Joseba Bikandi

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

Genes and molecules involved in Aspergillus fumigatus virulence

Aspergillus fumigatus causes a wide range of diseases that include mycotoxicosis, allergic reactions and systemic diseases (invasive aspergillosis) with high mortality rates. Pathogenicity depends on immune status of patients and fungal strain. There is no unique essential virulence factor for development of this fungus in the patient and its virulence appears to be under polygenetic control. The group of molecules and genes associated with the virulence of this fungus includes many cell wall components, such as beta-(1-3)-glucan, galactomannan, galactomannanproteins (Afmp1 and Afmp2), and the chitin synthetases (Chs; chsE and chsG), as well as others. Some genes and molecules have been implicated in evasion from the immune response, such as the rodlets layer (rodA/hyp1 gene) and the conidial melanin-DHN (pksP/alb1 gene). The detoxifying systems for Reactive Oxygen Species (ROS) by catalases (Cat1p and Cat2p) and superoxide dismutases (MnSOD and Cu, ZnSOD), had also been pointed out as essential for virulence. In addition, this fungus produces toxins (14 kDa diffusible substance from conidia, fumigaclavin C, aurasperon C, gliotoxin, helvolic acid, fumagilin, Asp-hemolysin, and ribotoxin Asp fI/mitogilin F/restrictocin), allergens (Asp f1 to Asp f23), and enzymatic proteins as alkaline serin proteases (Alp and Alp2), metalloproteases (Mep), aspartic proteases (Pep and Pep2), dipeptidyl-peptidases (DppIV and DppV), phospholipase C and phospholipase B (Plb1 and Plb2). These toxic substances and enzymes seems to be additive and/or synergistic, decreasing the survival rates of the infected animals due to their direct action on cells or supporting microbial invasion during infection. Adaptation ability to different trophic situations is an essential attribute of most pathogens. To maintain its virulence attributes A. fumigatus requires iron obtaining by hydroxamate type siderophores (ornitin monooxigenase/SidA), phosphorous obtaining (fos1, fos2, and fos3), signal transductional falls that regulate morphogenesis and/or usage of nutrients as nitrogen (rasA, rasB, rhbA), mitogen activated kinases (sakA codified MAP-kinase), AMPc-Pka signal transductional route, as well as others. In addition, they seem to be essential in this field the amino acid biosynthesis (cpcA and homoaconitase/lysF), the activation and expression of some genes at 37 degrees C (Hsp1/Asp f12, cgrA), some molecules and genes that maintain cellular viability (smcA, Prp8, anexins), etc. Conversely, knowledge about relationship between pathogen and immune response of the host has been improved, opening new research possibilities. The involvement of non-professional cells (endothelial, and tracheal and alveolar epithelial cells) and professional cells (natural killer or NK, and dendritic cells) in infection has been also observed. Pathogen Associated Molecular Patterns (PAMP) and Patterns Recognizing Receptors (PRR; as Toll like receptors TLR-2 and TLR-4) could influence inflammatory response and dominant cytokine profile, and consequently Th response to infec tion. Superficial components of fungus and host cell surface receptors driving these phenomena are still unknown, although some molecules already associated with its virulence could also be involved. Sequencing of A. fumigatus genome and study of gene expression during their infective process by using DNA microarray and biochips, promises to improve the knowledge of virulence of this fungus.

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)

Genetic evolution of the Spanish multidrug-resistant Salmonella enterica 4,5,12:i:- monophasic variant.

ABSTRACT We analyzed a collection of 60 Salmonella enterica 4,5,12:i:- phage type U302 multidrug-resistant monophasic variant strains, isolated in Spain between 2000 and 2007. Most strains showed resistance to ampicillin (A), chloramphenicol (C), sulfamethoxazole (Su), gentamicin (G), streptomycin (S), tetracycline (T), and co-trimoxazole (SxT) (an ACSuGSTSxT resistance pattern). Only one pulsed-field gel electrophoresis (PFGE) type was detected, with 19 subtypes (Simpsons index of diversity [SID] = 0.89). Multiple-locus variable-number tandem-repeat analysis (MLVA) showed more variability, with 32 profiles (SID = 0.97), but only showed diversity at the STTR5 and STTR6 loci. PCR and sequencing demonstrated all strains contained the same allantoin-glyoxylate pathway deletion. Four types of deletions were detected in the fljAB operon, all starting at the same position, at the STM2758 gene, and followed by an IS26 insertion. Furthermore, a representative set of strains of the four deletion types harbored plasmids with IS26. We propose that a Salmonella enterica serotype Typhimurium U302 multidrug-resistant (ACSuGSTSxT) strain, defective for the allantoin-glyoxylate pathway and containing IS26 at plasmid pU302L, could be the ancestor of the variant in Spain.

Comparison of morphotypic and genotypic methods for strain delineation in Candida

Summary. We compared two phenotypic methods, colony morphotyping on Sabouraud‐tripheniltetrazolium agar (STTZ) and serotyping, with two genotypic methods, karyotyping and Random Amplified Polymorphic DNA bands obtained by PCR amplification (RAPD‐PCR), for strain delineation in 33 Candida clinical isolates and two C. albicans strains from culture collections. Analysis of isolates on STTZ showed 11 different morphotypes. In two patients there was a switch in the morphotype coincidential with a change in the susceptibility of the isolates to azole antifungals. C. albicans isolates were divided into two serotypes. Sixteen and 18 different patterns were identified among the Candida isolates by karyotyping and RAPD‐PCR, respectively. No relationship was found between any of the typing methods used and the source of the isolates. The combination of karyotyping and morphotyping on STTZ yielded useful epidemiological information, since it allowed the differentiation among the Candida species studied and the discrimination of clusters within C. albicans as well as to check the capacity of a strain to generate variants with different susceptibility to some antifungals.

Reactivity of Candida albicans Germ Tubes with Salivary Secretory IgA

Salivary secretory IgA (sIgA) has been shown to react with a group of heat shock mannoproteins preferentially expressed on yeast cells grown at 37°C. Since at this temperature C. albicans can induce germ tubes, we explored the role of germ tube induction on human salivary sIgA reactivity in both germinative and agerminative C. albicans strains, in an attempt to investigate whether the germ tube expressed the heat shock mannoproteins reactive with sIgA. The reactivity with sIgA of the agerminative strain, grown at 25 and 37°C for different times, was measured spectrofluorometrically and was fairly constant with time. Yeast cells grown at 37°C tended to be more reactive than those grown at 25°C. In contrast, when compared with the yeast cells of the germinative strain grown at 25°C, there was a statistically significant decrease in reactivity with sIgA during germ tube formation. Serum IgA and IgG did not show statistically significant changes in reactivity with C. albicans during germination, suggesting differences in reactivity with C. albicans cell wall antigens between mucosal and systemic humoral responses. Cell wall mannoproteins of molecular masses > 60 kDa were characterized by Western blotting as responsible for the decrease in sIgA reactivity observed in the germ tube, and the fall in sIgA reactivity was related to the release of cell wall mannoproteins into the culture medium. The release of these mannoproteins may be a mechanism whereby C. albicans avoids the action of sIgA, and it may play an important role in the host-parasite relationship in oral candidiasis.

Serological Differentiation of Experimentally Induced Candida dubliniensis and Candida albicans Infections

ABSTRACT Using a rabbit model of systemic infection, we show that it is possible to differentiate infections caused by Candida dubliniensis and other Candida species by detecting the antibody response mounted by the infected animals. These results confirm our previous observation in a patient with C. dubliniensis candidemia and suggest that detection of C. dubliniensis-specific antibodies is useful in the diagnosis of invasive candidiasis caused by this yeast.

Influence of Environmental pH on the Reactivity of Candida albicans with Salivary IgA

Salivary secretory IgA reacts with a group of heat-shock mannoproteins preferentially expressed on Candida albicans yeast cells and germ tubes grown at 37°C. Since other environmental factors can also modulate the expression of those antigens, we have investigated the influence of the pH of the culture medium on the expression of the antigens reacting with human salivary IgA by C. albicans. By indirect immunofluorescence, yeast cells grown in Sabouraud glucose broth at 37°C showed a statistically significant increase in reactivity with salivary IgA (p < 0.0001) when compared with cells grown at 25°C at the 4 pH values studied (3.3, 5.9, 7.5, and 9.5), the highest reactivity and the major heat-shock effect being observed at pH 5.9. The decrease in reactivity with salivary IgA observed in C. albicans cells grown at pH values of 3.3 and 9.5 was confirmed by Western blotting. Salivary IgA reacted with polydispersed materials from the cell walls of molecular masses > 55 kDa, which were more expressed at neutral pH than at acidic or alkaline pH values. A similar reactivity was observed when the antigenic extracts were stained with an antiserum directed against oligosaccharides present in antigen 6 of C. albicans serotype A. The differences in reactivity presented by salivary IgA may be related to a decrease in the expression of polysaccharides present on the surfaces of the yeast cells of C. albicans grown at acidic or alkaline pH values. The low reactivity of salivary IgA with C. albicans cells grown at acidic pH values may help to explain the association between acidic saliva and the carriage of Candida in the oral cavity, as well as with oral candidiasis.

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.

Identification of antigens reacting with anti-Candida albicans germ tube antibodies

Anti-Candida albicans germ tube antibodies can be induced in rabbits immunized with different C. albicans extracts. Antigens responsible for the induction of those antibodies have molecular weights of approximately 230–250, 62, 43 and 41 kDa. These antigens are present in the cell wall of both C. albicans morphological forms, although their location seems to be different.