Analysis of mitochondrial function is central to the study of intracellular energy metabolism, mechanisms of cell death and pathophysiology of a variety of human diseases, including myopathies, neurodegenerative diseases and cancer. However, important properties of mitochondria differ in vivo and in vitro. Here, we describe a protocol for the analysis of functional mitochondria in situ, without the isolation of organelles, in selectively permeabilized cells or muscle fibers using digitonin or saponin. A specially designed substrate/inhibitor titration approach allows the step-by-step analysis of several mitochondrial complexes. This protocol allows the detailed characterization of functional mitochondria in their normal intracellular position and assembly, preserving essential interactions with other organelles. As only a small amount of tissue is required for analysis, the protocol can be used in diagnostic settings in clinical studies. The permeabilization procedure and specific titration analysis can be completed in 2 h.

We quantitatively analyzed particle tracking data on insulin granules expressing fluorescent fusion proteins in MIN6 cells to better understand the motions contributing to intracellular transport and, more generally, the means for characterizing systems far from equilibrium. Care was taken to ensure that the statistics reflected intrinsic features of the individual granules rather than details of the measurement and overall cell state. We find anomalous diffusion. Interpreting such data conventionally requires assuming that a process is either ergodic with particles working against fluctuating obstacles (fractional Brownian motion) or nonergodic with a broad distribution of dwell times for traps (continuous-time random walk). However, we find that statistical tests based on these two models give conflicting results. We resolve this issue by introducing a subordinated scheme in which particles in cages with random dwell times undergo correlated motions owing to interactions with a fluctuating environment. We relate this picture to the underlying microtubule structure by imaging in the presence of vinblastine. Our results provide a simple physical picture for how diverse pools of insulin granules and, in turn, biphasic secretion could arise. Eukaryotic cells package proteins into vesicles for trafficking and spatially localized secretion. These essential functions are highly regulated, and defects in them can lead to disease (1, 2). Although optical microscopy, combined with molecular and cellular biology, can provide important insight into intracellular dynamics, in the past, most measurements detected variations in intensities from many molecular events and thus averaged in some way. These include fluorescence correlation spectroscopy (FCS) (3), fluorescence recovery after photobleaching (FRAP) (4), and image correlation spectroscopy (5). Recent advances in experimental methods now enable tracking single particles in cells (6). Although these measurements still involve a degree of time averaging (7), the resulting individual time trajectories contain more information than the mean values extracted from the aforementioned approaches.Qualitatively, the time trajectories reveal complex behaviors: combinations of random, directed, transiently stalled and constrained motions (e.g., refs. 7, 8). These different types of motion reflect the interplay of various molecular components in crowded environments. Quantifying their relative importance can constrain mechanisms, but extracting this information from the particle tracking data requires new theoretical tools. Operationally, one strategy is to classify segments of trajectories according to their motions (e.g., active and passive) (9, 10), but this requires long trajectories. A less data-demanding approach is to identify different types of anomalous diffusion (11).What features can give rise to the observed anomalous behavior? Simple crowding is insufficient, as it results in standard Brownian motion but with a reduced diffusion coefficient (12). Instead, anomalous b...

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SummaryFOXO transcription factors induce apoptosis and regulate cellular production of reactive oxygen species (ROS). To identify the sequence of molecular events underlying FOXO3 (FKHRL1)-induced apoptosis, we studied the regulation and function of FOXO3 by expressing an ECFP-tagged FOXO3 or a 4OH-tamoxifen (4OHT)-inducible FOXO3-ERtm fusion protein in SH-EP and STA-NB15 neuronal cells. After knockdown of FOXO3 or expression of a dominant-negative FOXO3 mutant we observed that etoposide-and doxorubicin-induced elevation of cellular ROS depends on FOXO3 activation and induction of its transcriptional target BCL2L11 (Bim). Activation of FOXO3 on its own induced two sequential ROS waves as measured by reduced MitoTrackerRed in live cell microscopy. Induction of Bim by FOXO3 is essential for this phenomenon because Bim knockdown or ectopic expression of BCL2L1 (BclxL) prevented FOXO3-mediated overproduction of ROS and apoptosis. Tetracycline-controlled expression of Bim impaired mitochondrial respiration and caused ROS production, suggesting that FOXO3 induces uncoupling of mitochondrial respiration through Bim. FOXO3 also activated a ROS rescue pathway by inducing the peroxiredoxin SESN3 (Sestrin3), which is responsible for the biphasic ROS accumulation. Knockdown of SESN3 caused an increase of FOXO3-induced ROS and accelerated apoptosis. The combined data clearly demonstrate that FOXO3 activates overproduction of ROS as a consequence of Bim-dependent impairment of mitochondrial respiration in neuronal cells, which leads to apoptosis.

analysis ͉ dispersion ͉ flow ͉ microscale ͉ pulse