Computational tools for the study of allergens

Allergy is a major cause of morbidity worldwide. The number of characterized allergens and related information is increasing rapidly creating demands for advanced information storage, retrieval and analysis. Bioinformatics provides useful tools for analysing allergens and these are complementary to traditional laboratory techniques for the study of allergens. Specific applications include structural analysis of allergens, identification of B- and T-cell epitopes, assessment of allergenicity and cross-reactivity, and genome analysis. In this paper, the most important bioinformatic tools and methods with relevance to the study of allergy have been reviewed.

Allergen databases

Allergies represent a significant medical and industrial problem. Molecular and clinical data on allergens are growing exponentially and in this article we have reviewed nine specialized allergen databases and identified data sources related to protein allergens contained in general purpose molecular databases. An analysis of allergens contained in public databases indicates a high level of redundancy of entries and a relatively low coverage of allergens by individual databases. From this analysis we identify current database needs for allergy research and, in particular, highlight the need for a centralized reference allergen database.

Automated ribotyping differentiates vibrio parahaemolyticus O3:K6 strains associated with a Texas outbreak from other clinical strains

Automated ribotyping with a Qualicon Riboprinter was used to determine whether clinical isolates of Vibrio parahaemolyticus O3:K6 recovered during two U.S. outbreaks of oyster-associated gastroenteritis in 1998 were related to each other and to a previously identified highly virulent Asian clone of this serotype. The patterns produced using the restriction enzymes Eco RI and Pst I suggest that the outbreak in the Northeastern United States was caused by a single strain closely related to the Asian clone. In contrast, it appears that multiple strains were involved in the Texas outbreak and that the predominant type was genetically distinct from the Northeastern and Asian clone.

Differentiation between types and strains of Clostridium botulinum by riboprinting

The ability of automated ribotyping to differentiate between major types and individual strains of Clostridium botulinum was tested using the Qualicon Riboprinter Microbial Characterization System. Pure spores of C. botulinum type A, proteolytic type B, nonproteolytic type B, and type E strains were inoculated onto modified anaerobic egg yolk agar and incubated 24 h at 35 degrees C. Plates were rinsed with buffer (2 mM Tris + 20 mM EDTA) to remove vegetative cells that were heated for 10 min at 80 degrees C, treated with a lysing agent, and ribotyped in the Qualicon Riboprinter utilizing the enzyme EcoRI. Riboprint patterns were obtained for 30 strains of the four major types of C. botulinum most commonly involved in human foodborne botulism. Proteolytic strains yielded the best and most consistent results. Fifteen ribogroups were identified among the 31 strains tested. Interestingly, in two cases, a single ribogroup contained patterns from isolates belonging to evolutionarily distinct Clostridium lineages. This degree of differentiation between strains of C. botulinum may be useful in hazard analysis and identification, hazard analysis and critical control point monitoring and validation, environmental monitoring, and in inoculation studies.

Ribotype analysis of strain distribution in Listeria monocytogenes

Changes in the temporal and spatial patterns of strain distribution for the foodborne pathogen Listeria monocytogenes were studied by ribotyping using the Qualicon Riboprinter system. Ribotype patterns were obtained by using the restriction enzymes EcoRI and PvuII for 72 isolates of L. monocytogenes recovered from smoked salmon samples over a period of 3 years. Each pattern was classified both by comparison to a pattern library and by comparison among the 72 isolate patterns. Eleven EcoRI-based ribogroups and 16 PvuII groups were identified. Eight of the 11 EcoRI ribogroups were found in isolates obtained over a period of >12 months, and 75% of the EcoRI ribogroups that were found in more than one food sample were distributed nationally. Within the set of isolates, there were 26 instances where more than one isolate was obtained from a single food sample. In 35% of these instances, the co-isolates produced different ribotype patterns, indicating that multiple strains of L. monocytogenes commonly coexist in the same environment. Overall, these data indicate that the population of L. monocytogenes consists of a number of widely dispersed strains with little geographic or temporal stratification.

Specificity of the BAX polymerase chain reaction system for detection of the foodborne pathogen Listeria monocytogenes

The polymerase chain reaction (PCR) can be used for rapid and specific detection of foodborne pathogens. One commercial kit, the Qualicon BAX system uses PCR to detect Listeria monocytogenes in enrichment cultures derived from food and environmental samples. The specificity and sensitivity of the BAX system for detecting L. monocytogenes were characterized by using both pure and mixed cell cultures, and optimal conditions for production of cell lysates were determined. The BAX system was highly specific for L. monocytogenes, and no interference was seen in the presence of either other Listeria species or microbes from other genera. The assay detected L. monocytogenes at 10(5)-10(6) colony-forming units/mL. This sensitivity is adequate for detecting viable cells after enrichment but prevents false-positive signals from nonviable cells.

Evaluation of DNA preparation techniques for detection of the SLT-1 gene of Escherichia coli O157: H7 in bovine faeces using the polymerase chain reaction

The polymerase chain reaction (PCR) has the potential to detect low levels of the human pathogen Escherichia coli O157: H7 in bovine faeces. To improve the utility of PCR for this application, several methods for preparing template DNA from bovine faeces, both directly and after non-selective enrichment, were tested. These were boiling, enzyme treatment, enzyme treatment plus phenol-chloroform extraction, and enzyme treatment plus phenol-chloroform extraction plus Geneclean purification. Of these, the boiling method was the most consistent and had a sensitivity of approximately 3 cfu g-1 faeces, with an assay time of less than 32 h. The boiling method was also combined with immunomagnetic separation (IMS) to detect E. coli O157: H7 in less than 8 h, but with a sensitivity of approximately 10(3) cfu g-1 faeces. These methods can be used to prepare template for PCR screening of bovine faeces using any appropriate PCR primers.

Effects of sodium saccharin and linoleic acid on mRNA levels of Her2/neu and p53 in a human breast epithelial cell line

The effects of two food-related chemicals (sodium saccharin and linoleic acid) on the levels of Her2/neu and p53 mRNA in a non-cancerous human breast epithelial cell line (HBL-100) were tested in comparison with the effects of the known tumor promoter phorbol 12-myristate 13-acetate (TPA). Treatments were made both with and without prior treatment with two well-known tumor initiators, N-nitroso-N-methylurea (NMU) or 7,12-dimethylbenz[a]anthracene (DMBA). The effects in general were small, the greatest being increases of 46-67% in Her2/neu mRNA levels in response to treatments with TPA or sodium saccharin following NMU treatments. These results demonstrate that sodium saccharin following NMU treatments might be involved in transcriptional regulation of Her2/neu in HBL-100 cells and suggest that its effects may not be limited to urinary bladder.

Impedance based sensing of the specific binding reaction between Staphylococcus enterotoxin B and its antibody on an ultra-thin platinum film

Immunobiosensing techniques to measure specific antigen-antibody binding reactions are important in the development of biosensor applications in biotechnology, in vitro diagnosis, medicine and food technology. An immunobiosensor was constructed to measure the specific binding reaction between Staphylococcus enterotoxin B (SEB) and anti-SEB antibodies. The biosensor comprised an anti-SEB bioactive layer covalently immobilized on an ultra-thin platinum (Pt) film sputtered onto a 100 nm thick silicon dioxide layer on a silicon chip. The Pt film was discontinuous with a normal thickness of 25 A. The impedance of the Pt film decreased during the binding of the anti-SEB to SEB in phosphate buffered saline (PBS) at room temperature. The impedance decreases were irreversible in PBS before saturation of the specific binding sites. When saturated, the impedance at 100 Hz was 14% of the value obtained for the fresh anti-SEB layer in PBS. The magnitude of the impedance (Z) decrease followed a simple relationship with SEB concentration in the range between 0.389 and 10.70 ng/ml SEB. The specificity of the biosensor was demonstrated by showing that no irreversible impedance decreases occurred when the sensor was exposed to 100 ng/ml kappa-casein, or alpha-lactalbumin, in PBS.

Effects of staining of RNA with ethidium bromide before electrophoresis on performance of northern blots

Staining of RNA with ethidium bromide (EtdBr) prior to running agarose gels has been reported to afford certain advantages over staining gels after electrophoresis. We have examined prior staining of RNA with a wide range of EtdBr concentrations, particularly with respect to its effects on Northern blot hybridizations using antisense RNA probes. Prior staining with EtdBr at concentrations of 100-1000 micrograms/ml caused significant alterations in RNA mobilities and significantly decreased hybridization with antisense RNA probes compared with unstained RNA. Prior staining with EtdBr at 10-50 micrograms/ml resulted in the best combination of staining sensitivity, absence of alterations in RNA mobility and efficiency of hybridization. Conventional staining of gels after electrophoresis also resulted in decreased hybridization efficiency with RNA probes compared with unstained RNA.

Instability of Tn5 in a plasmid cloning vector for the cyanobacterium Anacystis nidulans

Transposon Tn5 was used to produce insertions within the region of a cyanobacterial shuttle vector previously identified as necessary for transformation of Anacystis nidulans. These transposon-containing plasmids were used to transform a plasmid-cured derivative of Anacystis strain R2 and tested for structural stability of the transforming plasmid. The transposon DNA was deleted from all the plasmids containing Tn5 within the cyanobacterial replication region. Inserts in the vector DNA were physically stable and expressed the kanr gene. The internal Tn5 HindIII fragment was also cloned into each of the three HindIII sites in the shuttle plasmid. Inserts in two of these sites were stable, whereas inserts into the third site were not.

Polyelectrolyte precipitation of β-galactosidase fusions containing poly-aspartic acid tails

Protein recovery from industrial microbial processes can be very expensive, often exceeding the cost of protein production. We have genetically engineered 3 beta-galactosidase (beta-gal) fusion proteins containing poly-aspartic acid tails to test the effect of the tails on recovery by the relatively inexpensive method of polyelectrolyte precipitation. The fusion proteins, designated T1, T2, and T3, were constructed with C-terminal tails of 5, 11, and 16 aspartic acid residues, respectively. The fusion proteins were expressed in Escherichia coli, and purified by affinity chromatography. T1 and T2 had specific activities similar to that of wildtype beta-gal, whereas the specific activity of T3 was about half that of T1 and T2. The increased net charge of the fusion proteins compared to wildtype beta-gal was indicated both by ion-exchange chromatography and their migration pattern in non-denaturing polyacrylamide gel electrophoresis. All three tails enhanced polyethyleneimine (PEI) precipitation of the fusion proteins compared to wildtype beta-gal. At a low PEI/protein ratio (0.01, g g-1), recovery by precipitation of T2 and T3 was more than 2 X that of the beta-gal control, whereas that of T1 was only slightly greater than that of the control. At a higher PEI/protein ratio (0.03, g g-1) the amount of precipitation of all three fusion proteins was nearly the same, about 1.5 X that of the control.

Instability of Tn5 inserts in cyanobacterial cloning vectors

Transposon Tn5 was used to produce random insertions in two hybrid cloning vectors for the unicellular cyanobacterium Anacystis nidulans. The transposon-containing plasmids were used to localize essential replication functions and to characterize the stability of large inserts in these vectors. The effect of the insertions on plasmid function was tested by transformation into a derivative of A. nidulans that had been cured of the endogenous plasmid used to construct the vectors. A region of approximately 4 kilobases was essential for successful plasmid transformation and replication. This region has also been shown to be involved in plasmid replication by deletion analysis. High rates of excision of Tn5 inserts within this region and restoration of normal replication function were observed when transformants were selected by using a resistance marker outside the replication region in the absence of selection for the transposon-coded kanamycin resistance. Transposon inserts outside this region were not deleted.