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May 15, 2011 (Vol. 31, No. 10)

Novel Applications for Sample Preparation

Tool Providers Launch Innovative Products to Meet Researchers' Protein-Related Demands

  • Disposability

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    According to Claremont BioSolutions, its PureLyse kits provide ultrarapid lysis and DNA extraction.

    Simplification and disposability are the key attributes of PureLyse® according to Claremont BioSolutions. This device facilitates both protein and DNA sample preparation, Bruce Irvine, CTO, explained. “It is fast and only has two steps. It is very conducive to integration into the field or point-of-care devices.”

    PureLyse uses a disposable micro-motor and specially designed impellor to lyse cells. As the sample lyses, nucleic acid or protein binds to the lysing particles. Because it flows through a chamber during lysis and binding, a wide range of volumes can be processed, with DNA binding up to 10 µg. “It works the same for protein and for DNA,” Irvine said, and produces results with better than 95% purity.

    “Alternatively, our OmniLyse® cartridge can be used for cell lysis only, and the lysed sample can then be delivered for further processing. The lysing particles can also be functionalized for affinity capture of proteins.” For example, HIS-tagged proteins bind to a nickel column in the HisExpress™ version. Two additional versions are planned for release this spring.

    Irvine reported a strong yield of protein using the PureLyse system, and noted that proteins can be extracted and purified in less than 10 minutes. (For DNA, the process requires less than three minutes.)

    This project grew from a defense contract, Irvine explained. “An efficient, disposable method to lyse cells was needed.” Claremont BioSolutions is also developing a benchtop version of PureLyse, called the RapidLyser™ with higher shear force and flow through configuration.

  • Streamlined Prep

    Stratec Molecular, until recently known as Invitek, is simplifying sample preparation with a chemistry “that allows us to combine some of the separation steps, creating, essentially, a master mix,” explained Len Vanderbosch, director of sales and marketing. Known as RTP® (Ready-to-Prep) technology, “this is an up-front solution to purifying quality nucleic acids for analysis. Our nonchaotropic chemistry prevents degradation of enzymes so samples can be prepared in fewer steps. Add the sample and you’re ready to go.”

    “The technology is for blood and blood-related products, but we have kits for a variety of different samples.” These kits create a more user-friendly approach to sample preparation which, he explains, is particularly important for molecular diagnostics labs in which researchers often have limited sample-preparation experience.

    RTP technology reduces error rates by minimizing human handling. “Our customers say the results equal those of traditional methods, but that this approach fits their workflow better. It doesn’t necessarily reduce preparation time, but streamlines the sample-preparation process.”

  • FFPE Samples

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    Qiagen offers a range of solutions for processing FFPE samples and performing subsequent assays, including those used in protein biomarker research.

    Clinical tissue samples represent a comprehensive source of material for analyzing protein-expression patterns associated with diseases such as cancer. Millions of FFPE tissue sections are stored around the world, representing a valuable and extensive collection of samples for biomedical research. While formalin-fixation is the standard for preserving and archiving biological material, FFPE samples can be challenging to work with, in particular when analyzing proteins. Without further processing, the formalin crosslinking between proteins that occurs upon sample fixation means that the starting material is unsuitable for proteomic studies, explained Peter Porschewski, Ph.D., senior scientist at Qiagen.

    Qiagen offers a range of solutions for processing FFPE samples and performing subsequent assays, including those used in protein biomarker research. “The Qproteome FFPE Tissue Kit provides an optimized protocol that uses innovative chemistry to extract total protein from FFPE tissue sections. After deparaffinization, the sample is treated with a buffer that reverses formalin crosslinking, releasing the protein molecules. Then, after preparation, the proteins can be used for downstream applications such as mass spectrometry or Western blotting.”

    Additionally, Qiagen has developed an alternative to formalin fixation for preserving tissue samples. “Recently, we successfully demonstrated that PAXgene, a new formalin-free tissue fixative, allows the extraction of nondegraded and immunoreactive proteins ready for subsequent downstream applications.” After storing treated samples for a few days, they can be embedded in paraffin, similar to traditional treatment. “PAXgene is a new technology that has the potential to become a novel fixative for modern pathology, enabling extensive proteomics studies on clinical tissues.”

  • Protein Removal

    At EMD Millipore, Sébastien Ribault, Ph.D., head of predevelopment-technology-collaboration, biomonitoring R&D, lab solutions, detailed a nucleic sample preparation kit called MilliPrep. “We’re not developing protein sample preparation with it. We’re removing protein from the sample.” This kit, he said, is a response to a sample-preparation technology that was time-consuming, generated false positives because of the steps required for sample preparation, and was not adapted for the molecular biologists’ workflow.

    MilliPrep fully integrates the sample-preparation steps within a single, three-step, closed system that combines membrane-based filtration and magnetic bead nucleic acid purification.

    To separate eukaryotic cells from mycoplasms, for example, users pipette the sample into the upper chamber of the device and place the device into a centrifuge, where the eukaryotic cells are retained on a membrane between the sample chamber and the capture chamber. “In this step, 99.9 percent of the protein and other contaminants are removed,” Dr. Ribault said.

    Mycoplasma are trapped on an asymmetric membrane, and fluid is drained into a waste tank at the bottom of the cartridge. “The remaining 0.1 percent of contaminants is removed with the fluid.” Then, a lysing reagent is added. The sample is incubated and then centrifuged again to recover targeted mycoplasma nucleic acids.

    According to Dr. Ribault, “The process eliminates false positives. It processes 20 mL volumes, which are 20 times higher than traditional column methods. Hands-on time is less than 30 minutes for ten devices.”

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