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Biomedical subjects

A Pesce

Publications and source records attributed to A Pesce.

At least 19 recordsLinked to original sources
PubMed2003

[Assessment of the habits of physicians involved in the management of HIV-infected patients. A clinical audit on the biological follow-up].

BACKGROUND: The aim of this study was to assess the habits of hospital and community-based physicians involved in the management of HIV-infected patients and to measure the gap between their practice and follow-up guidelines. METHOD: The guidelines considered as reference were the 1998 Dormont report. Data were prospectively collected from the medical files of the first 10 HIV-infected patients who presented for an out-patient visit (laboratory tests at initial consultation, type and frequency of follow-up during the previous year, relation between biological data and treatment strategy). RESULTS: 22 physicians (14 hospital-based physicians (HP) and 8 community-based general practitioners (GP) participated in the survey. Initial biological data were available for 211 patients; 45% had tests strictly conforming to the recommendations (HP: 57%, GP 23%; p<0.001). Among patients followed by a GP, the initial biological assessment was adequate in 7% of cases when an opiate substitute was prescribed versus 33% in the absence of opiate substitute prescription (p=0.05). For all patients, syphilis serology was the test most frequently lacking (38%). Among 78 patients with HIV-RNA levels>5,000 copies/ml, 18% did not benefit from a change in treatment. Among the patients treated by a GP, 15% had a three-fold increase in HIV-RNA, compared to their initial measurement. Of these, 3/4 were redirected to a hospital out-patient unit. CONCLUSION: This study highlights the discrepancy between initial laboratory testing and expert recommendations, particularly concerning patients attended by a GP. Improvement in data collection is essential. However, recommendations concerning patients' biological follow-up are applied, with the exception of the delay between the initial prescription or treatment modification and HIV-RNA measurement, which should be shortened.

Diagnostic Tests, Routine↗
PubMed2003

Static and dynamic water molecules in Cu,Zn superoxide dismutase.

Understanding protein hydration is a crucial, and often underestimated issue, in unraveling protein function. Molecular dynamics (MD) computer simulation can provide a microscopic description of the water behavior. We have applied such a simulative approach to dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase, comparing the water molecule sites determined using 1.0 ns MD simulation with those detected by X-ray crystallography. Of the water molecules detected by the two techniques, 20% fall at common sites. These are evenly distributed over the protein surface and located around crevices, which represent the preferred hydration sites. The water mean residence time, estimated by means of a survival probability function on a given protein hydration shell, is relatively short and increases for low accessibility sites constituted by polar atoms. Water molecules trapped in the dimeric protein intersubunit cavity, as identified in the crystal structure, display a trajectory mainly confined within the cavity. The simulation shows that these water molecules are characterized by relatively short residence times, because they continuously change from one site to another within the cavity, thus hinting at the absence of any relationship between spatial and temporal order for solvent molecules in proximity of protein surface.

Algorithms↗
PubMed2003

Active-site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase.

The influence of the constitutive metal ions on the equilibrium properties of dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase has been studied for the wild-type and for two mutant protein forms bearing a negative charge in the amino acid clusters at the dimer association interface. Depletion of copper and zinc dissociates the two mutant proteins into monomers, which reassemble toward the dimeric state upon addition of stoichiometric amounts of zinc. Pressure-dependent dissociation is observed for the copper-depleted wild-type and mutated enzymes, as monitored by the fluorescence shift of a unique tryptophan residue located at the subunit association interface. The spectral shift occurs slowly, reaching a plateau after 15-20 minutes, and is fully reversible. The recovery of the original fluorescence properties, after decompression, is fast (less than four minutes), suggesting that the isolated subunit has a relatively stable structure, and excluding the presence of stable intermediates during the dimer-monomer transition. The dimer dissociation process is still incomplete at 6.5 kbar for the copper-depleted wild-type and mutated enzymes, at variance with what is generally observed for oligomeric proteins that dissociate below 3 kbar. Measurement of the degree of dissociation, at two different protein concentrations, allows us to calculate the standard volume variation upon association, Delta V, and the dissociation constant K(d0), at atmospheric pressure, (25 ml/mol and 3 x 10(-7)M, respectively). The holoprotein is fully dimeric even at 6.5 kbar, which allows us to evaluate a lower Delta G degrees limit of 11.5 kcal/mol, corresponding to a dissociation constant K(d0)<10(-9)M.

Binding Sites↗
PubMed2001

Crystallization and preliminary X-ray analysis of neural haemoglobin from the nemertean worm Cerebratulus lacteus.

The nemertean worm Cerebratulus lacteus neural tissue haemoglobin (109 amino acids, the shortest known haemoglobin) has been overexpressed in Escherichia coli, purified and crystallized. A highly redundant native data set has been collected at the Cu K(alpha) wavelength to 2.05 A resolution. The crystals belong to the orthorhombic P2(1)2(1)2(1) space group, with unit-cell parameters a = 42.5, b = 43.1, c = 60.2 A and one molecule per asymmetric unit. The anomalous difference Patterson map clearly reveals the position of the haem Fe atom, thus paving the way for MAD/SAD structure determination.

Animals↗
PubMed2001

Mycobacterium tuberculosis hemoglobin N displays a protein tunnel suited for O2 diffusion to the heme.

Macrophage-generated oxygen- and nitrogen-reactive species control the development of Mycobacterium tuberculosis infection in the host. Mycobacterium tuberculosis 'truncated hemoglobin' N (trHbN) has been related to nitric oxide (NO) detoxification, in response to macrophage nitrosative stress, during the bacterium latent infection stage. The three-dimensional structure of oxygenated trHbN, solved at 1.9 A resolution, displays the two-over-two alpha-helical sandwich fold recently characterized in two homologous truncated hemoglobins, featuring an extra N-terminal alpha-helix and homodimeric assembly. In the absence of a polar distal E7 residue, the O2 heme ligand is stabilized by two hydrogen bonds to TyrB10(33). Strikingly, ligand diffusion to the heme in trHbN may occur via an apolar tunnel/cavity system extending for approximately 28 A through the protein matrix, connecting the heme distal cavity to two distinct protein surface sites. This unique structural feature appears to be conserved in several homologous truncated hemoglobins. It is proposed that in trHbN, heme Fe/O2 stereochemistry and the protein matrix tunnel may promote O2/NO chemistry in vivo, as a M.tuberculosis defense mechanism against macrophage nitrosative stress.

Amino Acid Sequence↗
PubMed2001

Very high resolution structure of a trematode hemoglobin displaying a TyrB10-TyrE7 heme distal residue pair and high oxygen affinity.

Monomeric hemoglobin from the trematode Paramphistomum epiclitum displays very high oxygen affinity (P(50)<0.001 mm Hg) and an unusual heme distal site containing tyrosyl residues at the B10 and E7 positions. The crystal structure of aquo-met P. epiclitum hemoglobin, solved at 1.17 A resolution via multiwavelength anomalous dispersion techniques (R-factor=0.121), shows that the heme distal site pocket residue TyrB10 is engaged in hydrogen bonding to the iron-bound ligand. By contrast, residue TyrE7 is unexpectedly locked next to the CD globin region, in a conformation unsuitable for heme-bound ligand stabilisation. Such structural organization of the E7 distal residue differs strikingly from that observed in the nematode Ascaris suum hemoglobin (bearing TyrB10 and GlnE7 residues), which also displays very high oxygen affinity. The oxygenation and carbonylation parameters of wild-type P. epiclitum Hb as well as of single- and double-site mutants, with residue substitutions at positions B10, E7 and E11, have been determined and are discussed here in the light of the protein atomic resolution crystal structure.

Amino Acid Sequence↗
PubMed2001

Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase.

The functional properties and X-ray structures of five mutant forms of Photobacterium leiognathi Cu,Zn superoxide dismutase carrying single mutations at residues located at the dimer association interface have been investigated. When compared to the wild-type enzyme, the three-dimensional structures of the mutants show structural perturbations limited to the proximity of the mutation sites and substantial identity of active site geometry. Nonetheless, the catalytic rates of all mutants, measured at neutral pH and low ionic strength by pulse radiolysis, are higher than that of the wild-type protein. Such enzymatic activity increase is paralleled by enhanced active site accessibility to external chelating agents, which, in the mutated enzyme, remove more readily the active site copper ion. It is concluded that mutations at the prokaryotic Cu,Zn superoxide dismutase subunit interface can transduce dynamical perturbation to the active site region, promoting substrate active site accessibility. Such long-range intramolecular communication effects have not been extensively described before within the Cu,Zn superoxide dismutase homology family.

Amino Acid Substitution↗
PubMed2001

HPLC analysis of reduced and oxidized coenzyme Q(10) in human plasma.

BACKGROUND: The percentage of reduced coenzyme Q(10) (CoQ(10)H(2)) in total coenzyme Q(10) (TQ(10)) is decreased in plasma of patients with prematurity, hyperlipidemia, and liver disease. CoQ(10)H(2) is, however, easily oxidized and difficult to measure, and therefore reliable quantification of plasma CoQ(10)H(2) is of clinical importance. METHODS: Venous blood was collected into evacuated tubes containing heparin, which were immediately placed on ice and promptly centrifuged at 4 degrees C. The plasma was harvested and stored in screw-top polypropylene tubes at -80 degrees C until analysis. After extraction with 1-propanol and centrifugation, the supernatant was injected directly into an HPLC system with coulometric detection. RESULTS: The in-line reduction procedure permitted transformation of CoQ(10) into CoQ(10)H(2) and avoided artifactual oxidation of CoQ(10)H(2). The electrochemical reduction yielded 99% CoQ(10)H(2). Only 100 microL of plasma was required to simultaneously measure CoQ(10)H(2) and CoQ(10) over an analytical range of 10 microg/L to 4 mg/L. Intra- and interassay CVs for CoQ(10) in human plasma were 1.2-4.9% across this range. Analytical recoveries were 95.8-101.0%. The percentage of CoQ(10)H(2) in TQ(10) was approximately 96% in apparently healthy individuals. The method allowed analysis of up to 40 samples within an 8-h period. CONCLUSIONS: This optimized method for CoQ(10)H(2) analysis provides rapid and precise results with the potential for high throughput. This method is specific and sufficiently sensitive for use in both clinical and research laboratories.

Calibration↗
PubMed2000

Single mutation at the intersubunit interface confers extra efficiency to Cu,Zn superoxide dismutase.

The Val28-->Gly single mutant at the subunit interface of Cu,Zn superoxide dismutase from Photobacterium leiognathi displays a k(cat)/K(M) value of 1.7x10(10) M(-1) s(-1), twice that of the native enzyme. Analysis of the three-dimensional structure indicates that the active site Cu,Zn center is not perturbed, slight structural deviations being only localized in proximity of the mutation site. The enzyme-substrate association rate, calculated by Brownian dynamics simulation, is identical for both enzymes, indicating that the higher catalytic efficiency of the Val28-->Gly mutant is not due to a more favorable electrostatic potential distribution. This result demonstrates the occurrence of an intramolecular communication between the mutation site and the catalytic center, about 18 A away and indicates a new strategy to encode extra efficiency within other members of this enzymatic family.

Amino Acid Substitution↗
PubMed2000

Functional and crystallographic characterization of Salmonella typhimurium Cu,Zn superoxide dismutase coded by the sodCI virulence gene.

The functional and three-dimensional structural features of Cu,Zn superoxide dismutase coded by the Salmonella typhimurium sodCI gene, have been characterized. Measurements of the catalytic rate indicate that this enzyme is the most efficient superoxide dismutase analyzed so far, a feature that may be related to the exclusive association of the sodCI gene with the most pathogenic Salmonella serotypes. The enzyme active-site copper ion is highly accessible to external probes, as indicated by quenching of the water proton relaxation rate upon addition of iodide. The shape of the electron paramagnetic resonance spectrum is dependent on the frozen or liquid state of the enzyme solution, suggesting relative flexibility of the copper ion environment. The crystal structure (R-factor 22.6%, at 2.3 A resolution) indicates that the dimeric enzyme adopts the quaternary assembly typical of prokaryotic Cu,Zn superoxide dismutases. However, when compared to the structures of the homologous enzymes from Photobacterium leiognathi and Actinobacillus pleuropneumoniae, the subunit interface of Salmonella Cu,Zn superoxide dismutase shows substitution of 11 out of 19 interface residues. As a consequence, the network of structural water molecules that fill the dimer interface cavity is structured differently from the other dimeric bacterial enzymes. The crystallographic and functional characterization of this Salmonella Cu,Zn superoxide dismutase indicates that structural variability and catalytic efficiency are higher in prokaryotic than in the eukaryotic homologous enzymes.

Amino Acid Sequence↗
PubMed2000

A novel two-over-two alpha-helical sandwich fold is characteristic of the truncated hemoglobin family.

Small hemoproteins displaying amino acid sequences 20-40 residues shorter than (non-)vertebrate hemoglobins (Hbs) have recently been identified in several pathogenic and non-pathogenic unicellular organisms, and named 'truncated hemoglobins' (trHbs). They have been proposed to be involved not only in oxygen transport but also in other biological functions, such as protection against reactive nitrogen species, photosynthesis or to act as terminal oxidases. Crystal structures of trHbs from the ciliated protozoan Paramecium caudatum and the green unicellular alga Chlamydomonas eugametos show that the tertiary structure of both proteins is based on a 'two-over-two' alpha-helical sandwich, reflecting an unprecedented editing of the classical 'three-over-three' alpha-helical globin fold. Based on specific Gly-Gly motifs the tertiary structure accommodates the deletion of the N-terminal A-helix and replacement of the crucial heme-binding F-helix with an extended polypeptide loop. Additionally, concerted structural modifications allow burying of the heme group and define the distal site, which hosts a TyrB10, GlnE7 residue pair. A set of structural and amino acid sequence consensus rules for stabilizing the fold and the bound heme in the trHbs homology subfamily is deduced.

Amino Acid Motifs↗
PubMed2000

Cancer risk among men with, or at risk of, HIV infection in southern Europe.

OBJECTIVE: To evaluate the cancer risk in southern European men with, or at risk of, HIV infection. DESIGN: An analysis of longitudinal data to assess time-dependent rare events. METHODS: Data from a cohort of HIV seroconverters, and from two hospital-based HIV seroprevalent cohorts were combined and analysed. The number of cancer cases observed was compared with the expected number, obtained from cancer incidence rates among men in the general population. Age-standardized incidence ratios (SIR) and their 95% confidence intervals (CI) were computed. RESULTS: A total of 19,609 person-years of observation were accumulated among HIV-positive men, and 7957 person-years among HIV-negative men. Among HIV-positive men, statistically significant increased SIR were seen for Hodgkin's disease (HD) (SIR = 8.7), liver cancer (SIR = 11.0), and cancer of the salivary glands (SIR = 33.6). An excess of lung cancer was seen among intravenous drug users (IDU), but not among homosexual men. When the risk of all non-AIDS-defining cancers was considered, HIV-positive men had a nearly twofold excess (95% CI: 1.2-2.8). A risk of similar magnitude emerged among HIV-negative IDU (95% CI: 1.0-4.5), largely attributable to lung cancer and HD. CONCLUSION: These findings confirm that HIV infection increases the risk of HD, whereas they suggest that the risk of hepatocellular carcinoma may also be enhanced by HIV infection. The observation of an elevated risk of lung cancer in both HIV-positive and HIV-negative IDU points to personal behaviours unrelated to HIV infection.

Adult↗
PubMed1999

Anticooperative ligand binding properties of recombinant ferric Vitreoscilla homodimeric hemoglobin: a thermodynamic, kinetic and X-ray crystallographic study.

Thermodynamics and kinetics for cyanide, azide, thiocyanate and imidazole binding to recombinant ferric Vitreoscilla sp. homodimeric hemoglobin (Vitreoscilla Hb) have been determined at pH 6.4 and 7.0, and 20.0 degrees C, in solution and in the crystalline state. Moreover, the three-dimensional structures of the diligated thiocyanate and imidazole derivatives of recombinant ferric Vitreoscilla Hb have been determined by X-ray crystallography at 1.8 A (Rfactor=19.9%) and 2.1 A (Rfactor=23.8%) resolution, respectively. Ferric Vitreoscilla Hb displays an anticooperative ligand binding behaviour in solution. This very unusual feature can only be accounted for by assuming ligand-linked conformational changes in the monoligated species, which lead to the observed 300-fold decrease in the affinity of cyanide, azide, thiocyanate and imidazole for the monoligated ferric Vitreoscilla Hb with respect to that of the fully unligated homodimer. In the crystalline state, thermodynamics for azide and imidazole binding to ferric Vitreoscilla Hb may be described as a simple process with an overall ligand affinity for the homodimer corresponding to that for diligation in solution. These data suggest that the ligand-free homodimer, observed in the crystalline state, is constrained in a low affinity conformation whose ligand binding properties closely resemble those of the monoligated species in solution. From the kinetic viewpoint, anticooperativity is reflected by the 300-fold decrease of the second-order rate constant for cyanide and imidazole binding to the monoligated ferric Vitreoscilla Hb with respect to that for ligand association to the ligand-free homodimer in solution. On the other hand, values of the first-order rate constant for cyanide and imidazole dissociation from the diligated and monoligated derivatives of ferric Vitreoscilla Hb in solution are closely similar. As a whole, ligand binding and structural properties of ferric Vitreoscilla Hb appear to be unique among all Hbs investigated to date.

Crystallography, X-Ray↗
PubMed1999

[Visceral leishmaniasis associated with Wegener disease. Use of lipid complex amphotericin B and liposomal amphotericin B].

BACKGROUND: Leishmaniasis in a patient with Wegenerís disease raises the problem of amphotericin toxicity further compromising the pre-existing renal disorder. CASE REPORT: An anemic patient treated for Wegenerís disease developed visceral leishmaniasis. This renal failure patient was treated with lipid complex amphotericin B and liposomal amphotericin B. We report outcome at 10 months follow-up. DISCUSSION: The new formulations of amphotericin B allow effective treatment of visceral leishmaniasis in renal failure patients. Long-lasting results are probably favored by the interruption of immuno-suppressive therapy.

Acute Kidney Injury↗
PubMed1999

Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.

Prokaryotic Cu,Zn superoxide dismutases are characterized by a distinct quaternary structure, as compared to that of the homologous eukaryotic enzymes. Here we report a newly determined crystal structure of the dimeric Cu,Zn superoxide dismutase from Photobacterium leiognathi (crystallized in space group R32, refined at 2.5 A resolution, R-factor 0.19) and analyse it in comparison with that of the monomeric enzyme from Escherichia coli. The dimeric assembly, observed also in a previously studied monoclinic crystal form of P. leiognathi Cu,Zn superoxide dismutase, is based on a ring-shaped subunit contact region, defining a solvated interface cavity. Three clusters of neighbouring residues play a direct role in the stabilization of the quaternary assembly. The present analysis, extended to the amino acid sequences of the other 11 known prokaryotic Cu,Zn superoxide dismutases, shows that at least in five other prokaryotic enzymes the interface residue clusters are under strong evolutionary constraint, suggesting the attainment of a quaternary structure coincident with that of P. leiognathi Cu,Zn superoxide dismutase. Calculation of electrostatic fields for both the enzymes from E. coli and P. leiognathi shows that the monomeric/dimeric association behaviour displayed by prokaryotic Cu, Zn superoxide dismutases is related to the distribution of surface charged residues. Moreover, Brownian dynamics simulations reproduce closely the observed enzyme:substrate association rates, highlighting the role of the active site neighbouring residues in determining the dismutase catalytic properties.

Amino Acid Sequence↗
PubMed1999

Epidemiology of resistance to antimicrobial drugs in the major respiratory pathogens circulating in Europe.

There is an overwhelming consensus on the fact that Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis represent the prevailing bacterial pathogens of community-acquired lower respiratory tract infections. Their specific incidence as causative agents of the more common syndromes is known to vary even profoundly depending on geographic location, and the same holds true for the rates of resistance to antimicrobial drugs. Europe does not escape the threat posed by the present pandemic spread of penicillin resistance in S. pneumoniae although, as expected, countries like Spain and France are greatly affected, while others including Germany, Italy, The Netherlands and the Scandinavian region are comparatively spared. In several sites multiple resistance has been described in S. pneumoniae and the most affected drugs include penicillin, the macrolides, co-trimoxazole and tetracycline. In H. influenzae synthesis of beta-lactamases the main trait of resistance is expressed. Lack of susceptibility to beta-lactams dictated by a different mechanism remains extremely rare. Considerable variations in the incidence of this characteristic are apparent when European countries are considered. France and Spain are again widely affected, while Germany, The Netherlands and Italy display rates of beta-lactamase-positive H. influenzae of about 10%. M. catarrhalis must be considered generally resistant to non-protected aminopenicillins since over 90% of these organisms produce beta-lactamases.

Anti-Bacterial Agents↗
PubMed1999

Factors related to the prescription of antibiotics for young children with viral pharyngitis by general practitioners and paediatricians in southeastern France.

This study evaluates the antibiotic-prescribing practices of physicians as well as other related issues in the context of viral pharyngitis. In a telephone interview, 535 physicians practising in southeastern France were submitted a clinical case description of an episode of acute pharyngitis in a 2-year-old child. Questions concerned antibiotic treatment and physicians' reasons for their treatment decision. The viral origin of the pharyngitis was more likely to be suspected by paediatricians than by general practitioners (92% vs. 78%, P<0.01); 57% of allopaths (compared with 26% of homeopaths/acupuncturists and 14% of paediatricians, P<0.001) declared they would prescribe an antibiotic in this situation (amoxicillin only in 42% of cases). This difference between allopaths and other physicians was still significant after controlling for knowledge regarding antibiotic therapy. In order to limit the risk of emerging resistant bacteria, it is urgent that training be upgraded for physicians, especially for allopaths.

Anti-Bacterial Agents↗