Proteomic investigation tools

Another application of microfluidic enzymatic reactors is in the enormous and diverse challenges of proteomic investigations. Enzymatic microreactors present proteomics with a valuable analytical tool for protein analysis. Most of applications of IMERs are currently directed at protein analysis by protein digestion and peptide mapping. 

Other stressing treatments employed to improve the microbial stability of some meat products merit consideration. This is the case for high hydrostatic pressure (HHP) treatment in use in several countries for the preservation of various sausage or dry-cured ham. By a proteomic investigation, it was notably shown that Lact. sakei can react differently from other bacterial species after an HHP treatment (Jofre et al. 2007). In addition, flow cytometry was successfully used to test the ability of Lact. sakei cells to survive different stresses like acidic or high temperature stresses (Bonomo et al. 2013) illustrating one of the numerous tools available for starter culture selection. 

Consequently, proteomics is a valuable tool for identification and validation of drug targets in early phases, the investigation of the mechanism of pharmacological drug activity and toxicity, and hence, individualized drug therapy. Use of biomarkers may lead to development of nonanimal models. 

Proteomics is the omics tool that separates and identifies individual proteins from an initial protein mixture. Proteomics is termed global if it identifies proteins from total preparations, or targeted if, for example, a protein superfamily or protein subset is investigated (Blackstock and Weir, 1999 Pandey and Mann, 2000). 

In general, the proteome can be analysed by a broad spectrum of methods. All of them follow similar principles. After treatment of laboratory animals/cells, parallel protein extraction and protein separation is performed. Changes in the proteome are then investigated by differential expression analysis with bioinfor-matics/biostatistics tools before the identification of proteins of interest is done (Anderson and Anderson 1998 Ryan and Patterson 2001 Schrattenholz 2004). The most powerful protein separation technologies... 

Synthetic derivatives and analogs of prenyl diphosphates have historically played a key role in defining key featnres of the mechanism of enzymes that ntilize these key intermediates in the isoprenoid pathway. This has also been the case with the investigation of the protein prenyl-transferases. A brief introduction to the protein prenyltransferase enzymes is given along with outlines on the previous use of prenyl diphosphate tools and key aspects of their synthesis. The development of prenyl diphosphate-based FTase inhibitors is described. The use of prenyl diphosphate derivatives as mechanistic and structural probes is next discussed. In particular, the use of fluorinated, isotopically labeled, and photoaffinity derivatives is presented. An overview of the extensive work on the determination of FTase isoprenoid substrate specificity is then given, and the chapter concludes with a section on the development of prenyl diphosphate tools for proteomic studies. 

Different tools and approaches can be used at different levels for dynamical and integrative investigations, from nanotechnology to high-throughput (HTP) analyses such as proteomic studies, from biophysics studies to physiological measurements. 

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