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We have posted several times in the past about the fun and constructive online game Foldit! that helps gamers contribute important information to a protein structure database while playing a fun video game. We called it “guilt free computer gaming.” (See our previous posts Crowdsourcing as a model for protein structure discovery and Foldit! Guilt-Free Computer Gaming for Protein Scientists).
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Posts Tagged ‘Proteomics’
Video games can be used as effective scientific tools
:: Posted by American Biotechnologist on 11-08-2011
Five great tips for proteomic researchers
:: Posted by American Biotechnologist on 11-03-2011Here are some great application tips from Bio-Rad Laboratories for those researchers working with proteins:
- Generally, the best method for keeping a protein in solution is to add any combination of nonionic detergents, zwitterionic detergents, and chaotropic agents to the sample mixture. Also use reducing agents such as DTT and DTE (less than 20 mM) to decrease disulfide bond formation between proteins.
- When working with membrane or insoluble proteins, increase the amount of SDS in the equilibration and running buffers (up to 0.2%) to allow the proteins to effectively migrate out of the IPG strip.
- To reduce the amount of SDS in samples generated by preparative SDS-PAGE, substitute the elution buffer with one that does not contain SDS.
- Nucleic acid contamination is a common cause of horizontal gel streaking. Treat samples with nucleases to remove nucleic acids prior to isoelectric focusing.
- Never heat samples in urea-containing buffers. The urea rapidly breaks down to carbamic acid and carbamylates the proteins, modifying their charge. Urea breakdown and subsequent protein carbamylation is the cause of charge trains on 2-D gels. A charge train is a series of spots on a 2-D gel that are of different pIs and the same size.
For more great tips visit www.expressionproteomics.com
New technique for watching proteins in action in intact cells
:: Posted by American Biotechnologist on 11-01-2011Proteins are literally the movers and the shakers of the intracellular world. If DNA is the film director, then they are the actors. And much can be learned about cell function – and dysfunction – by watching proteins on the move.
Until now, scientists have only been able to see this process indirectly. Now researchers at Vanderbilt University in Nashville, Tenn., have come up with a promising new technique that uses a scanning transmission electron microscope (STEM) to view proteins tagged with gold nanoparticles in whole, intact cells.
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Changing the way gel imaging is done
:: Posted by American Biotechnologist on 10-26-2011The GelDoc EZ was ranked among the top 10 innovations of 2010. Watch the testimonial below to learn why researchers at Harvard University think that the award was well deserved.
Strategies for proteomics sample preparation
:: Posted by American Biotechnologist on 10-25-2011Two-dimensional (2-D) gel electrophoresis is a popular and proven separation technique for proteome analysis. The 2-D procedure is straightforward: Proteins are first separated according to their isoelectric point (pI) by isoelectric focusing (IEF) and then by their molecular weight by SDS-PAGE. For most researchers, 2-D gel electrophoresis is easy to learn, because advances in immobilized pH gradient (IPG) technology have eliminated the need for tricky and tedious IEF in ampholyte gel gradients. Nevertheless, problems with smearing, streaking, and poor resolution and reproducibility tend to leave researchers dissatisfied with the results of 2-D experiments. These common compalints are often due to improper sample preparation.
One of teh most undervalued aspects of the 2-D process, sample preparation prior to the first-dimension IEF separation contributes significantly to the overall reproducibility and accuracy of protein expression analysis. Some important considerations include:
- Care must be taken to prevent protolysis during protein extraction, and proteins must be solubilized in a buffer that is compatible with IEF
- Contaminants such as salts and detergents must be removed to ensure successful separation
- Fractionation is essential to reduce protein sample complexity when analysis of subpopulations or low-abundance proteins is required
Without proper sample preparation, protein precipitations, gel streaking, and overall poor resolution are often the unfortunate result.
Click on this link to learn some great strategies for proteomic sample preparation.
Click to learn about Bio-Rad’s new Protean i12 IEF Cell.