Electrophoresis: The State of the Gel

For a 30-year-old experimental method, gel electrophoresis remains popular. Originally devised as a method to extract nucleic acids from solution, it has evolved into a method for the analysis of everything from protein expression to matching RNA expression to proteins. "When we opened this facility three years ago, some people told me that in three years you won't do gel electrophoresis any more, so why invest in the equipment?" says Thomas Franz, head of the proteomics core facility at the European Molecular Biology Laboratory in Heidelberg, Germany. "Instead we've had an increase in demand of gel electrophoresis of 100% every year for the last three years." That's not to say that there aren't contenders for the throne. As liquid chromatography continues to improve, it gains more and more adherents in the field of proteomics. And there are plenty of emerging technologies, including surface plasmon resonance and planar waveguide technology for protein microarrays, which promise to quickly identify defined targets. Gel electrophoresis, however, keeps getting better with age. In just the past decade, 2-D gels have become the norm, measuring both the isoelectric point and the size of the proteins. Now a process called Differential Gel Electrophoresis (DiGE) is quickly catching on in labs throughout the world as the gold standard of protein expression analysis. "It is possible to use DiGE to detect and quantify differences between pairs of samples on the same gel," says Kenneth Williams, director of the Keck Laboratory at Yale University. That's important because it aids reproducibility – the great bugaboo of gel electrophoresis. "The single greatest problem in doing electrophoresis experiments is that it's so difficult to run the same experiment under the same conditions and get exactly the same results," says Franz. The ability to run a complete experiment on the same gel optimizes the environmental conditions for experimental success. Often, differing results are not the fault of the million-dollar machines or the highly trained technicians running the equipment, but in the gel itself. "No matter how much effort a manufacturer puts into creating the perfect gel, it's going to have some irregularities," says Chao-Xing Yuan, technical director of the proteomics core facility at the University of Pennsylvania. "It might be a little more brittle at one edge, or contain a speck of dust or something else that will disrupt the process of protein separation." That's where most of the advances in imaging and documentation systems have been focused. Franz, for instance, always runs four gels for every gel that's requested. A digital image of each gel is captured and then all four images are combined into a 'virtual gel' which is then subjected to image-analysis software. "No matter how good you are at running gels and no matter how much money you have spent on your equipment, you can never guarantee a perfect gel," he says. "By combining the images, we increase our chances of getting it right three-fold." More importantly, he adds, it reduces the risks of getting it wrong. Thanks to advanced algorithms and years of perfecting the software, it's much easier to get usable data from image-analysis programs than it was even a few years ago. "There have been great strides in image manipulation and algorithms that make gels much more useful tools than they were even a few years ago," says David Wishart, a bioinformatics professor at the University of Alberta. He also points out that there's a darker side to advances in such software. "The more powerful manipulation leads to greater temptations to see what you want to see in the gel. The only thing stopping the individual researcher from going too far is trust. That might come back to bite us in the end." Wishart suggests that it's time for all raw gel images to be made available online (something which is often done anyway), so that anyone can check data with their own software. With all the improvements and modifications it has undergone, gel electrophoresis seems likely to be around for a while. Thanks to creative adjustments and improvements, the technique continues to grow in terms of resolution and reliability. Its greatest shortcoming today is in its ability to detect trace amounts of proteins in a larger sample. "We can easily find about two thousand proteins in an average blood serum sample," says Yuan. "But we know that there are another 98,000 human proteins floating out there." The biggest problem, he says, is that nobody has created a method yet for the amplification of unknown proteins. "When that happens, it will change everything. That will be the only thing that might make electrophoresis extinct. Or, on the other hand, it might make it even more useful." - Sam Jaffe sjaffe@the-scientist.com On the following pages, we compare selected suppliers of gel apparatuses, gel documentation systems, scanners, pre-cast gels, and software. For more complete tables, visit us online at http://www.the-scientist.com. Gel Documentation Systems Have you noticed that everyone seems to have a shiny, new digital camera these days? That's because manufacturing costs have plummeted, flattening the pricing curve for high-end multi-megapixel sensors. While that's good news for family papparazi, it's also a boon for any lab that runs gels. That's because the same cameras that can be used for your Monday bowling party work just as well capturing a gel image. As a result, low-end, high-resolution imaging equipment has flooded the market. "It's gotten to the point where all you need is the family camera and a darkroom hood," says Ramana Tadepalli, marketing chief at Hoefer, whose revamped product line doesn't even include an imaging system. "The most critical piece of equipment now is the rubber gasket that keeps the light out of the space between the camera and the hood. When a rubber gasket is all the value you can add, it's time to get out of the business." While low-end systems have been revolutionized, high-end machines have kept up with progress too. Take, for instance, UVP's EpiChemi, which sells for a little under $20,000. It has an advanced Peltier cooling unit to keep the camera cool as ice so that temperature doesn't alter the image. The gel itself is also cooled, ensuring that warping doesn't occur. Here's a table of the image capture and documentation systems that are available for today's labs, from the high-end to the bargain basement. Gel Apparatus Buying an electrophoresis apparatus can be an intimidating task. First you have to decide if you want a horizontal (or submarine) device or a vertical one. Then you have to determine which size format – mini, midi, or large – works best for your lab tasks. Then you must wade through all the different models from the myriad manufacturers. It's enough to make the process of buying a new home seem simple in comparison. Thus, there's little surprise that many buyers simply choose a manufacturer and stick with it throughout the course of their career. That can be a costly mistake, though. If a simple device is all you need, you might be better off with an off-the-shelf unit from a little-known company with which you can use cheaper standard consumables. If you want a more specialized machine, it's worth your time to spend some time shopping. Integrated devices, while expensive, are filled with features that could make a big difference in your lab. NextGen Science's a2DE, for instance, automates the casting process and the actual gel run itself: Just pipette the sample into the machine and a finished gel comes out 24 hours later. "It saves a tremendous amount of time if your lab does high-throughput electrophoresis," says marketing manager Lorna Watson. A similar system from Proteome Systems takes a slightly different tack. While you cast the gels yourself, its ElectrophoretIQ apparatus runs the gel, analyzes it and even teams with a robotic spot-picker, all with minimal human intervention. Market leader GE Healthcare (formerly known as Amersham Biosciences), sells a conglomeration of its equipment for its proprietary Differential Gel Electrophoresis (DiGE) process, which allows multiple staining on the same gel. Below you'll find a selected list of apparatus makers and their wares, separated into separate tables for integrated, horizontal, and vertical systems. Article Extras Related Tables Selected Gel Doc Systems (Excel document, 744K) Selected Electrophoresis Appartus (horizontal) (Excel document, 286K) Selected Electrophoresis Appartus (vertical) (Excel document, 281K) Selected Suppliers of Scanner-Based Systems (Excel document, 738K) Selected Suppliers of Precast Gels Amresco http://www.amresco-inc.com Bio-Rad Laboratories http://www.bio-rad.com Biotech Holdings * Gelux http://www.biotechholdings.com Cambrex http://www.cambrex.com Continental Lab Products http://www.clpdirect.com Crescent Chemical Company http://www.crescentchemical.com Elchrom Scientific http://www.elchrom.com Embi Tec http://www.embitec.com ESA http://www.esainc.com GE Healthcare http://www.amershambiosciences.com The Gel Company http://www.gelcompany.com Genomic Solutions http://www.genomicsolutions.com Geno Technology http://www.genotech.com Gradipore http://www.gradipore.com/lifescience Hoefer http://www.hoeferinc.com Invitrogen http://www.invitrogen.com ISC BioExpress http://www.bioexpress.com JT Baker http://www.jtbaker.com Jule Biotechnologies http://www.precastgels.com Mirador DNA Design http://www.mirador.ca MP Biomedicals http://www.mpbio.com Owl Separation Systems http://www.owlsci.com Pierce Biotechnology http://www.piercenet.com Serva http://www.serva.de Sigma-Aldrich http://www.sigmaaldrich.com Stratagene http://www.stratagene.com 6mgel http://www.6mgel.com Software While gel electrophoresis has been around for more than three decades, the advanced computing packages designed to analyze gels are recent developments. The ability to minutely analyze the smallest spots is probably the greatest technological advance in gel technology. "The software available today has kept electrophoresis alive as a viable technology," says Chao-Xing Yuan, head of the proteomics core facility at the University of Pennsylvania. "Gels were once little more than illustrations of expression patterns. Now, they're loaded with relevant data." Most gel-analysis software packages take a high-resolution digital image and process it in multiple ways. For instance, contrast can be increased and borders can be sharpened to make individual spots more clear. More advanced programs can estimate even small differences in protein concentrations and some can quantify concentration levels. Software designed for integrated systems with spot-picking robots can then determine exactly how to excise a spot with micrometer precision. Some software packages concentrate on saving money. Silk Scientific, for instance, provides a $400 package for small labs that can be used with a plain old flatbed scanner to analyze an image. An even cheaper option is open-source software. GelScape http://www.gelscape.ualberta.ca, for instance, is a free Java-enabled, browser-based tool for annotating, manipulating, comparing, and storing 1-D and 2-D protein images. Most labs are tied to the software systems that come with the equipment they buy, however. And more sophisticated analysis, of course, generally requires a commercial package. Below, we have compiled a selected list of gel-related software suppliers, from electrophoresis system manufacturers to independent software providers. Selected Suppliers of Electrophoresis Software AMPL Software http://www.ampl.com.au Applied Maths http://www.applied-maths.com Beckman Coulter http://www.beckman.com Biosystematica http://www.biosystematica.com GelScape http://www.gelscape.ualberta.com Genetix http://www.genetix.com Imaging Research http://www.imagingresearch.com MadgeBio http://www.madgebio.co.uk Media Cybernetics http://www.mediacy.com Nonlinear Dynamics http://www.nonlinear.com PerkinElmer http://www.perkinelmer.com Scanalytics http://www.scanalytics.com Silk Scientific http://www.silkscientific.com Systat http://www.systat.com

Electrophoresis: The State of the Gel

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Sam Jaffe

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August 2004

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