Phenotype Screens

This approach requires more upstream tools than the other approaches but the reward can be high-quality, information-rich leads acting at defined novel target sites. Dow AgroSciences partnered with Exelixis (South San Francisco, CA) and Exehxis Plant Sciences (Portland, OR) to implement such a multidisciplinary approach to find novel herbicide sites of action. 

The three components of a chemical genetic process to uncover novel sites of pesticide action, chemical libraries, phenotype screens and target site identification, can be organized and deployed in a variety of different ways and with varying degrees of complexity, depending on project objectives. 

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Phenotypic screens seek compounds with a specific effect on cell physiology, by adding compounds to living cells, and scoring for an effect. The measurable... 

Gray SG, Ekstrom TJ (2001) The human histone deacetylase family. Exp Cell Res 262 75—83 Greiner D, Bonaldi T, Eskeland R, Roemer E, Imhof A (2005) Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3-9. Nat Chem BioH 143-145 Grozinger CM, Chao ED, Blackwell HE, Moazed D, Schreiber SL (2001) Identification of a class of small molecule inhibitors of the sirtuin family of NAD-dependent deacetylases by phenotypic screening. J Biol Chem 276(42) 38837-38843... 

Aza-Blanc P, Cooper CL, Wagner K et al (2003) Identification of modulators ofTRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol Cell 12 627-637... 

Mercier C, Ciccolini J, Dupuis C et al. Prospective phenotypic screening for DPD deficiency in patients upon fluoropyrimidines administration Impact on the reduction of drug-induced toxicities. Asco Annual Meeting Proceedings. J Clin Oncol. 2007 25. 

Wei, Y., Marchi, V., Wang, R., and Rao, R., 1999, An N-terminal EF hand-hke motif modulates ion transport by Pmrl, the yeast Golgi Ca2+/Mn2+-ATPase. Biochemistry 38, 14534-14541 Wei, Y., Chen, J., Rosas, G., Tompkins, D.A., Holt, P.A., and Rao, R., 2000, Phenotypic screening of mutations in Pmrl, the yeast secretory pathway Ca2+/Mn2+-ATPase, reveals residues critical for ion selectivity and transport. J. Biol. Chem. 275, 23927-23932 Wilk, M., Rietschel, M., Korner, J., Moller, H.J., Nothen, M.M., Bauer, R., and Kreisel, H.W., 1994, Pemphigus chronicus benignus familiaris (Hailey-Hailey disease) and bipolar affective disease in three members of a family. Hautarzt 45, 313-317... 

Brown, S. D., Chambon, P. and de Ange-lis, M. H. (2005) EMPReSS standardized phenotype screens for functional annotation of the mouse genome. Nat Genet 37, 1155. 

The direction of evolution is dictated by the experimenter in the form of a screen (or selection) for the desired phenotype. Screening strategies are discussed below and in more detail by Gershenson and Arnold (2000). The single-step nature of the evolutionary walk, however, also places some limitations on the properties that can be evolved. Properties (or combinations of properties) that require multiple, simultaneous amino acid substitutions will not be acquired. 

Plants are not different from other natural product samples in that they too tend to interfere with various screening formats in nonspecific ways as nuisance compounds displaying unwanted color, inherent fluorescence, promiscuous or aggregate behaviors, detergent-like activities, or toxicity (Feng et al., 2005 Appleton, Buss, and Butler, 2007). Biochemical assays (cell-free defined systems) are notoriously sensitive to such interference by natural product extracts. Cell-based reporter assays and cell-based so-called phenotypic screens always require parental cell controls to determine extract toxicity. However, plants contain their own sets of components that are problematic to screening assays and compound identification. 

Seibert, M., Flynn, T., and Benson, D. 2001a. Method and apparatus for rapid biohydrogen phenotypic screening of microorganisms using a chemochromic sensor, U.S. Patent 6,277,589. 

S. L. Schreiber, Identification of a class of small molecule inhibitors of the sirtuin family of NAD-dependent deacetylases by phenotypic screening,... 

Differentiation is the developmental process by which early pluripotent cells acquire the features of late-stage, mature cells such as neurons, hepatocytes, or heart muscle cells. Currently, few examples of devised, highly selective, and efficient conditions for stem cell differentiation into specific homogeneous cell types have been reported because of a lack of understanding of stem cell signaling at the molecular level. Small-molecule phenotypic screens provide another means to generate desired cell types in a controlled manner. Several small molecules have been identified by this method that modulate specific differentiation pathways of embryonic or adult stem cells. 

Other cells, viruses, tissues phenotypic screens, RNAi, pathology 18-20, 22, 52, 54... 

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