1H NMR at 600 MHz. The properties of the redox-active dinuclear CuA site in the paramagnetic mixed-valence Cu(I)-Cu(II) state were investigated in detail. A group of relatively sharp signals found between 30 and 15 ppm in the 1H NMR spectrum correspond to the imidazole protons of the coordinated histidines (H181 and H224). A second group of broader and farther shifted signals between 50 and 300 ppm are assigned to Hbeta protons of the bridging cysteines (C216 and C220); the protons from the weak M227 and E218 ligands do not shift outside of the diamagnetic envelope. About 40% of the total spin density appears delocalized over the cysteine-bridging ligands while a much smaller amount is delocalized on the two ligand histidines. The latter have similar spin density distributions. Analysis of the pattern of the hyperfine shifts of the Cys H beta protons shows that the ground state bears 2B3u character, in which the sulfur lobes in the singly occupied molecular orbital are aligned with the Cu-Cu axis. Analysis of the temperature dependence of the shifts of the Cys H beta signals leads to the conclusion that the 2B2u excited state is thermally accessible at room temperature (Delta E approximately kT).

Copper↗

PubMed1998

The dynamic properties of the M121H azurin metal site as studied by NMR of the paramagnetic Cu(II) and Co(II) metalloderivatives.

The M121H azurin mutant in solution presents various species in equilibrium that can be detected and studied by 1H NMR of the Cu(II) and Co(II) paramagnetic metalloderivatives. In both cases up to three species are observed in slow exchange, the proportions of which are different for the two metalloderivatives. Above pH 5 the major species displays a tetrahedral coordination in which the His121 can be observed as a coordinated residue. Its metal site corresponds to a new type of site that is defined as a type 1.5 site. The second and third species resemble the wild type (type 1) azurin and, above pH 4.5, they are present only at a low concentration. At low pH a protonation process increases the proportion of both type 1 species at the expense of the type 1.5 species. This process, characterized by a pKa = 4.3, is assigned to the protonation of His121. At high pH the NMR spectrum of the Co(II)-M121H azurin experiences an additional transition, which is not observed in the case of the Cu(II) protein. The dynamic properties of the M121H metal site appear to be related to changes in the coordination geometry and the strength of the axial interaction between the Ndelta1 (His121) and the metal.

Azurin↗

PubMed1998

A comprehensive biochemical and genetic analysis of the yeast U1 snRNP reveals five novel proteins.

The U1 snRNP is essential for recognition of the pre-mRNA 5'-splice site and the subsequent assembly of the spliceosome. Yeast U1 snRNP is considerably more complex than its metazoan counterpart, which suggests possible differences between yeast and metazoa in early splicing events. We have comprehensively analyzed the composition of yeast U1 snRNPs using a combination of biochemical, mass spectrometric, and genetic methods. We demonstrate the specific association of four novel U1 snRNP proteins, Snu71p, Snu65p, Nam8p, and Snu56p, that have no known metazoan homologues. A fifth protein, Npl3p, is an abundant cellular component that reproducibly co-purifies with the U1 snRNP, but its association is salt-sensitive. Therefore, we are unable to establish conclusively whether it binds specifically to the U1 snRNP. Interestingly, Nam8p and Npl3p were previously assigned functions in (pre-m)RNA-metabolism; however, so far, no association with U1 snRNP has been demonstrated or proposed. We also show that the yeast SmB protein is a U1 snRNP component. Yeast U1 snRNP therefore contains 16 different proteins, including seven snRNP core proteins, three homologues of the metazoan U1 snRNP-specific proteins, and six yeast-specific U1 snRNP proteins. We have simultaneously continued the characterization of additional mutants isolated in a synthetic lethal (MUD) screen for genes that functionally cooperate with U1 snRNA. Consistent with the biochemical results, mud10, mud15, and mud16 are alleles of SNU56, NAM8, and SNU65, respectively. mud10 and mud15 affect the in vivo splicing efficiency of noncanonical introns. Moreover, mud10p strongly affects the in vitro formation of splicing complexes, and extracts from the mud15 strain contain a U1 snRNP that migrates aberrantly on native gels. Finally, we show that Nam8p/Mud15p contributes to the stability of U1 snRNP.

Amino Acid Sequence↗