Sample Company Description for Biotechnology Homework

Ciphergen Biosystems Inc (acquired by Bio-Rad )
Equalizer Bead Technology

Ciphergen Biosystems Inc,(acquired by Bio-Rad and launched under the name Proteominer) A major obstacle in biomarker (of disease) discovery from body fluids (plasma, sera, cerebrospinal fluid, urines) is that the most interesting molecules in the proteome are masked by high abundance proteins ( such as albumins, IgG’s) and therefore are hard to identify in subsequent 2-D electrophoresis and/or spectroscopy techniques. Currently, the most common method used to overcome this difficulty is the immunodepletion technique in which the bio-sample goes through a column which contains antibodies (usually IgG or avian IgY’s) with affinity to the highest abundance proteins. Therefore, the higher abundance proteins are removed (as much as 98%-99%) and some of the medium and lower abundance proteins can now be detected. This immunodepletion method has 2 major caveats. First, many of the lower-abundance proteins are washed away together with the high abundance proteins (mostly due to the fact that these low abundance proteins have binding interactions with the high abundance proteins). Second, the technique removes only 98-99% of proteins and this is still not sufficient for discovering the rare biomarkers. It should be noted, that the most efficient immunodepletion column has about 20 affinities (or in other words, can only remove only the 20 of the most abundant proteins from a sample) A new technology that was developed by Ciphrogen, called the Equalizer Bead Technology overcomes some of the above obstacles and caveats. The technology relies on building a solid-phase combinatorial chemical library (made with hexapeptides incorporating all 20 natural amino acids) onto beads. The technology creates a situation where each bead has millions of the same unique ligand. At the end of the chemical process, there are about 64 million different ligands (and about 64 million beads), and the beads can theoretically bind ANY protein in a complex proteome. When a sample is treated with these beads, higher abundance proteins will bind to the beads, but due to their excess, many of them will remain unbound, and washed in subsequent step. On the other hand, the lower abundance proteins will also bind to the beads for which they have highest affinity, but they will not saturate the beads (no excess will be washed). Essentially, this technique reduces the protein concentration differences in a given sample. In other words, the concentration of the most abundant proteins is reduced, while the concentration of the rare proteins is enhanced. The final step in the process is elution. This technique can also be integrated into the purification of recombinant proteins from host cell for proteins that are made for human consumption and therefore, making rDNA technology safer for consumers. About the bead making technology: the beads are made of hexapeptides synthesized via a short spacer on poly(hydroxymethacrylate) beads using a modified Merrifield approach. This novel approach entails multiple sequential chemical reactions: “The first synthesis step is a batch of millions of microscopic resin beads divided into [20] different reaction vessels and the first building block, e.g., a protected amino acid, is coupled to the resin. The beads are then mixed together and washed extensively, the amino group of the coupled amino acid is deprotected, and the beads are distributed randomly into a second set of [20] reaction vessels and coupled with the next set of [amino acid] building blocks. This process is repeated until a ligand of the desired length is obtained. “ (P. G. Righetti et al. Electrophoresis 2005, 26, 297–319) [20^6 = 64M]