Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects

The SH3 domain from the Fyn tyrosine kinase possesses a buried hydrogen bond between the side chains of a glutamate (Glu24) and a serine (Ser41) residue. Multiple amino acid substitutions were made at these positions to determine the role of this interaction in the stability and conformational specificity of the domain and to assess the relationship between the thermodynamic stability of mutants and sequence conservation seen in the SH3 domain family. Analysis of single and double alanine mutations indicated that the Glu24-Ser41 interaction contributes 0.50 kcal/mol to the stability of the domain. However, disruption of the Glu24-Ser41 interaction did not impair peptide binding function, suggesting that the interaction is not critical for conformational specificity. The stability of the domain was not increased by the replacement of these residues with different combinations of hydrophobic residues or with potential salt bridge forming residues. Despite their similar structural roles in the Fyn SH3 domain, the Ser41 position was considerably more tolerant to substitution than was the Glu24 position. An alignment of >350 different SH3 domains has been completed in our laboratory. A statistically significant correlation was found between the conservation data for the Glu24 and Ser41 positions and the thermodynamic stabilities of the mutants constructed at these positions. Surprisingly, our analysis of sequence alignment data provided a more accurate prediction of the stability of mutants than did examination of the three-dimensional structure of the domain.     

Variants of the 3' region of the cagA gene in Helicobacter pylori isolates from patients with different H. pylori-associated diseases

The CagA protein of Helicobacter pylori is an immunogenic antigen of variable size and unknown function that has been associated with increased virulence as well as two mutually exclusive diseases, duodenal ulcer and gastric carcinoma. The 3' region of the cagA gene contains repeated sequences. To determine whether there are structural changes in the 3' region of cagA that predict outcome of H. pylori infection, we examined 155 cagA gene-positive H. pylori isolates from Japanese patients including 50 patients with simple gastritis, 40 with gastric ulcer, 35 with duodenal ulcer, and 30 with gastric cancer. The 3' region of the cagA gene was amplified by PCR followed by sequencing. CagA proteins were detected by immunoblotting using a polyclonal antibody against recombinant CagA. One hundred forty-five strains yielded PCR products of 642 to 651 bp; 10 strains had products of 756 to 813 bp. The sequence of the 3' region of the cagA gene in Japan differs markedly from the primary sequence of cagA genes from Western isolates. Sequence analysis of the PCR products showed four types of primary gene structure (designated types A, B, C, and D) depending on the type and number of repeats. Six of the seven type C strains were found in patients with gastric cancer (P < 0.01 in comparison to noncancer patients). Comparison of type A and type C strains from patients with gastric cancer showed that type C was associated with higher levels of CagA antibody and more severe degrees of atrophy. Differences in cagA genotype may be useful for molecular epidemiology and may provide a marker for differences in virulence among cagA-positive H. pylori strains.     

Dervation of a Fast Algorthm to Account for Distortions Due to Terrain in Earth-Viewing Satellite Sensor Images

Earth-viewing satellite sensors (e. g., the Landsat 4/5 Thematic Mapper) produce images with nontrivial amounts of geometric distortion due to local terrain variations. Although correction formulas are easy to derive, the high frequency of terrain variation relative to pixel size means that excessive computer time is required to process a large digital image. This paper derives approximations to the correction geometry that reduce computer time by orders of magnitude. A statistical sensitivity analysis shows that the approximations do not adversely affect the accuracy of the results even under a very demanding error budget.     

Culture amplification in human colon adenocarcinoma cell line (CaCo-2) combined with an ELISA as a supplementary assay for accurate diagnosis of rotavirus

Culture amplification in colon adenocarcinoma cell line (CaCo-2) combined with enzyme immunoassay (Pathfinder ELISA) was developed as a supplementary tool for rotavirus diagnosis. One hundred and thirty stools in which results by polyacrylamide gel electrophoresis (PAGE) were in agreement with those obtained by ELISA were amplified in the CaCo-2 cell line. After the first passage 100% specimens were revealed as positive by ELISA. This result was confirmed by PAGE and direct electron microscopy (EM) which increased the rates of rotavirus detection up to 100% after the third and fifth cell passages, respectively. All of the amplified negative stools were confirmed as negative. Among discordant results, three of the eight specimens positive by ELISA but negative by PAGE were confirmed as true positive after the third cell passage. False positive ELISA results could be discarded when the samples were culture amplified and retested by the same ELISA. Using the CaCo-2 amplification-ELISA as supplementary assay, sensitivity and specificity were 1.000 and 0.953 for ELISA and 0.917 and 1.000 for PAGE, respectively. The combined CaCo-2 cell line amplification-immunoassay method proved to be suitable both to evaluate increase in sensitivity of newly developed rotavirus assays and for rotaviral amplification before antigen assays.     

Metronidazole has no antibacterial effect in Cornell model murine tuberculosis

SETTING: Experiments in vitro on the bactericidal activity of metronidazole and in the Cornell model of murine tuberculosis. OBJECTIVE: To assess the sterilising activity of maximal metronidazole dosage and its activity against bacilli held dormant by immunity in the mouse. DESIGN: In vitro experiments showed that metronidazole was only bactericidal at attainable concentrations (50-100 microg/ml) under anaerobic conditions. In the Cornell model, isoniazid 25 mg/kg and high dosage pyrazinamide 1000 mg/kg was given in the diet with and without 1500 mg/kg metronidazole for the initial 14 weeks of sterilising chemotherapy. In the subsequent sterile state, metronidazole at 0, 100 and 250 mg/kg was given by daily gavage for 6 weeks. Finally, the mice were given 3 weeks of high dosage steroids and their organs were cultured in selective liquid medium. RESULTS: Metronidazole had no activity either in the initial sterilising phase or in the subsequent sterile state. CONCLUSION: The O2 tension in the cellular lesions of murine tuberculosis is unlikely to be sufficiently low to allow metronidazole to act. Its activity should be assessed in caseous lesions.     

Optimization and diagnostic accuracy of computerized tomography with tridimensional spiral technique in the study of craniostenosis

INTRODUCTION: Conventional Computed Tomography (CT) with three-dimensional (3D) reconstructions is considered the most complete and accurate imaging modality to diagnose craniosynostosis. However, the introduction of Spiral CT (SCT) opened new possibilities for 3D studies of the skull in pediatric patients with craniosynostosis. The purpose of our study is two fold: first, to optimize the scanning and imaging parameters to obtain diagnostic images in a single spiral scan; second, to assess the diagnostic accuracy of such images in the identification of normal and abnormal cranial vault sutures. MATERIAL AND METHODS: Seventy-eight pediatric patients (age range: 1-35 months; mean: 11.8 months) with craniosynostosis were submitted to SCT of the head. The images were acquired with the following parameters: 3- and 5-mm nominal slice thickness, 5-6 mm/s table feed (pitch 1-2), 165 mAs and 120 kV. Two different algorithms and increases were used for image reconstructions. A first set of images was reconstructed with 2-mm increases and a soft tissue algorithm: these images were used for brain studies and for 3D reconstructions. A second set of slices was reconstructed with 5-mm increases and a bone algorithm to visualize the sutures of the axial plane. The 3D images were processed with the Shaded Surface Display software with threshold values ranging 120-150 HU. All images were acquired with a single spiral scan lasting less than 30 seconds. Two blinded radiologists analyzed the 3D and the planar images independently to evaluate the course and depth of each cranial suture. The sensitivity, specificity and diagnostic accuracy of both 3D and planar SCT images were evaluated. The frequency of artifacts (the Lego effect, boiled egg, pseudoforamina, movement, and chainsaw artifacts) and their influence on the final diagnosis were studied on 3D SCT images. RESULTS: The diagnostic accuracy rates of 3D SCT images, by suture, were: sagittal 90.7%, metopic 100%, left lamboid 90.9%, right lamboid 93.9%, left coronal 85.7%, right coronal 91.1%. The diagnostic accuracy rates of the axial images, by suture, were: sagittal 90.7%, metopic 95.5%, left lamboid 86.4%, right lamboid 90.9%, left coronal 83.7%, right coronal 91.1%. The interobserver agreement on 3D images was: sagittal 91.1%, metopic 100%, left lamboid 88.9%, right lamboid 91.1%, left coronal 88.9%, right coronal 84.4%. The Lego effect artifact was the most frequent one (82%) and affected image evaluation in 6.3% of cases. CONCLUSIONS: Our results prove that 3D SCT is a very accurate technique for identifying normal and abnormal sutures and presents many advantages over conventional 3D CT in the examination of pediatric patients with craniosynostosis. The quality of 3D SCT images was adequate and the artifacts did not affect the final diagnostic yield significantly.     

Relevance of training in transbronchial fine-needle aspiration technique

The activity of four natural triterpenoids on a 12-O-tetradecanoylphorbol-13-acetate multiple-dose model of skin chronic inflammation was studied. Erythrodiol and ursolic acid were significantly effective. The most important features concerning structure-activity relationship and previous data on the effect of these triterpenoids on other inflammatory conditions are discussed.