Rosario San Millán

In silico analysis of complete bacterial genomes: PCR, AFLP--PCR and endonuclease restriction

UNLABELLED We have developed a website, www.in-silico.com, which runs a software program that performs three basic tasks in completely sequenced bacterial genomes by in silico analysis: PCR amplification, amplified fragment length polymorphism (AFLP-PCR) and endonuclease restriction. For PCR, after selection of the genome and introduction of primers, fragment size, DNA sequence and corresponding open reading frame (ORF) identity of the resulting PCR product is computed. Plasmids of sequenced species may be included in the analysis. Theoretical AFLP-PCR analyzes similar parameters, and includes a suggestion tool providing a list of commercial restriction enzyme pairs yielding up to 50 amplicons in the selected genome. Endonuclease restriction analysis of complete genomes and plasmids calculates the number of restriction sites for endonucleases in a given genome. If the number of fragments is 50 or fewer, pulsed field gel electrophoresis image and restriction maps are illustrated. Other tools that have been included in this site are ORF search by name and DNA to protein translation as well as restriction digestion of user-defined DNA sequences. AVAILABILITY This is a new molecular biology resource freely available over the Internet at http://www.in-silico.com

The aetiology of paediatric inflammatory vulvovaginitis

Vulvovaginitis is the most common gynaecological problem in prepubertal girls and clear-cut data on the microbial aetiology of moderate to severe infections are lacking. Many microorganisms have been reported in several studies, but frequently the paediatrician does not know the pathogenic significance of an isolate reported in vaginal specimens of girls with vulvovaginitis. A multicentre study was performed, selecting 74 girls aged 2 to 12 years old with a clinical picture of vulvovaginitis and inflammatory cells on Gram stain. All the specimens were cultured following standard microbiological techniques and the paediatricians completed a questionnaire to highlight risk factors after interviewing the parents or tutors. The data were compared with those obtained in a control group of 11 girls without vulvovaginitis attending a clinic. Streptococcus pyogenes and Haemophilus spp.were isolated in 47 and 12 cases, respectively. Upper respiratory infection in the previous month ( P <0.001) and vulvovaginitis in the previous year ( P <0.05) were identified as significant risk factors. Foreign bodies, sexual abuse, poor hygiene and bad socioeconomic situation were not identified as risk factors for the infection. Conclusion: Paediatric inflammatory vulvovaginitis is mainly caused by pathogens of the upper respiratory tract and the most common risk factor for this infection is to have suffered an upper respiratory tract infection in the previous month.

Effect of salivary secretory IgA on the adhesion of Candida albicans to polystyrene.

Attachment of Candida albicans to plastic materials of dental prostheses or to salivary macromolecules adsorbed on their surface is believed to be a critical event in the development of denture stomatitis. In an earlier study, it was shown that adhesion of C. albicans to polystyrene, a model system to study the adhesion of C. albicans to plastic materials, can be partially inhibited with an mAb directed against cell wall polysaccharides of C. albicans. In the present study, the role of whole saliva in the adhesion of C. albicans to polystyrene has been investigated, and three mAbs directed against epitopes of cell wall mannoproteins have been used to mimic the inhibitory effect observed with salivary secretory IgA (sIgA) on the adhesion of C. albicans to polystyrene. In the absence of whole saliva, adherence of C. albicans 3153 increased with germination. However, the presence of whole saliva enhanced the adhesion to polystyrene of C. albicans 3153 yeast cells but decreased the adhesion of germinated cells. The enhancement of adhesion of yeast cells to polystyrene mediated by saliva was confirmed with an agerminative mutant of C. albicans 3153. The inhibition of the adhesion of C. albicans 3153 germ tubes to polystyrene was due to the salivary sIgA since sIgA-depleted saliva enhanced the adhesion of C. albicans 3153 to polystyrene. The inhibitory effect mediated by sIgA was not related to the inhibition of germination but to the blockage of adhesins expressed on the cell wall surface of the germ tubes. The three mAbs studied reduced the adhesion of C. albicans 3153 to polystyrene at levels equivalent to those for purified sIgA. The highest reduction in the adhesion was obtained with the IgA mAb N3B. The best results were obtained when the three mAbs were combined. The results suggest that whole saliva plays a different role in the adhesion of C. albicans to polystyrene depending on the morphological phase of C. albicans. These results may give new insights into the conflicting role of saliva in the adhesion of C. albicans to plastic materials of dental prostheses.

Multicenter Evaluation of ATB Fungus: A Standardized Micromethod for Yeast Susceptibility Testing

The micromethod for yeast susceptibility testing, ATB Fungus, was evaluated with 30 reference strains in three laboratories. Ready-to-use strips with 5-fluorocytosine, amphotericin B, nystatin, miconazole, econazole and ketoconazole were used. The test allowed the categorization of each strain as susceptible, intermediate or resistance to all the antifungals tested, and 5-fluorocytosine and amphotericin B MIC determination. The results were compared with the MIC for each reference strain obtained by a microdilution method on RPMI 1640 buffered with MOPS. The repeatability and intralaboratory and interlaboratory reproducibility were evaluated. ATB Fungus was a reliable and reproducible method with a repeatability of 96.6%, a reproducibility of 95.4% and showed an excellent correlation 91.7%) with reference MICs.

Variability in expression of antigens responsible for serotype specificity in Candida albicans

The monoclonal antibody (mAb) B9E, which reacts with a cell wall surface determinant of Candida albicans serotype A, and a polyclonal monospecific antiserum against the antigen 6 (IF6) were used to investigate the expression of the antigens responsible for the serotype specificity in C. albicans under different growth conditions. By indirect immunofluorescence, both antibodies reacted with the cell wall surface of serotype A yeast cells and germ tubes grown in vitro but no reactivity was observed with serotype B yeast cells. In some cases, only a weak reactivity restricted to a zone close to the parent yeast cell was observed in serotype B germ tubes stained with mAb B9E. Both antibodies reacted strongly with yeast cells and germ tubes present in kidney abscesses from rabbits infected with both serotypes, but only serotype A yeast cells and germ tubes present in smears from patients with vulvovaginal candidiasis reacted with B9E and IF6 antibodies. The expression of antigens reactive with both antibodies was modulated by the pH of the environment in which the fungus was grown. Both antibodies showed a similar pattern of reactivity when studied with a spectrofluorometer. Serotype A yeast cells showed maximum reactivity when cells were grown on Sabouraud dextrose broth supplemented with yeast extract at pH 4.6. The lowest reactivity was observed in cells grown at pH 2.0. Conversely, the reactivity of serotype B yeast cells increased at alkaline pH values, the highest being in cells grown at pH values of 7.2 and 9.5.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of monoclonal antibodies directed against Candida albicans cell wall antigens on the adhesion of the fungus to polystyrene.

The adhesion of Candida albicans to polystyrene and the effect of three monoclonal antibodies (mAbs) reactive with C. albicans cell wall surface antigens on this process was assessed in vitro with several C. albicans strains. In the absence of mAbs, adhesion of C. albicans to polystyrene increased in parallel with germ-tube formation. However, the growth of the strains in the yeast phase at 25 degrees C or the use of an agerminative mutant inhibited adhesion to polystyrene. Serotype A and B strains showed similar kinetics of adhesion to polystyrene and no statistically significant differences in germination or adhesion were observed when strains from the two serotypes were compared. The three mAbs had different effects on both germination and adhesion of C. albicans. mAbs 3D9 showed no influence on either germination or adhesion to polystyrene in two C. albicans strains. mAb B9E decreased both adhesion (45.6%) and filamentation (52.6%), and mAb 21E6 decreased filamentation (34.0%) but enhanced adhesion by 23.3%. This enhancement was also observed with the agerminative mutant and it was dose-dependent. It was not related to the binding capacity of the MAb to polystyrene nor to an increase in cell surface hydrophobicity of the antibody-treated cells. In conclusion, both growth phases of C. albicans can adhere to polystyrene, although the conditions for this process seem to be different in each phase. The two types of adhesion of C. albicans to polystyrene might have a role in the colonization of medical implants. The disparate effects shown by mAbs directed against cell wall mannoproteins of C. albicans on the adhesion of the fungus to polystyrene should be taken into consideration when designing strategies to block the adhesion of C. albicans to plastic materials with mAbs.

Clonal Dissemination of Yersinia enterocolitica Strains with Various Susceptibilities to Nalidixic Acid

ABSTRACT Ten epidemiologically related Yersinia enterocolitica clinical isolates were studied. Six isolates were nalidixic acid resistant (MIC > 512 μg/ml), with mutations in the quinolone resistance-determining region (QRDR) of the gyrA gene, suggesting clonal dissemination of a nalidixic acid-susceptible Y. enterocolitica strain which has acquired different mutations generating resistance to nalidixic acid.

In vitro survival and germination of Candida albicans in the presence of nitrogen compounds

The in vitro effect of nitric oxide (NO) and nitrite on blastoconidia and hyphae of Candida albicans was studied. Sodium nitroprusside (SNP) and S-nitroso-N-acetylpenicillamine (SNAP) were used as NO donors. Both minimal and complex media at two pH values, 7.0 and 4.5, were used for the assays. Blastoconidia were more susceptible than hyphae to NO. The NO effect on blastoconidia was greater at acidic pH. Nitrite affected the viability of blastoconidia in complex medium. The percentage germination and the relative rate of elongation of hyphae were both enhanced when NO was present in acidic conditions.

Online exercise for the design and simulation of PCR and PCR-RFLP experiments.

BackgroundPolymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool.FindingsAn online PCR and PCR-RFLP exercise has been create that requires users to find the target genes, compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive.ConclusionsThe exercise is freely available at http://insilico.ehu.es/edu.

Evaluación de dos métodos inmunocromatográficos comerciales para el diagnóstico rápido de Giardia duodenalis y Cryptosporidium spp. en muestras de heces

INTRODUCTION To assess and compare the performance of two immunochromatographic tests for the simultaneous detection of Giardia duodenalis and Cryptosporidium spp. in faeces. MATERIALS AND METHODS In this study 254 faeces samples were tested using the two immunochromatography strips Cryto-Giardia (CerTest Biotec) and Stick Crypto-Giardia (Operon). RESULTS In the diagnosis of G. duodenalis, the sensitivity and specificity of the kits were 97% and 100%, respectively for the CerTest; and 97% and 95% for Operon. In the diagnosis of Cryptosporidium spp. Certest strip rendering a sensitivity of 100%, compared to with a sensitivity of 92% using Operon. There were no false positives using either technique. CONCLUSIONS Both methods yielded good sensitivity and specificity values and are thus useful tools for a rapid diagnosis of G. duodenalis and Cryptosporidium spp. The benefits of immunochromatography methods are that there is no requirement for expert microscopists or special equipment.