Processing of DNA and Protein Electrophoresis Gels by Image processing

Year 2015, Volume: 36 Issue: 3, 3486 - 3494, 13.05.2015

Mohsen Fırooz Abadı

Abstract

Abstract. With recent legislation allowing for the registration of new cultivars, the analysis of DNA and protein electrophoresis gels is becoming increasingly important for cultivar identification. DNA fragments or proteins of different molecular weights are separatedusing electrophoresis, giving a series of bands with positions corresponding to the molecular weight. Image analysis of the gels removes much of the subjectivity of manual comparison of band position and intensity between samples.The first step in processing corrects for geometric distortions, called smiling, caused by variations in conditions during electrophoresis. Most of the effects of smiling may be eliminated by detecting and straightening a pair of bands (one at each end of the lane) common to most of the lanes. Next, the individual lanes corresponding to each sample are automatically detected. The background fog is estimated and removed by subtracting it from the image. The bands are then detected and the positions and densities of each band are determined. By including a series of proteins or nucleotides of known molecular weights in one of the lanes, the unknown molecular weights of the bands in each sample are able to be estimated based on their position.The use of image analysis techniques in this application provides a relatively quick and inexpensive method of objectively identifying differences between samples.

Keywords

Image processing, DNA, Electrophoresis

References

• Williams C.E. and St. Clair D.A. Phenetic relationships and levels of variability detected by restriction fragment length polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersicon esculentum. Genome, 36:619- 630. (1993)
• Shapiro A.L., Vineula E., Maizel J. V. Molecular weight estimation of polypeptide chains by electrophoresis in SDS-polyacrylamide gels. Biochem. and Biophysical Research Communications 28:815-20 (1967)
• Weber K. and Osborne M. The reliability of molecular weight determinations by dodecyl sulphate-polyacrylamide gel electrophoresis. Journal of Biological Chemistry 244:4406-12 (1969)
• Aaij C. and Borst P. The gel electrophoresis of DNA. Biochimica et Biophysica Acta 269:192-200 (1972)
• Meyer J.A., Sanchez D., Elwell L.P. and Falkow S. Simple agarose gel electrophoretic method for the identification and characterisation of plasmid deoxyribonucleic acid. Journal of Bacteriology 127:1529-37 (1976)
• Southern E.M. Measurement of DNA length by gel electrophoresis. Analytical Biochemistry 100:319-23 (1979)
• Plikaytis B.D., Carlone G.M., Edmonds P. and Mayer L.W. Robust standard estimation of standard curves for protein molecular weight and linear duplex DNA base pair number after gel electrophoresis. Analytical Biochemistry 152:346-64 (1986)
• Owen R.J. and Beck A. Evaluation of three procedures using a laser densitometer and microcomputer for estimating molecular sizes of restriction endonuclease digest fragments and application to Campylobacter jejuni chromosomal DNA. Letters in Applied Microbiology 4:5-8 (1987).