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Mazzarella L, Vergara A, Vitagliano L, Merlino A, Bonomi G, Scala S, Verde C, di Prisco G. High resolution crystal structure of deoxy hemoglobin from Trematomus bernacchii at different pH values: The role of histidine residues in modulating the strength of the root effect. Proteins 2006; 65:490-8. [PMID: 16909420 DOI: 10.1002/prot.21114] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Root effect is a widespread property in fish hemoglobins (Hbs) that produces a drastic reduction of cooperativity and oxygen-binding ability at acidic pH. Here, we report the high-resolution structure of the deoxy form of Hb isolated from the Antarctic fish Trematomus bernacchii (HbTb) crystallized at pH 6.2 and 8.4. The structure at acidic pH has been previously determined at a moderate resolution (Ito et al., J Mol Biol 1995;250:648-658). Our results provide a clear picture of the events occurring upon the pH increase from 6.2 to 8.4, observed within a practically unchanged crystal environment. In particular, at pH 8.4, the interaspartic hydrogen bond at the alpha(1)beta(2) interface is partially broken, suggesting a pK(a) close to 8.4 for Asp95alpha. In addition, a detailed survey of the histidine modifications, caused by the change in pH, also indicates that at least three hot regions of the molecule are modified (Ebeta helix, Cbeta-tail, CDalpha corner) and can be considered to be involved at various levels in the release of the Root protons. Most importantly, at the CDalpha corner, the break of the salt bridge Asp48alpha-His55alpha allows us to describe a detailed mechanism that transmits the modification from the CDalpha corner far to the alpha heme. More generally, the results shed light on the role played by the histidine residues in modulating the strength of the Root effect and also support the emerging idea that the structural determinants, at least for a part of the Root effect, are specific of each Hb endowed with this property.
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Vergara A, Arrue I, Dominuez JD, Vanaclocha F. Generalized pustular psoriasis precipitated by aceclofenac. J Eur Acad Dermatol Venereol 2006; 20:1028-9. [PMID: 16922973 DOI: 10.1111/j.1468-3083.2006.01622.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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103
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Vergara A, Capuano F, Paduano L, Sartorio R. Lysozyme Mutual Diffusion in Solutions Crowded by Poly(ethylene glycol). Macromolecules 2006. [DOI: 10.1021/ma0605705] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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104
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Losito P, Vergara A, Muscariello LT, Ianieri A. Antimicrobial susceptibility of environmental Staphylococcus aureus strains isolated from a pigeon slaughterhouse in Italy. Poult Sci 2006; 84:1802-7. [PMID: 16463981 DOI: 10.1093/ps/84.11.1802] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
No information is available concerning the antimicrobial susceptibility of Staphylococcus aureus isolated from pigeon slaughterhouses. In the present study, 59 staphylococcal strains isolated from a pigeon slaughterhouse in central Italy were compared according to their antibiotic resistance. On the basis of cultural and biochemical properties, all isolates could be identified as S. aureus. The strains were checked for the productions of enterotoxins A, B, C, D by reversed passive latex agglutination. Resistance to 26 antibiotics was also determined paying particular attention to resistance to those antimicrobial agents frequently used in human medicine and in poultry breeding. Only one strain was positive for the production of enterotoxins type C and D. It was isolated from the evisceration tube after slaughtering. Enterotoxin B was produced by 2 strains isolated from the eyebrows and conjunctivas of the worker operating the crop rinsing tube. As to the susceptibility to antibiotics, all strains were sensitive to amoxicillin/clavulanic acid, bacitracin, cephalothin, fusidic acid, gentamicin, kanamycin, linezolid, oxacillin, quinupristin/dalfopristin, rifampicin, tobramycin, trimethoprim-sulfamethoxazole, vancomycin. Some (15.2%) of the strains were resistant to ampicillin and to penicillin G; 6.8% were resistant to chloramphenicol, 20.3% to enrofloxacin, 16.9% to erythromycin and to ciprofloxacin, 8.5% to clindamycin, and 11.9% to lincomycin. The highest percentages of strains were resistant to tetracycline and oleandomicin (37.3 and 25.4% respectively). Methicillin-resistant staphylococci were also found (3.4%). Only one strain had a multiple antibiotic resistance index > 0.30. The results were statistically analyzed and clustered in 6 groups. This work provides the antibiotic resistance pattern of S. aureus strains isolated from a pigeon slaughtering plant and represents a study on a quite unknown field in meat production.
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López-Medrano F, Vergara A, García-Donoso C, Menassa A, Aguado JM. Mujer proveniente de Bolivia con fiebre, exantema y «signo del torniquete» positivo. A propósito de un caso de dengue. Rev Clin Esp 2006; 206:212. [PMID: 16750102 DOI: 10.1157/13086813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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106
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Mazzarella L, Bonomi G, Lubrano MC, Merlino A, Riccio A, Vergara A, Vitagliano L, Verde C, di Prisco G. Minimal structural requirements for root effect: Crystal structure of the cathodic hemoglobin isolated from the antarctic fish Trematomus newnesi. Proteins 2005; 62:316-21. [PMID: 16299734 DOI: 10.1002/prot.20709] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The cathodic hemoglobin component of the Antarctic fish Trematomus newnesi (HbCTn) is a Root-effect protein. The interpretation of its functional properties in relation to its sequence is puzzling. Indeed, HbCTn sequence is characterized by an extremely low histidyl content, and in particular by the lack of His146beta and His69beta, which are believed to be important in Bohr and Root effects, respectively. Furthermore, previous analyses suggested that the local environment of Asp95alpha, Asp99beta, and Asp101beta should not be appropriate for the formation of Asp-Asp interactions, which are important for the Root effect. Here, we report the high-resolution crystal structure of the deoxy form of HbCTn. Our data provide a structural interpretation for the very low oxygen affinity of the protein and insights into the structural determinants of the Root effect protein. The structure demonstrates that the presence of Ile41alpha and Ser97alpha at the alpha1beta2 interface does not prevent the formation of the inter-Asp interactions in HbCTn, as previous studies had suggested. The present data indicate that the hydrogen bond formed between Asp95alpha and Asp101beta, which is stabilized by Asp99beta, is per se sufficient to generate the Root effect, and it is the minimal structural requirement needed for the design of Root-effect Hbs.
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Vergara A, Lorber B, Sauter C, Giegé R, Zagari A. Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology. Biophys Chem 2005; 118:102-12. [PMID: 16150532 DOI: 10.1016/j.bpc.2005.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 06/23/2005] [Accepted: 06/23/2005] [Indexed: 11/24/2022]
Abstract
The crystallographic quality of protein crystals that were grown in microgravity has been compared to that of crystals that were grown in parallel on earth gravity under otherwise identical conditions. A goal of this comparison was to assess if a more accurate 3D-structure can be derived from crystallographic analysis of the former crystals. Therefore, the properties of crystals prepared with the Advanced Protein Crystallisation Facility (APCF) on earth and in orbit during the last decade were evaluated. A statistical analysis reveals that about half of the crystals produced under microgravity had a superior X-ray diffraction limit with respect of terrestrial controls. Eleven protein structures could be determined at previously unachieved resolutions using crystals obtained in the APCF. Microgravity induced features of the most relevant structures are reported. A second goal of this study was to identify the cause of the crystal quality enhancement useful for structure determination. No correlations between the effect of microgravity and other system-dependent parameters, such as isoelectric point or crystal solvent content, were found except the reduced convection during the crystallisation process. Thus, crystal growth under diffusive regime appears to be the key parameter explaining the beneficial effect of microgravity on crystal quality. The mimicry of these effects on earth in gels or in capillary tubes is discussed and the practical consequences for structural biology highlighted.
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Vitagliano L, Bonomi G, Franzese M, Merlino A, Vergara A, Verde C, di Prisco G, Mazzarella L. Structural characterization of the oxidation pathway of antarctic fish hemoglobins. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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109
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López-Medrano F, Vergara A, García-Donoso C, Menassa A, San Juan R, Aguado J. Caso 4. Mujer proveniente de Bolivia con fiebre, exantema y «signo del torniquete» positivo. Rev Clin Esp 2005. [DOI: 10.1016/s0014-2565(05)72593-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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110
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111
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Vergara A. Cover Picture: Macromol. Theory Simul. 1/2005. MACROMOL THEOR SIMUL 2005. [DOI: 10.1002/mats.200590000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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112
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Vergara A, Annunziata O, Paduano L, Miller DG, Albright JG, Sartorio R. Multicomponent Diffusion in Crowded Solutions. 2. Mutual Diffusion in the Ternary System Tetra(ethylene glycol)−NaCl−Water. J Phys Chem B 2004. [DOI: 10.1021/jp036219s] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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113
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Capuano F, Vergara A, Paduano L, Annunziata O, Sartorio R. Electrostatic and Excluded Volume Effects on the Transport of Electrolytes in Poly(ethylene glycol)−Water “Mixed Solvents”. J Phys Chem B 2003. [DOI: 10.1021/jp034223y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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114
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Vergara A. Hard-Sphere Hydrodynamics as Reference State in Velocity Cross-Correlation Analysis of Real Systems. J Phys Chem B 2003. [DOI: 10.1021/jp034100d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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115
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Mangiapia G, Paduano L, Vergara A, Sartorio R. Novel Method for Calculating the Diffusion Coefficients of a Ternary System Containing a Polydisperse Component. Applications to the Gouy Interferometry. J Phys Chem B 2003. [DOI: 10.1021/jp027435o] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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116
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Annunziata O, Vergara A, Paduano L, Sartorio R, Miller DG, Albright JG. Precision of Interferometric Diffusion Coefficients in a Four-Component System Relevant to Protein Crystal Growth: Lysozyme−Tetra(ethylene glycol)−NaCl−H2O. J Phys Chem B 2003. [DOI: 10.1021/jp0301094] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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117
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Castagnolo D, Piccolo C, Carotenuto L, Vergara A, Zagari A. Crystallization of the collagen-like polypeptide (PPG)10 aboard the International Space Station. 3. Analysis of residual acceleration-induced motion. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2003; 59:773-6. [PMID: 12657808 DOI: 10.1107/s0907444903002178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2002] [Accepted: 01/24/2003] [Indexed: 11/10/2022]
Abstract
(PPG)(10) crystallization experiments onboard the ISS using the Advanced Protein Crystallization Facility have shown parallel and coherent crystal motions. The residual acceleration profiles and the History of the ISS Increment 3 mission allow a quantitative interpretation of these motions. Two events determine the observed crystal motions: the undocking of the Space Shuttle and a change in the ISS attitude required for power generation. No correlation between these motions and the crystal quality is apparent.
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118
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Colavita G, Sessa M, Giaccone V, Vergara A. Effect of NaCl Concentration on the Survival and Growth of Coliforms in Raw Seasoned Sausages. Vet Res Commun 2003; 27 Suppl 1:293-5. [PMID: 14535413 DOI: 10.1023/b:verc.0000014163.13439.3a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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119
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Vergara A, Lorber B, Zagari A, Giegé R. Physical aspects of protein crystal growth investigated with the Advanced Protein Crystallization Facility in reduced-gravity environments. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2003; 59:2-15. [PMID: 12499533 DOI: 10.1107/s0907444902021443] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2002] [Accepted: 11/20/2002] [Indexed: 11/10/2022]
Abstract
The physicochemical aspects of protein crystallization in reduced-gravity environments ( micro g) have been investigated with the Advanced Protein Crystallization Facility during six space missions. This review summarizes the results, dealing with the mechanisms of nucleation and crystal growth and with the quality of the crystals that were obtained under reduced gravity as well as under normal gravity on earth. Statistical analyses of the experimental data strongly support the fact that micro g has a positive effect on crystallization and on crystal quality. A comparison of experiments and theories of protein crystallization in reduced-gravity environments is presented. Recommendations for improving the performance of protein crystallization experiments in micro g and on earth are discussed.
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Vergara A, Ianieri A, Colavita G, Paparella A. Behaviour of Listeria monocytogenes in Anchovies during Marination. Vet Res Commun 2003; 27 Suppl 1:319-21. [PMID: 14535420 DOI: 10.1023/b:verc.0000014170.03343.9c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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121
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Castagnolo D, Vergara A, Paduano L, Sartorio R, Annunziata O. Analysis of the influence of coupled diffusion on transport in protein crystal growth for different gravity levels. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2002; 58:1633-7. [PMID: 12351876 DOI: 10.1107/s0907444902014361] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2002] [Accepted: 08/07/2002] [Indexed: 02/26/2023]
Abstract
Diffusion has a central role in protein crystal growth both in microgravity conditions and on ground. Recently several reports have been focused on the importance to use the generalized Fick's equations in n-component systems where crystals grow. In these equations the total flux of each component is produced by the own concentration gradient (main flow) and by the concentration gradient of the other components (cross-flow) present in the system. However in literature the latter effect is often neglected, and the so-called pseudo-binary approximation is used. Lin et al. (1995) proposed a mathematical model to evaluate the concentration profile of the species present around a growing protein crystal. Although the model is reliable, it suffers of the pseudo-binary approximation (neglecting cross term diffusion coefficients and using binary diffusion coefficients), probably because of the lack of multicomponent diffusion data. The present model is based on the experimental set-up proposed by Lin et al. (1995). Nevertheless we have included the coupled diffusion effects, according to the correct description of the matter transport through the generalized Fick's equations. The crystal growth rate is calculated for different gravity levels. The model has been applied to the ternary lysozyme-NaCl-water and quaternary lysozyme-poly(ethylene glycol) (PEG)-NaCl-water systems using recent diffusion data.
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Berisio R, Vitagliano L, Vergara A, Sorrentino G, Mazzarella L, Zagari A. Crystallization of the collagen-like polypeptide (PPG)10 aboard the International Space Station. 2. Comparison of crystal quality by X-ray diffraction. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2002; 58:1695-9. [PMID: 12351888 DOI: 10.1107/s0907444902014427] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2002] [Accepted: 08/07/2002] [Indexed: 11/10/2022]
Abstract
Crystals of the collagen-like polypeptide (PPG)(10) were obtained within the Advanced Protein Crystallization Facility on board the International Space Station, during the STS-105/STS-108 mission. The duration of this mission was such to ensure that the crystallization process had reached its end. Crystals were grown both in the presence and in the absence of agarose gel, to compare the quality of the crystals obtained from these different environments. As a result, crystals grown in the absence of agarose on Earth as well as in microgravity showed X-ray diffraction up to 1.15 A. The intensity/sigma ratio was slightly higher for microgravity grown crystals. Crystals grown in agarose gel, both in microgravity and on ground, showed a comparable diffraction power, with a resolution limit of 1.45 A.
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Vergara A, Corvino E, Sorrentino G, Piccolo C, Tortora A, Carotenuto L, Mazzarella L, Zagari A. Crystallization of the collagen-like polypeptide (PPG)10 aboard the International Space Station. 1. Video observation. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2002; 58:1690-4. [PMID: 12351887 DOI: 10.1107/s0907444902014269] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2002] [Accepted: 08/07/2002] [Indexed: 11/10/2022]
Abstract
Single chains of the collagen model polypeptide with sequence (Pro-Pro-Gly)(10), hereafter referred to as (PPG)(10), aggregate to form rod-shaped triple helices. Crystals of (PPG)(10) were grown in the Advanced Protein Crystallization Facility (APCF) both onboard the International Space Station (ISS) and on Earth. The experiments allow the direct comparison of four different crystallization environments for the first time: solution in microgravity ((g), agarose gel in (g, solution on earth, and gel on earth. Both on board and on ground, the crystal growth was monitored by a CCD video camera. The image analysis provided information on the spatial distribution of the crystals, their movement and their growth rate. The analysis of the distribution of crystals reveals that the crystallization process occurs as it does in batch conditions. Slow motions have been observed onboard the ISS. Different to Space-Shuttle experiment, the crystals onboard the ISS moved coherently and followed parallel trajectories. Growth rate and induction time are very similar both in gel and in solution, suggesting that the crystal growth rate is controlled by the kinetics at the interface under the used experimental conditions. These results provide the first data in the crystallogenesis of (PPG)(10), which is a representative member of non-globular, rod-like proteins.
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Torres-Tortosa M, Canueto J, Bascuñana A, Vergara A, Sánchez-Porto A, Moreno-Maqueda I, López-Suárez A, González-Serrano M, Cruz E. Prognostic evaluation of bacteremia and fungemia in patients with acquired immunodeficiency syndrome. Eur J Clin Microbiol Infect Dis 2002; 21:262-8. [PMID: 12072936 DOI: 10.1007/s10096-002-0700-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The incidence of bacterial infections in general and of bacteremia in particular is high among patients with acquired immunodeficiency syndrome (AIDS). The factors influencing the prognosis of bacteremia in these patients are not well known. In order to better define those factors associated with a poor prognosis, all episodes of bacteremia or fungemia in patients with AIDS who were hospitalized in four general hospitals between 1 September 1987 and 31 December 1996 were studied prospectively. Among 1,390 patients diagnosed with AIDS, 238 (17.1%) developed 274 episodes of bacteremia or fungemia. Mortality related to bacteremia was 21.3%. Variables associated with high mortality were fungemia (odds ratio [OR], 6.19; 95% confidence interval [CI], 1.99 - 19.28), hypotension (OR, 19.65; 95%CI, 7.42 - 52.07), inappropriate antimicrobial treatment (OR, 16.94; 95%CI, 4.92 - 58.32), and unknown origin of bacteremia (OR, 3.93; 95%CI, 1.58 - 9.76). The mortality rate among patients with at least one of these factors was 46.7%, whereas in patients without any of these factors, the rate was 4.9% ( P < 0.001). Bacteremic episodes of unknown origin were significantly more frequently associated with community acquisition ( P = 0.001), inappropriate antimicrobial treatment ( P = 0.04), and etiology by gram-negative microorganisms or fungi ( P < 0.001) and were significantly less frequently associated with the presence of a previous intravenous catheter ( P = 0.004), resulting in peculiar etiologic and epidemiological profiles. The factors that influence the outcome of AIDS patients who develop bacteremia are sometimes avoidable or known during the first days after admission. Therefore, knowledge about these factors could improve the prognosis of bloodstream infections in this population.
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125
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Vergara A, Paduano L, Sartorio R. Mechanism of Protein−Poly(ethylene glycol) Interaction from a Diffusive Point of View. Macromolecules 2002. [DOI: 10.1021/ma011390s] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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