Protein extraction studies standardization

Proteomics studies in plants are not fundamentally different from animal proteomics A protein extraction is needed first then the analytical methods are the standard ones, such as polyacrylamide gel electrophoresis, two-dimensional... 

In terms of improving the quality of chitosan, partial autolysis plays a crucial role because it facilitates exposure of CaC03 directly to the chemicals used during the demineralization process. For the industrial practice of chitin extraction, this means that a shorter time and lower concentration of HCl may be adequate to demineralize and thus avoid damage due to the hydrolytic action of HCl on the polymeric backbone structure of chitin. However, it was found that the protein content after treatment of autolyzed biomaterial with 2% NaOH was similar to the protein content after standard 4% NaOH treatment. Obviously, this study could help... 

In principle, this increase in reproducibihty would allow for the detection of small features and/or differences between the mass spectra of closely related microorganisms. Assnming the direct transfer method has a variance similar to that of the dried-droplet method used in this study (Fig. 2.6), it can be inferred that a significant rednction in the variance can be realized by simply premixing the intact bacteria with the matrix solution prior to its deposition onto the MALDl plate, rather than performing sequential depositions of bacteria followed by matrix. This improvement in the reproducibility would also be expected to be observed in the protein extraction protocols, adding only a single dilution step in the overall procedure (1 1 sample/matrix). However, to date, all standard protocols (Freiwald and Sauer 2009) used in profile-based MALDI-MS analyses implement a dried-droplet approach to deposit the sample onto the MALDl plate. 

Recent studies have shown that HIAR is also effective for physically fixed materials, un-embedded and plastic-embedded specimens, and immunoelec-tron microscopy. Heating has also been shown to be useful for the extraction of proteins and nucleic acids from FFPE materials. The elucidation of the mechanisms described above should support the usefulness of such applications and lead to the establishment of standardized protocols for immunohis-tochemical staining. 

We have demonstrated that this insect cell-free protein synthesis system is one of the most effective protein synthesis systems among those based on animal extracts (2). Furthermore, it has the potential to perform eukaryote-specific protein modifications such as protein W-myristoylation and prenylation (3, 4). Thus, we expect that the insect cell-free protein synthesis system will be a useful method for target protein production in the reverse chemical genetics era, as well as for postgenomic studies. In this chapter, we describe standard protocols to synthesize proteins of interest using the insect cell-free protein synthesis system. 

Fig. 13.8. Correlation between expression levels and the measured aggregation rates for a set of human proteins. The aggregation rates represent all the data obtained from a comprehensive search of the amyloid aggregation literature, for studies carried out at pH values between 4.0 and 8.0. The expression levels are estimated from the cellular mRNA concentration and are taken from published databases. The standard deviations of the aggregation rates are reported only in four cases, as these values are generally not available or difficult to extract from the literature. Data for two proteins not involved in any known medical conditions are included in the plot while the other points correspond to proteins that are associated with amyloid diseases. From [4]...

---