You are currently browsing the archives for the Protocols category.

Archive for the ‘Protocols’ Category

A new technology for studying protein interactions within the brain

 :: Posted by American Biotechnologist on 12-21-2011

Despite the difficulties associated with measuring in-situ protein-protein interactions in neural networks, Dr. Akira Chiba of the University of Miami recently announced that his team has embarked on a project to develop a protein interaction map within brain cells. Why have these studies been so difficult to perform until now and what does Dr. Chiba have that will make him successful? The answer lies in the small size of neural proteins and the technical limitations associated with even the highest resolution microscope.

Using a a custom- built 3D FLIM (fluorescent lifetime imaging microscopy), Chiba’s team has been able to spatially and temporally quantify fluorescently tagged protein-protein interactions in genetically modified fruit flies.

According to Chiba, “collaborating fluorescent chemistry, laser optics and artificial intelligence, my team is working in the ‘jungle’ of the molecules of life within the living cells. This is a new kind of ecology played out at the scale of nanometers—creating a sense of deja vu 80 years after the birth of modern ecology.”

Thanks to the University of Miami for this story.

Watch the video below, (already set to the appropriate frame…just press play), as Karl Svoboda of the Howard Hughes Medical Institute explains how FLIM works.

Proteomic Application Tips Grand Finale

 :: Posted by American Biotechnologist on 12-14-2011

In previous posts we provided you with several great tips for proteomic researchers (see five great tips for researchers working with proteins and more great proteomic applications tips). Today we will present you with the final in the series of application tips which are sure to improve the quality of your proteomic experiments.

  • To ensure proper and consistent visualization with a silver stain, use ultrapure water with all organic contaminants removed for the final rinse of your staining vessel. In addition, reserve that vessel exclusively for silver staining, and separate it from other glassware in your laboratory.
  •  

  • Proteins must be soluble if they are to be separated and identified on 2-D gels. Protein insolubility (precipitation) leads to loss of sample spots and streaking on 2-D gels.
  •  

  • Fractionation may improve your 2-D result by reducing sample complexity, improving the range of detection, and enriching low-abundance proteins. Fractionation can be performed according to many protein properties, including subcellular location, solubility, size, charge, and pI.
  •  

  • Improve the resolution and reproducibility of 2-D gels by performing sample cleanup to remove salts, charged detergents, phenolics, lipids, sugars, and nucleic acids. Cleanup will also reduce disulfide bonds.
  •  

  • NaCl increases conductivity, extends the time required for focusing, causes electroendosmosis, and results in uneven water distribution in the gel. In general, the tolerated concentrations of NaCl for proper in-gel rehydration and cup loading are 10 mM and 40 mM, respectively.
  •  

  • Nucleic acids bind proteins through electrostatic interaction, thereby interfering with isoelectric focusing. Nucleic acids can also clog the pores of the acrylamide matrix. Remove nucleic acids with nucleases and ultracentrifugation in the presence of carrier ampholytes. In addition, benzonase can be used in a sample together with urea to remove DNA or RNA contamination.
  •  

  • Insoluble material in a sample obstructs gel pores, resulting in poor focusing and severe streaking. Remove these materials by high-speed centrifugation (for example, 20,000 x g for 30 minutes at 20°C).
  •  

  • To monitor the initial progress of the electrophoresis on the IPG strips, add up to 0.001% of Bromophenol Blue to both the rehydration and equilibration buffers.

For more great tips visit www.expressionproteomics.com

More great proteomic application tips

 :: Posted by American Biotechnologist on 11-28-2011

In a previous post we provided you with five great tips for researchers working with proteins. Today we will present you with five more tips which are sure to improve the quality of your proteomic experiments.

  • Negatively charged polysaccharides that contain sialic acid can produce horizontal streaks similar to those generated by nucleic acid contaminants. Ultracentrifugation is often sufficient to remove carbohydrates from samples.
  •  

  • To prevent vertical streaking, limit the amount of protein added onto an IPG strip. Compensate for such decreases in sample load by using a more sensitive staining technique, such as silver staining.
  •  

  • Reusing electrophoresis running buffer can result in poor separation and vertical streaking due to the depletion of ions and SDS in the running buffer. Avoid this practice, especially if vertical streaking is a persistent problem.
  •  

  • Vertical streaking on second-dimension gels is often caused by gaps between the IPG strips and the gels. Ensure the second-dimension gel has a straight and level top edge, and that the IPG strip is in direct contact with the gel along its entire length.
  •  

  • If some of the bands on your gel are not staining or appear faint, use silver stain as usual, then agitate it slowly in deionized water for 30 minutes and repeat. Then apply the silver stain again, starting with the silver reagent step. Proteins that did not stain on the first cycle will stain to full intensity.

For more great tips visit www.expressionproteomics.com

Protein blotting home video

 :: Posted by American Biotechnologist on 11-15-2011

We found the amateur home video on protein blotting and western blot analysis posted on teachinhawaii’s YouTube channel. The video is a decent step-by-step demonstration of how to perform protein blotting and western blot analysis. It is appropriate for novice or first-time users. The video shows how to do protein blotting with Bio-Rad’s Mini-Trans Blot or Criterion Protein Blotting Systems. Of course, faster protein blotting can now be perfomed in under 3 minutes with Bio-Rad’s Trans-Blot Turbo Transfer System (as opposed to the 1-2 hours suggested in this video).

We are in the process of collecting protein blotting home videos. If you are aware of an interesting video, please let us know.

Five great tips for proteomic researchers

 :: Posted by American Biotechnologist on 11-03-2011

Here 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