Effects of mitochondria-selective fluorescent probes on mitochondrial movement in Arabidopsis mesophyll cells evaluated by using the quantification

Mitochondria-selective fluorescent probes such as MitoTracker are often used for mitochondria imaging in various plants. Although some of the probes are reported to induce mitochondria dysfunction in animal cells, the effect on plant cells remains to be determined. In the present study, we applied quantitative methods to analyze mitochondrial movement, speed frequency, and speed-angle changes, based on trajectory analysis of mitochondria in mesophyll protoplast cells of Arabidopsis thaliana expressing the mitochondria-localized fluorescent protein. Using the quantitative method, we assessed whether MitoTracker Red (FM and CMXRos) induce mitochondria dysfunction in A. thaliana. Although both the fluorescent probes well-stained mitochondria, the CMXRos probe, not the FM probe, gave a severe effect on mitochondrial movement at the low concentration (10 nM), indicating a MitoTracker-induced mitochondria dysfunction in A. thaliana. These results revealed that our quantitative method based on mitochondrial movement can be used to determine the appropriate concentrations of mitochondria-selective fluorescent probes in plants.     

Cytochrome C is a potent catalyst of dichlorofluorescin oxidation: implications for the role of reactive oxygen species in apoptosis

The generation of reactive oxygen species has been suggested to occur at increased rates during apoptosis, but the validity and significance of this remain contentious. In several key studies levels of reactive oxygen species have been monitored using the intracellular probe dichlorofluorescin (DCFH(2)), which undergoes oxidation to the fluorescent dichlorofluorescein (DCF). We report here that cytochrome c, which is released from mitochondria during cell death, is a potent catalyst of DCF formation. In a model system using xanthine oxidase to generate superoxide radicals, the rate of DCF formation was insensitive to changes in the rate of superoxide production over a 17-fold range, but extremely sensitive to nanomolar concentrations of cytochrome c. Thus we conclude that the DCF fluorescence observed in dying cells is a reflection of increased cytosolic cytochrome c. Moreover, we suggest that the suppression of DCF formation by the anti-apoptotic oncoprotein Bcl-2, which has been suggested to have antioxidant properties, can be explained on the basis of its prevention of mitochondrial cytochrome c release.     

Subunit composition of ATP-sensitive potassium channels in mitochondria of rat hearts

Mitochondrial ATP-sensitive potassium (mitoKATP) channels play a pivotal role in early and late ischemic preconditioning, but the subunit composition of mitoKATP channels remains unclear. In this study, we investigated the subunit composition of mitoKATP channels in rat hearts using confocal microscopy, immunofluorescence, and Western blot analysis. The green fluorescent probe glibenclamide-BODIPY was colocalized with the red fluorescent mitochondrial marker MitroTracker Red in isolated ventricular myocytes and in ventricular myocyte mitochondria, indicating the presence of sulfonylurea receptors (SURs) in the mitochondria. Anti-Kir6.1, anti-Kir6.2, and anti-SUR2 immunofluorescence was colocalized with that of MitoTracker Red in isolated mitochondria, suggesting that Kir6.1, Kir6.2, and SUR2 subunits are present in the mitochondria. Similarly, Kir6.1 (approximately 46 kDa), Kir6.2 (approximately 46 and approximately 40 kDa), and SUR2 (approximately 140 kDa) proteins were found to be expressed in mitochondria using Western blot analysis. By contrast, SUR1 was not present in mitochondria. These results suggest that mitoKATP channels in rat hearts might comprise a combination of Kir6.1, Kir6.2, and SUR2 subunits.     

Direct oxidation of 2',7'-dichlorodihydrofluorescein by pyocyanin and other redox-active compounds independent of reactive oxygen species production

Formation of dichlorofluorescein (DCF), the fluorescent oxidation product of 2',7'-dichlorodihydrofluorescein (DCFH2), in cells loaded with the latter compound is often used to detect ROS formation. We previously found that exposure of DCFH2-loaded A549 cells to the Pseudomonas aeruginosa secretory product pyocyanin results in DCF formation, consistent with ROS production. However, since pyocyanin directly accepts electrons from NAD(P)H, we hypothesized that pyocyanin might directly oxidize DCFH2 to DCF without an ROS intermediate. Incubation of DCFH2 with pyocyanin rapidly resulted in DCF formation, the rate of which was proportional to the [pyocyanin] and was not inhibited by SOD or catalase. Phenazine methosulfate, a pyocyanin analog, was more effective than pyocyanin in generating DCF. Mitoxantrone and ametantrone also produced DCF. However, menadione, paraquat, plumbagin, streptonigrin, doxorubicin, daunorubicin, and 5-iminodaunorubicin did not. Pyocyanin, phenazine methosulfate, mitoxantrone, and ametantrone also oxidized dihydrofluorescein and 5- (and 6-) -carboxy-2',7'-dichlorodihydrofluorescein, whereas dihydrorhodamine was oxidized only by pyocyanin or phenazine methosulfate. Under aerobic conditions, the interaction of DCFH2 with pyocyanin or phenazine methosulfate (but not mitoxantrone or ametantrone) produced superoxide, as detected by spin trapping. Direct oxidation of the fluorescent probes needs to be controlled for when employing these compounds to assess ROS formation by biological systems exposed to redox active compounds.     

Evidence for free radical formation during the oxidation of 2'-7'-dichlorofluorescin to the fluorescent dye 2'-7'-dichlorofluorescein by horseradish peroxidase: possible implications for oxidative stress measurements.

The oxidation of 2'-7'-dichlorofluorescin (DCFH) to the fluorescent 2'-7'-dichlorofluorescein (DCF) by horseradish peroxidase (HRP) was investigated by fluorescence, absorption, and electron spin resonance spectroscopy (ESR). As has been previously reported, HRP/H2O2 oxidized DCFH to the highly fluorescent DCF. However, DCF fluorescence was still observed when H2O2 was omitted, although its intensity was reduced by 50%. Surprisingly, the fluorescence increase, in the absence of exogenous H2O2, was still strongly inhibited by catalase, demonstrating that H2O2 was present and necessary for DCF formation. H2O2 was apparently formed during either chemical or enzymatic deacetylation of 2'-7'-dichlorofluorescin diacetate (DCFH-DA), probably by auto-oxidation. Spectrophotometric measurements clearly showed that DCFH could be oxidized either by HRP-compound I or HRP-compound II with the obligate generation of the DCF semiquinone free radical (DCF*-). Oxidation of DCF*- to DCF by oxygen would yield superoxide (O2*-). ESR spectroscopy in conjunction with the spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) revealed the presence of both superoxide and hydroxyl radicals in the DCFH/H2O2/HRP system. Both radicals were also detected in the absence of added H2O2, although the intensities of the resultant adducts were decreased. This work demonstrates that DCF fluorescence cannot be used reliably to measure O2*- in cells because O2*- itself is formed during the conversion of DCFH to DCF by peroxidases. The disproportionation of superoxide forms H2O2 which, in the presence of peroxidase activity, will oxidize more DCFH to DCF with self-amplification of the fluorescence. Because the deacetylation of DCFH-DA, even by esterases, can produce H2O2, the use of this probe to measure H2O2 production in cells is problematic.     

A method for the direct identification of differentiating muscle cells by a fluorescent mitochondrial dye

Identification of differentiating muscle cells generally requires fixation, antibodies directed against muscle specific proteins, and lengthy staining processes or, alternatively, transfection of muscle specific reporter genes driving GFP expression. In this study, we examined the possibility of using the robust mitochondrial network seen in maturing muscle cells as a marker of cellular differentiation. The mitochondrial fluorescent tracking dye, MitoTracker, which is a cell-permeable, low toxicity, fluorescent dye, allowed us to distinguish and track living differentiating muscle cells visually by epi-fluorescence microscopy. MitoTracker staining provides a robust and simple detection strategy for living differentiating cells in culture without the need for fixation or biochemical processing.     

Generation of a novel fluorescent product, monochlorofluorescein from dichlorofluorescin by photo-irradiationdagger

Dichlorofluorescin (DCFH), a widely used fluorescent probe for reactive oxygen species (ROS) was decomposed completely and generated two distinct fluorescent products by photo-irradiation at 254 nm for 30 min. In the previous study, we had shown that one was dichlorofluorescein (DCF), a well known oxidized product of DCFH. In this study we investigated the other product and identified it as monochlorofluorescein (MCF) by ¹H-NMR and fast atom bombardment/mass spectrum (FAB/MS) analyses. MCF was generated by photo-irradiation, but not by ROS. On the other hand, DCF was produced by both photo-irradiation and ROS. MCF showed similar fluorescent emission spectrum to DCF, however, its fluorescence intensity was more than that of DCF. The kinetic study suggested that MCF was not generated from DCF but from monochlorofluorescin, which might be generated from DCFH by photo-irradiation.     

Generation of a novel fluorescent product,monochlorofluorescein from dichlorofluorescin by photo-irradiation†

Dichlorofluorescin (DCFH), a widely used fluorescent probe for reactive oxygen species (ROS) was decomposed completely and generated two distinct fluorescent products by photo-irradiation at 254 nm for 30 min. In the previous study, we had shown that one was dichlorofluorescein (DCF), a well known oxidized product of DCFH. In this study we investigated the other product and identified it as monochlorofluorescein (MCF) by ¹H-NMR and fast atom bombardment/mass spectrum (FAB/MS) analyses. MCF was generated by photo-irradiation, but not by ROS. On the other hand, DCF was produced by both photo-irradiation and ROS. MCF showed similar fluorescent emission spectrum to DCF, however, its fluorescence intensity was more than that of DCF. The kinetic study suggested that MCF was not generated from DCF but from monochlorofluorescin, which might be generated from DCFH by photo-irradiation.     

Properties of the radical intermediate obtained on oxidation of 2',7'-dichlorodihydrofluorescein, a probe for oxidative stress

Reduced "leuco" dyes such as dichlorodihydrofluorescein (DCFH(2)) are widely used as profluorescent probes for oxidative stress, although they require a catalyst to be oxidized by hydrogen peroxide and react indiscriminately with oxidizing radicals and the fluorescent product (DCF) is a potential photosensitizer of superoxide generation. In this study, key properties of the radical intermediate in oxidation ("semiquinone," DCFH(.-)/DCF(.)(-)) were measured, to help understand the reactions that can occur in biological systems. The intermediate was generated by oxidizing DCFH(2) or reducing DCF by radiolytically generated radicals and monitoring the reactions using kinetic spectrophotometry. The semiquinone showed pH-sensitive absorption spectral changes, decay kinetics (both in the absence and in the presence of oxygen), and reduction potential, all corresponding to prototropic dissociations with pK(a)'s of approximately 7.1 and 9.0. DCFH(2) has pK(a)'s in a similar region (8-9) and hence pH variations are potentially important in the use of this probe. The rate constant for reaction of the semiquinone with oxygen at pH 7.4 is 5.3 x 10(8) M(-1) s(-1): this reaction, rather than disproportionation of DCFH(.-)/DCF(.)(-), generates DCF in biological systems, concomitantly forming superoxide and hence H(2)O(2) to cycle the catalyst. The midpoint reduction potential of the couple DCF,H(+)/DCFH() is approximately -0.75 V vs. NHE at pH 7.4; DCF is unlikely to be reduced rapidly by common flavoprotein reductases.     

Intracellular generation of reactive oxygen species by contracting skeletal muscle cells

The aim of this work was to examine the intracellular generation of reactive oxygen species in skeletal muscle cells at rest and during and following a period of contractile activity. Intracellular generation of reactive oxygen species was examined directly in skeletal muscle myotubes using 2',7'-dichlorodihydrofluorescein (DCFH) as an intracellular probe. Preliminary experiments confirmed that DCFH located to the myotubes but was readily photoxidizable during repeated intracellular fluorescence measurements and strategies to minimize this were developed. The rate of oxidation of DCFH did not change significantly over 30 min in resting myotubes, but was increased by approximately 4-fold during 10 min of repetitive, electrically stimulated contractile activity. This increased rate was maintained over 10 min following the end of the contraction protocol. DCF fluorescence was distributed evenly throughout the myotube with no evidence of accumulation at any specific intracellular sites or localization to mitochondria. The rise in DCF fluorescence was effectively abolished by treatment of the myotubes with the intracellular superoxide scavenger, Tiron. Thus these data appear to represent the first direct demonstration of a rise in intracellular oxidant activity during contractile activity in skeletal muscle myotubes and indicate that superoxide, generated from intracellular sites, is the ultimate source of oxidant(s) responsible for the DCFH oxidation.     

Genetic modification of the manganese superoxide dismutase/glutathione peroxidase 1 pathway influences intracellular ROS generation in quiescent, but not contracting, skeletal muscle cells

Increased amounts of reactive oxygen species (ROS) are generated by skeletal muscle during contractile activity, but their intracellular source is unclear. The oxidation of 2',7'-dichlorodihydrofluorescein (DCFH) was examined as an intracellular probe for reactive oxygen species in skeletal muscle myotubes derived from muscles of wild-type mice and mice that were heterozygous knockout for manganese superoxide dismutase (Sod2(+/-)), homozygous knockout for glutathione peroxidase 1 (GPx1(-/-)), or MnSOD transgenic overexpressors (Sod2-Tg). Myoblasts were stimulated to fuse and loaded with DCFH 5-7 days later. Intracellular DCF epifluorescence was measured and myotubes were electrically stimulated to contract for 15 min. Quiescent myotubes with decreased MnSOD or GPx1 showed a significant increase in the rate of DCFH oxidation whereas those with increased MnSOD did not differ from wild type. Following contractions, myotubes from all groups showed an equivalent increase in DCF fluorescence. Thus the oxidation of DCFH in quiescent skeletal muscle myotubes is influenced by the content of enzymes that regulate mitochondrial superoxide and hydrogen peroxide content. In contrast, the increase in DCFH oxidation following contractions was unaffected by reduced or enhanced MnSOD or absent GPx1, indicating that reactive oxygen species produced by contractions were predominantly generated by nonmitochondrial sources.     

Photosensitized oxidation of 2',7'-dichlorofluorescin: singlet oxygen does not contribute to the formation of fluorescent oxidation product 2',7'-dichlorofluorescein

2',7'-Dichlorofluorescin (DCFH) is often employed to assess oxidative stress in cells by monitoring the appearance of 2',7'-dichlorofluorescein (DCF), its highly fluorescent oxidation product. We have investigated the photosensitized oxidation of DCFH in solution and elucidated the role played by singlet molecular oxygen (1O(2)) in this reaction. We used rose bengal (RB), protoporphyrin, and DCF as photosensitizers. Irradiation (550 nm) of RB (20 microM) in 50 mM phosphate (pH 7.4) in the presence of DCFH (50 microM) resulted in the rapid formation of DCF, measured as an increase in its characteristic absorbance and fluorescence. The oxidation rate was faster in deoxygenated solution, did not increase in D(2)O, and even increased in the presence of sodium azide. The presence of antioxidants that react with 1O(2), thus removing oxygen, accelerated DCF formation. Such results eliminate any potential direct involvement of 1O(2) in DCF formation, even though DCFH is an efficient (physical) quencher of 1O(2) (k(q) = 1.4 x 10(8) M(-1)s(-1) in methanol). DCF is also a moderate photosensitizer of 1O(2) with a quantum yield of circa phi = 0.06 in D(2)O and phi = 0.08 in propylene carbonate, which unequivocally indicates that DCF can exist in a triplet state upon excitation with UV and visible light. This triplet can initiate photo-oxidization of DCFH via redox-and-radical mechanism(s) similar to those involving RB (vide supra). Our results show that, upon illumination, DCF can function as a moderate photosensitizer initiating DCFH oxidation, which may prime and accelerate the formation of DCF. We have also shown that, while 1O(2) does not contribute directly to DCF production, it can do so indirectly via reaction with cellular substrates yielding peroxy products and peroxyl radicals, which are able to oxidize DCFH in subsequent dark reactions. These findings suggest that DCFH should not be regarded as a probe sensitive to singlet molecular oxygen, and that care must be taken when using DCFH to measure oxidative stress in cells as a result of both visible and UV light exposure.     

Method to overcome photoreaction,a serious drawback to the use of dichlorofluorescin in evaluation of reactive oxygen species

Non-fluorescent dichlorofluorescin (DCFH) was converted to fluorescent products by photo-irradiation during observations with spectrofluorometer and fluorescence microscopy. Photo-irradiation of DCFH at 250, 300, 330, 400, 500, or 600 nm generated fluorescent dichlorofluorescein (DCF), an oxidation product of DCFH, and an unrecognized fluorescent product. The ratio of the unknown product to DCF varied from 0.15 to 8.21 depending on wavelength. Although reactive oxygen species scavengers, such as catalase, superoxide dismutase, and sodium azide, did not suppress the increase in non-specified fluorescence, reagents such as ascorbic acid, mercaptopropionyl glycine, and methoxycinnamic acid, in a cell-free system, almost completely suppressed it with little effect on the fluorescence of DCF. Meanwhile, ascorbic acid also suppressed non-specified fluorescence in cells, but not completely. At low concentrations of DCFH, the speed of increasing fluorescence was considerably retarded, to such a degree that the fluorescence increase in cells during fluorescence microscopic observation was negligible. The addition, at the time of evaluation, of the above reagents to cell-free systems and, in cell systems, reducing the concentration of DCFH, effectively suppressed the photoreaction of DCFH.     

Developmental fate of mitochondria microinjected into murine zygotes

A greater understanding of the fate of mitochondria injected into early preimplantation embryos would provide insights into mitochondrial biology and dynamics associated with development and disease. The ability to introduce foreign mitochondria into mouse embryos provides a means of tracking or following mitochondrial populations in vivo. Previously, injection of foreign mitochondria into the cytoplasm of the zygote was used to produce heteroplasmic mice. However, populations of introduced mitochondria decreased rapidly during development beyond the blastocyst stage. Therefore, the fate of exogenous mitochondria introduced into mouse ova was examined to determine viability and localization in comparison to endogenous mitochondria. Microinjection of murine mitochondria labeled with mitochondria-specific MitoTracker fluorophores allowed evaluation of subsequent viability and functionality of exogenous mitochondria populations in vivo. Characterization of mitochondrial survival and migration following microinjection illustrated toxic effects of MitoTracker Red upon exposure to laser confocal examination. In contrast, mitochondrial-specific fluorophores effectively detected foreign mitochondrial migration post-microinjection. The subsequent viability of the introduced mitochondria was observed through the blastocyst stage. Through the use of mitochondria-specific fluorophores, newly introduced mitochondria were further characterized and tracked post-transfer.     

A photochemical study of cells loaded with 2',7'-dichlorofluorescin: implications for the detection of reactive oxygen species generated during UVA irradiation

There have been several attempts to implicate reactive oxygen species in UVA-induced damage by loading cells with 2',7'-dichlorofluorescin (DCFH) and following the appearance of 2',7'-dichlorofluorescein (DCF), its highly fluorescent oxidation product. However, both DCF and DCFH have significant absorption in the 300-400 nm range so it is possible that photochemical reactions will occur in cells containing these dyes when they are irradiated with UVA. HaCaT keratinocytes loaded with DCFH were irradiated with 0, 1, 2, or 4 J/cm(2) UVA and DCF fluorescence was measured. A dose-dependent increase in DCF fluorescence was observed, with the cells exposed to 4 J/cm(2) UVA exhibiting an almost 10-fold increase over dark controls. However, there was no difference in cell viability, as measured by the MTS assay or LDH release, between the dark and the 4 J/cm(2) UVA-exposed groups. Furthermore, a large increase in DCF fluorescence was observed when a cell-free system containing DCF, DCFH, and horseradish peroxidase was UVA irradiated. As a control, keratinocytes loaded with DCFH were incubated in the dark with either exogenously added H(2)O(2) or 5-hydroxy-1,4-naphthoquinone (juglone), which redox cycles to generate superoxide (and H(2)O(2)). In both cases, the cells showed a concentration-dependent increase in DCF fluorescence and a concomitant decrease in viability. Our findings suggest that DCFH can not be used to detect the UVA-induced generation of reactive oxygen species in cells when the dye is present during exposure.     

Adaptation of the dichlorofluorescein assay for detection of radiation-induced oxidative stress in cultured cells

The oxidation of 2'7'-dichlorofluorescin (DCFH) to 2'7'-dichlorofluorescein (DCF), a fluorescent DCFH oxidation product, is a highly sensitive indicator that is used to measure oxidative stress in cells. In the present study, a DCF assay has been adapted to quantify oxidative stress in human breast epithelial cell cultures after exposure to gamma rays. The results demonstrate that the sensitivity and specificity of the DCF assay is strongly influenced by the timing of DCFH diacetate (DCFH-DA) substrate loading in relation to radiation exposure and by the matrix in which the cells were loaded with DCFH-DA substrate. Under the conditions optimized in this study, the DCF assay is capable of detecting increased DCFH oxidation in cell cultures irradiated with gamma rays at a dose as low as 1.5 cGy. The increase in fluorescence was directly proportional to the radiation dose, which ranged from 0 to 2 Gy, and a minimal level of fluorescence was observed in sham-irradiated cells. These results indicate that the DCF assay optimized in this study is highly sensitive, linear and specific for measuring oxidative stress in irradiated cells.     

Role of mitochondria in calcium regulation of spontaneously contracting cardiac muscle cells.

Mitochondrial involvement in the regulation of cytosolic calcium concentration ([Ca2+]i) in cardiac myocytes has been largely discounted by many authors. However, recent evidence, including the results of this study, has forced a reappraisal of this role. [Ca2+]i and Ca2+ in the mitochondria ([Ca2+]m) were measured in this study with specific fluorescent probes, fluo-3 and di-hydro-rhod-2, respectively; mitochondrial membrane potential (DeltaPsim) was monitored with JC-1. Addition of uncouplers or inhibitors of the mitochondrial respiratory chain was found to cause a twofold decrease in the rate of removal of Ca2+ from the cytosol after a spontaneously generated Ca2+ wave. These agents also caused a progressive elevation of [Ca2+]i, an increase in the number of hotspots of Ca2+ release (Ca2+ sparks), and depression of mitochondrial potential. The Ca2+-indicative fluorophore dihydro-rhod-2 has a net positive charge that contributes to selective accumulation by mitochondria, as supported by its co-localization with other mitochondrial-specific probes (MitoTracker Green). Treatment of dihydro-rhod-2-loaded cells with NaCN resulted in rapid formation of "black holes" in the otherwise uniformly banded pattern. These are likely to represent individual or small groups of mitochondria that have depressed mitochondrial potential, or have lost accumulated rhod-2 and/or Ca2+; all of these eventualities are possible upon onset of the mitochondrial permeability transition. Release of Ca2+ from the sarcoplasmic reticulum and the resultant spontaneous contractility of cardiac muscle are proposed to be triggered by the induction of the mitochondrial permeability transition and the subsequent loss of [Ca2+]m.     

Vimentin intermediate filaments increase mitochondrial membrane potential

Mitochondria are the main source of energy in eukaryotic cells. They also play an important role in the number of other processes, such as regulation of calcium concentration and sequestration of apoptotic factors. Almost all functions of mitochondria depend on their ability to generate and maintain membrane potential by means of aerobic respiration. The level of mitochondrial potential is under the control of different inner and outer factors. However, mechanisms of this regulation are still poorly understood. In the present study we answer the question of how membrane potential of mitochondria depends on their motility. Using the potential-dependent dye MitoTracker Red, fluorescent microscopy of live cells, and the analysis of mitochondrial motility, two sub-populations of mitochondria were determined: (1) moving mitochondria transported along microtubules and (2) stationary mitochondria. We have shown that stationary mitochondria have higher membrane potential than moving mitochondria. It was also found that the level of potential of mitochondria is regulated by their interaction with vimentin intermediate filaments.     

Timing of Ca2+ response in pancreatic beta-cells is related to mitochondrial mass

The timing and magnitude of calcium response are cell-specific in individual beta-cells. This may indicate that the cells have different roles in the intact islet. It is unknown what mechanisms determine these characteristics. We previously found that the mechanisms setting cell-specific response timing are disturbed in beta-cells from hyperglycemic mice and one of the causes is likely to be an altered mitochondrial metabolism. Mitochondria play a key role in the control of nutrient-induced insulin secretion. Here, we used confocal microscopy with the fluorescent probe MitoTracker Red CMXRos and Fluo-3 to study how the amount of active mitochondria is related to the lag-time and the magnitude of calcium response to 20mM glucose in isolated beta-cells and in cells within intact lean and ob/ob mouse islets. Results show that the mitochondrial mass is inversely correlated with the lag-times for calcium response both in lean and ob/ob mouse beta-cells (r=-0.73 and r=-0.43, respectively, P<0.05). Thus, the state of mitochondria may determine the timing of calcium response.     

Analysis of mitochondrial free radical generation in animal models of neuronal disease

Mitochondria, the power plant of all eukaryotic cells, produce cellular energy in the form of ATP via electron transport and oxidative phosphorylation. However, the mitochondria leak electrons that can act as major sources of oxidative stress, and their dysfunction, have been proposed as causative events underlying neurodegeneration in stroke and neurodegenerative diseases. We examined whether MitoTracker Red CM-H(2)XRos, a rosamine derivative used to detect mitochondrial free radicals in vitro, would be applied to analyze the mitochondrial free radicals in various models of neurological diseases in vivo. The injections of MitoTracker Red CM-H(2)XRos revealed generation of mitochondrial free radicals primarily in vulnerable neurons following focal cerebral ischemia as well as administration of Fe(2+) or 3-nitropropionic acid. MitoTracker Red CM-H(2)XRos was retained after fixation, compatible with immunocytochemistry or nuclear staining, and can be applied to study roles of mitochondrial free radicals in the process of neurodegeneration in vivo.