qE has been studied by researchers from a broad range of fields. This diversity of approaches has led to a wide variety of theoretical and experimental tools that have been valuable in studying qE. Fig. 1 To understand the mechanism of qE requires an understanding of the dynamics of the trigger, the membrane change, and the photophysical mechanism. The techniques CB-839 that are used to study the different aspects of the mechanism are listed below the respective process In this paper, we review the methods and techniques that have been used in qE research. These methods, though often developed and primarily used to study plants, can

be used to study qE in any photosynthetic organism, and many can be used to study any NPQ mechanism. We focus on the applications of these methods PF-562271 in vitro to samples that are capable of performing qE in response to light, such as thylakoids, chloroplasts, and whole leaves, and do not review many experiments done on isolated and aggregated proteins. For a review of experiments on isolated

complexes, see Ruban et al. (2012). We also limit the scope of this review to the application of these methods to qE in plants, although other organisms, such as cyanobacteria, also exhibit NPQ processes that have similarities with qE. Some methods, such as the use of fluorescence yield measurements, chemical inhibitors, and qE mutants, have been used to extract information about all parts of the qE process: the trigger, membrane change, and photophysical mechanism of quenching. We discuss the use of these methods, as well as their strengths and limitations, in the “General tools for the study of qE” section. In the “Triggering of qE” section, we discuss the current understanding of the trigger by reviewing methods and models for correlating qE with the lumen pH. We discuss the techniques used to monitor membrane changes and to identify the quenching site(s) and photophysical mechanism(s) of NPQ in the “Formation TCL of qE in the grana membrane” section. Finally, in the “New tools for characterizing

qE in vivo” section, we discuss the development of measurements and techniques to study the dynamics of qE in vivo. General tools for the study of qE Discovery and early studies of qE qE was first observed in fluorescence studies of isolated chloroplasts subjected to chemical treatments. The amount of chlorophyll fluorescence was found to depend on the pH of the lumen. Figure 3 illustrates the series of experiments performed by Murata and Sugahara (1969) and Wraight and Crofts (1970). Chloroplasts were first treated with NU7026 clinical trial dichlorophenyl-dimethylurea (DCMU), which inhibits electron transfer at PSII and prevents photochemical quenching. Because excited chlorophyll could not be quenched photochemically (by charge separation at the RC), a high level of fluorescence was observed.