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:: Posted by American Biotechnologist on 04-13-2011
Lisa Grauer from BioTechniques recently discussed an elegant study by Dr. Benjamin Natelson of the University of Medicine and Dentistry of New Jersey, that highlights the utility of proteome-wide association studies in disease diagnosis.
Her article focused on a study that compared the protein profile in the cerebral spinal fluid (CSF) of “normal” individuals and those suffering from Chronic Fatigue Syndrome (CFS…talk about getting confused by acronyms) or neurologic post-treatment Lyme syndrome (nPTLS). The results showed 738 proteins that were uniquely expressed in the CFS group and 692 in the nPTLS group. These findings are a significant step in the study of CFS and nPTLS which until now have been classified as “medically unexplained illnesses” often resulting in patient complaints not being taken seriously by their primary care provider.
While more detailed downstream analysis remain to be done, this study provides a wonderful example of how population-scale proteomic studies help in the advancement of disease diagnosis.
:: Posted by American Biotechnologist on 09-15-2010
A recent article has demonstrated the validity of a new top-down proteomics approach to identifying low-abundance biomarkers in the one per cent of serum/plasma proteins known as the deep proteome. The study used a 4-step approach including sample collection, fractionation with proteominer technology, biomarker discovery with SELDI and biomarker identification using the Lucid system to identify a potential biomarker that might be used to track a patient’s recovery from a myocardial infarction (heart attack).
According to Bio-Rad product manager Dominic Casenas, ‘The workflow in this publication provides scientists with a promising approach for accessing, profiling, and identifying clinically relevant biomarkers.’
:: Posted by American Biotechnologist on 08-27-2010
As discussed in an earlier post, biomarker studies are quickly becoming the hottest research topic around. Many techniques such as 2D, SELDI and Mass Spectrometry are widely deployed in biomarker research. Nonetheless, whichever technique is utilized (a multifaceted approach is generally recommended as each technique contain its own set of advantages) adequate sample preparation is crucially important in obtaining accurate results.
Bio-Rad’s Proteominer technology is a fantastic tool for enriching low abundant proteins which helps identify the proverbial biomarker needle in the protein haystack. In this video, Kate Smith takes you on a tour of Proteominer Enrichment Technology and shows you how it will help you dig deeper into the Proteome.
:: Posted by American Biotechnologist on 05-06-2010
Biotechnologists engaged in protein biomarker studies are well aware of some of the challenges they face trying to identify biomarkers in albumin and IgG rich serum and plasma. Protein biomarkers generally tend to be low-abundance proteins which are very difficult to detect among highly complex samples. Furthermore, an ever-increasing amount of biomarker studies are focused on identifying biomarkers in other biological sources such as muscle tissue and cell lines. Traditional approaches to solving this problem include depletion methods for removing high abundant proteins so that the proverbial “needle in the haystack” biomarker is easier to locate. While this approach has its advantages, it suffers from being too specific and may not work well in sample types other than serum and plasma.
Bio-Rad Laboratories Inc. has developed the ProteoMiner protein enrichment technology which uses a library of hexapeptides to bind all proteins in a complex mixture allowing reduction of high-abundance proteins and enrichment of medium and low-abundance proteins.
This Tech Note discusses the use of ProteoMner protein enrichment kits for the enrichment of low- and medium- abundance proteins and the depletion of high-abundance proteins in tissue, cell line and bacterial samples, with detailed experimental parameters in a 2-D gel based proteomics workflow.
:: Posted by American Biotechnologist on 03-08-2010
Plasma and Serum are often used in biomarker discovery studies because they are easy to obtain from patients and are readily available. The biggest challenge with using these sources in biomarker studies is the HUGE overexpression of approximately 20 predominant proteins such as heat shock proteins and albumin (to name a few) which represent about 99% of the total protein mass. Since most analytical technologies are incapable of resolving expression levels over more than 5 orders of magnitude, proteins with low expression levels (which are most likely to be viable candidates for biomarker studies since differences in their expression levels between normal and diseased states are more easily resolved) are often masked and difficult to detect.
Unfortunately, many of the technologies available which aid in biomarker discovery rely on the depletion of high abundance proteins which often ends up depleting low abundant proteins as well thereby “throwing out the baby with the bathwater.”
Bio-Rad has recently launched a new and innovative method for resolving differences in low abundant proteins using a unique quantitative enrichment technology.