Quantitative comparison of electrophoretic traces of bacterial proteins

Physiological and biochemical characterization of Trichoderma harzianum, a biological control agent against soilborne fungal plant pathogens

Monoconidial cultures of 15 isolates of Trichoderma harzianum were characterized on the basis of 82 morphological, physiological, and biochemical features and 99 isoenzyme bands from seven enzyme systems. The results were subjected to numerical analysis which revealed four distinct groups. Representative sequences of the internal transcribed spacer 1 (ITS 1)-ITS 2 region in the ribosomal DNA gene cluster were compared between groups confirming this distribution. The utility of the groupings generated from the morphological, physiological, and biochemical data was assessed by including an additional environmental isolate in the electrophoretic analysis. The in vitro antibiotic activity of the T. harzianum isolates was assayed against 10 isolates of five different soilborne fungal plant pathogens: Aphanomyces cochlioides, Rhizoctonia solani, Phoma betae, Acremonium cucurbitacearum, and Fusarium oxysporum f. sp. radicis lycopersici. Similarities between levels and specificities of biological activity and the numerical characterization groupings are both discussed in relation to antagonist-specific populations in known and potential biocontrol species.

Automated lanes detection and comparison of bacterial electrophoretic protein fingerprints using fast Fourier transformation

A method of computer-automated analysis of bacterial fingerprints produced by electrophoresis of proteins in a one-dimensional slab gel system is described. Proteins were visualized by silver staining. Western blotting, or autoradiography. Gels were recorded with a CCD camera, and after initial manual removal of the unwanted image margins, track margins were identified and extracted and a normalized trace was produced automatically using Fourier routines to smooth plots required for this process. Normalized traces were then compared by Fourier correlation after application of a high-pass step filter.

Interlaboratory comparative study of the numerical analysis of one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoretic protein patterns of Campylobacter strains

Twenty-nine bacterial strains of the genus Campylobacter were examined independently at two collaborating institutes, the National Collection of Type Cultures, London and the Laboratorium voor Microbiologie, Rijksuniversiteit Gent. The one-dimensional polyacrylamide gel electrophoretic protein patterns of the strains were analysed using computerised numerical methods which employed a correlation coefficient and a clustering algorithm. The electrophoretic methods used at the two institutes included both major differences such as gel composition and running conditions and minor differences in buffer composition. Although the algorithm on which similarity and clustering were computed were the same, the detailed treatment of scan patterns differed. The resulting protein patterns in the gels differed markedly in appearance but after numerical analysis the two systems were equally effective in their ability to speciate the strains. There were, however, differences in the relationships between the species defined at the two institutes and these were at least partly due to the different background subtraction methods employed. In conclusion, the portability and reproducibility of the two systems for identification was demonstrated but for definitive classification further standardization may be required.

Numerical analysis of sodium dodecyl sulphate-polyacrylamide gel electrophoretic protein patterns for the classification, identification and typing of medically important bacteria

A numerical analysis of one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoretic protein patterns of three separate bacterial groups is described. Similarity between patterns was estimated using a correlation coefficient and is represented diagramatically by the unweighted pair-group with arithmetic averages method of clustering. Protein patterns were scanned using a laser densitometer interfaced directly to a microcomputer, where calculations were performed semi-automatically with specially written software. A method for the normalization of patterns from different gels is utilized. Whole cell protein patterns clearly distinguished strains representing various groups of Achromobacter. Similarly the two biovars of the Group EF-4 bacteria could be separated after analysis of partial "background patterns" as could the different species of Providencia. In addition, whole patterns could be used to type the various strains of P. rettgeri. These examples serve to illustrate the power, versatility and potential of the technique when applied to problems of classification, identification and typing of bacteria of medical interest. Its advantages and disadvantages, when compared to other available electrophoretic methodologies, are discussed, as is the future application of such technology to the hospital laboratory.

A method for the refinement of data arising from electrophoresis of biological fluids

Gingival crevicular fluid (GCF) is being analyzed by sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS/PAGE) in our laboratory. We wish to characterize the major protein species in GCF and to investigate their association with the progression of disease. Laser densitometry of SDS/PAGE provides estimates of log molecular weight (LMW) and relative abundance for each band in each sample. Our aim was to develop a method for the refinement of these data into clusters which could be treated as distinct protein species, whose relation to disease progression could be assessed. A reproducibility study showed that the estimated LMW would fall within 3% of the true LMW 95% of the time. The method clusters the estimated LMWs of each band in each sample so that clusters form at LMWs which occurred frequently. The data from each band in each sample are thus refined into cluster number and relative abundance. Application of the technique to data from the reproducibility study showed that clusters formed around the individual components in the mixture, with little misclassification. The technique was then applied to two data sets: from SDS/PAGE of 104 GCF samples from 74 adolescents without progressive periodontal disease, and from 2 patients suffering from advanced progressive disease. The clusters appeared accurately to reflect the appearance of the gels, and clear differences were observed between the two data sets. The method will enable changes in the composition of biological fluids to be associated with external factors such as disease status and should be widely applicable.

A study of the value of electrophoretic and other techniques for typing Acinetobacter calcoaceticus

Forty-four isolates of Acinetobacter calcoaceticus var anitratus collected during hospital outbreaks were studied using polyacrylamide gel electrophoresis (PAGE), plasmid analysis, antibiograms and biochemical tests to determine their degree of similarity. Reproducibility tests were also carried out on the PAGE and biochemical techniques to determine their validity when used to compare bacteria of the same type isolated intermittently. PAGE data was analysed densitometrically and isolates compared using a similarity matrix. All methods were able to subdivide the isolates, but results did not always correlate well between methods. Reproducibility data indicated that careful attention to technique is required when organisms are examined by PAGE sequentially. Results suggest that no single biotyping technique is likely to be adequate and that electrophoretic, biochemical and antibiogram data may complement one another and other epidemiological data in the typing of these organisms.

Automation in clinical microbiology: a new approach to identifying micro-organisms by automated pattern matching of proteins labelled with 35S-methionine

A new rapid automated method for the identification and classification of microorganisms is described. It is based on the incorporation of 35S-methionine into cellular proteins and subsequent separation of the radiolabelled proteins by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The protein patterns produced were species specific and reproducible, permitting discrimination between the species. A large number of Gram negative and Gram positive aerobic and anaerobic organisms were successfully tested. Furthermore, there were sufficient differences within species between the protein profiles to permit subdivision of the species. New typing schemes for Clostridium difficile, coagulase negative staphylococci, and Staphylococcus aureus, including the methicillin resistant strains, could thus be introduced; this has provided the basis for useful epidemiological studies. To standardise and automate the procedure an automated electrophoresis system and a two dimensional scanner were developed to scan the dried gels directly. The scanner is operated by a computer which also stores and analyses the scan data. Specific histograms are produced for each bacterial species. Pattern recognition software is used to construct databases and to compare data obtained from different gels: in this way duplicate "unknowns" can be identified. Specific small areas showing differences between various histograms can also be isolated and expanded to maximise the differences, thus providing differentiation between closely related bacterial species and the identification of differences within the species to provide new typing schemes. This system should be widely applied in clinical microbiology laboratories in the near future.