When can the Ogston-Morris-Rodbard-Chrambach model be applied to gel electrophoresis?

Gel Electrophoresis of a Hydrophobic Liquid Droplet with an Equipotential Slip Surface

A theoretical study has been carried out on the electrophoresis of charged dielectric liquid droplets with an equipotential and hydrodynamically slipping surface moving in a quenched polymeric charged hydrogel medium. The liquid inside the droplet is electrically neutral. The Brinkman-Debye-Bueche model is employed to study the gel electrophoresis of such a hydrophobic and equipotential liquid droplet considering the long-range hydrodynamic interaction between a migrating droplet and the gel skeleton. Within the weak field and Debye-Hückel electrostatic framework, we derive an original closed-form expression for electrophoretic mobility, which further recovers the existing mobility expressions derived under several limiting conditions. The derived expressions for electrophoretic mobility explicitly involve exponential integrals, which are not so convenient for practical applications. Thus, the exact forms of the electrophoretic mobility under various electrohydrodynamic conditions are further approximated to make them free from exponential integrals. The approximate forms are found to be in excellent agreement with the exact results with maximum relative errors of about 1.5%.

Image analysis tools and emerging algorithms for expression proteomics

Since their origins in academic endeavours in the 1970s, computational analysis tools have matured into a number of established commercial packages that underpin research in expression proteomics. In this paper we describe the image analysis pipeline for the established 2-DE technique of protein separation, and by first covering signal analysis for MS, we also explain the current image analysis workflow for the emerging high-throughput 'shotgun' proteomics platform of LC coupled to MS (LC/MS). The bioinformatics challenges for both methods are illustrated and compared, whereas existing commercial and academic packages and their workflows are described from both a user's and a technical perspective. Attention is given to the importance of sound statistical treatment of the resultant quantifications in the search for differential expression. Despite wide availability of proteomics software, a number of challenges have yet to be overcome regarding algorithm accuracy, objectivity and automation, generally due to deterministic spot-centric approaches that discard information early in the pipeline, propagating errors. We review recent advances in signal and image analysis algorithms in 2-DE, MS, LC/MS and Imaging MS. Particular attention is given to wavelet techniques, automated image-based alignment and differential analysis in 2-DE, Bayesian peak mixture models, and functional mixed modelling in MS, and group-wise consensus alignment methods for LC/MS.

Analysis of RNA folding by native polyacrylamide gel electrophoresis

Polyacrylamide gel electrophoresis under native conditions (native PAGE) is a well-established and versatile method for probing nucleic acid conformation and nucleic acid-protein interactions. Native PAGE has been used to measure RNA folding equilibria and kinetics under a wide variety of conditions. Advantages of this method are its adaptability, absolute determination of reaction endpoints, and direct analysis of conformational hetereogeneity within a sample. Native PAGE is also useful for resolving ligand-induced structural changes.

Electrophoresis of spheres with uniform zeta potential in a gel modeled as an effective medium

The effective medium model [H.C. Brinkman, Appl. Sci. Res. A 1 (1947) 27] is used to calculate the electrophoretic mobility of spheres in a gel with uniform zeta potential on their surface. In the absence of a gel support medium or ion relaxation (the distortion of the ion atmosphere from equilibrium due to the presence of an external flow or electric field), our results reduce to those of Henry [D.C. Henry, Proc. R. Soc. London Ser. A 133 (1931) 106]. The relaxation effect can be ignored for weakly charged particles, or for particles with low absolute zeta potential. Using a procedure similar to that employed by O'Brien and White [R.W. O'Brien, L.R. White, J. Chem. Soc. Faraday Trans. 2 74 (1978) 1607], the relaxation effect is accounted for in the present work and results are presented over a wide range of particle sizes, gel concentrations, and zeta potentials in KCl salt solutions. In the limit of no gel, our results reduce to those of earlier investigations. The procedure is then applied to the mobility of Au nanoparticles in agarose gels and model results are compared to recent experiments [D. Zanchet, C.M. Micheel, W.J. Parak, D. Gerion, S.C. Williams, A.P. Alivisatos, J. Phys. Chem. B 106 (2002) 11758; T. Pons, H.T. Uyeda, I.L. Medintz, H. Mattoussi, J. Phys. Chem. B 110 (2006) 20308]. Good agreement with experiment is found for reasonable choices of the model input parameters.

Computer-assisted 2-D agarose electrophoresis ofHaemophilus influenzae type B meningitis vaccines and analysis of polydisperse particle populations in the size range of viruses: A review

When protein-polysaccharide conjugated vaccines were first developed for the immunization of small children against meningitis caused by infection with Haemophilus influenzae type b (Hib), the vaccine preparations varied in immunogenicity. Testing for immunogenicity was time-consuming and alternative analytical procedures for determining vaccine quality were unsatisfactory. For example, due to the very high molecular weight of the vaccine particles, immunogens could only be physically characterized as a fraction in the void volume of Sepharose gel filtration. In search of better analytical methods, a computer-assisted electrophoretic technique for analyzing such vaccines was developed in the period from 1983 to 1995. This new approach made it possible to analyze highly negatively charged particles as large as or larger than intact viruses. 2-D gel patterns were generated that varied depending on the conditions of the particular vaccine preparation and were therefore characteristic of each vaccine sample. Thus, vaccine particle populations with a continuous size variation over a wide range (polydisperse) could be characterized according to size and free mobility (related to particle surface net charge density). These advances are reviewed in this article, since the developed methods are still a promising tool for vaccine quality control and for predicting immunogen effectiveness in the production of vaccines. The technique is potentially beneficial for Hib immunogens and other high-molecular-mass vaccines. Additional biomedical applications for this nondenaturing electrophoretic technique are briefly discussed and detailed information about computational and mathematical procedures and theoretical aspects is provided in the Appendices.

Warping two-dimensional electrophoresis gel images to correct for geometric distortions of the spot pattern

A crucial step in two-dimensional gel based protein expression analysis is to match spots in different gel images that correspond to the same protein. It still requires extensive and time-consuming manual interference, although several semiautomatic techniques exist. Geometric distortion of the protein patterns inherent to the electrophoresis procedure is one of the main causes of these difficulties. An image warping method to reduce this problem is presented. A warping is a function that deforms images by mapping between image domains. The method proceeds in two steps. Firstly, a simple physicochemical model is formulated and applied for warping of each gel image to correct for what might be one of the main causes of the distortions: current leakage across the sides during the second-dimensional electrophoresis. Secondly, the images are automatically aligned by maximizing a penalized likelihood criterion. The method is applied to a set of ten gel images showing the radioactively labeled proteome of yeast Saccharomyces cerevisiae during normal and steady-state saline growth. The improvement in matching when given the warped images instead of the original ones is exemplified by a comparison within a commercially available software.

An exactly solvable Ogston model of gel electrophoresis: VIII. Nonconducting gel fibers, curved field lines, and the Nernst-Einstein relation

In this article, we examine the low-field electrophoretic migration of infinitely small analytes in dilute sieving media made of nonconducting gel fibers. Using an Ogston obstruction model, we show that the electrophoretic mobility is not affected by the presence of curved field lines. In other words, the Nernst-Einstein relation between the mobility and the diffusion coefficient is valid regardless of the electrical properties of the gel fibers. Although this finding may greatly simplify the development of obstruction models of electrophoretic sieving, it also represents a critical test for any analytical or computational approach.

Theory of DNA electrophoresis: a look at some current challenges

Although electrophoresis is one of the basic methods of the modern molecular biology laboratory, new ideas are being suggested at an accelerated rate, in large part because of the pressing demands of the biomedical community. Although we now have, at least for some methods, a fairly good theoretical understanding of the physical mechanisms that lead to the observed peak spacings, widths and shapes, this knowledge is often too qualitative to be used to guide further technical developments and improvements. In this article, we review some selected elements of the current state of our theoretical ignorance, focusing mostly on DNA electrophoresis, and we offer several suggestions for further theoretical investigations.