Optical methods for probing mitochondrial function in brain slices.

Brain slice preparations have become useful tools for studying multiple facets of normal brain function and for investigations of brain pathophysiology. Recently, a variety of neurological disorders have been linked to dysfunction of brain mitochondria. In this report we discuss optical methods for probing mitochondrial function in brain slices. Absorption spectrophotometric and spectrofluorometric techniques are described for measuring changes in the redox activity of mitochondrial cytochromes and the primary respiratory chain substrate nicotinamide adenine dinucleotide (NADH), respectively. A spectrofluorometric method is described also for measuring changes in mitochondrial membrane potential using the potential-sensitive fluorescent indicator JC-1. These methods used together have proven to be useful for studying dysfunction of mitochondria following in vitro ischemia in hippocampal slices, and might also be valuable for investigations of mitochondrial involvement in other neurological disorders.     

Building the power house: recent advances in mitochondrial studies through proteomics and systems biology

The emerging field of systems biology seeks to develop novel approaches to integrate heterogeneous data sources for effective analysis of complex living systems. Systemic studies of mitochondria have generated a large number of proteomic data sets in numerous species, including yeast, plant, mouse, rat, and human. Beyond component identification, mitochondrial proteomics is recognized as a powerful tool for diagnosing and characterizing complex diseases associated with these organelles. Various proteomic techniques for isolation and purification of proteins have been developed; each tailored to preserve protein properties relevant to study of a particular disease type. Examples of such techniques include immunocapture, which minimizes loss of posttranslational modification, 4-iodobutyltriphenylphosphonium labeling, which quantifies protein redox states, and surface-enhanced laser desorption ionization-time-of-flight mass spectrometry, which allows sequence-specific binding. With the rapidly increasing number of discovered molecular components, computational models are also being developed to facilitate the organization and analysis of such data. Computational models of mitochondria have been accomplished with top-down and bottom-up approaches and have been steadily improved in size and scope. Results from top-down methods tend to be more qualitative but are unbiased by prior knowledge about the system. Bottom-up methods often require the incorporation of a large amount of existing data but provide more rigorous and quantitative information, which can be used as hypotheses for subsequent experimental studies. Successes and limitations of the studies reviewed here provide opportunities and challenges that must be addressed to facilitate the application of systems biology to larger systems. constraint-based modeling; kinetics-based modeling; data integration; standards; bioinformatics     

A randomized,double-blind,placebo-controlled phase 2 study evaluating the efficacy and safety of romiplostim treatment of patients with low or intermediate-1 risk myelodysplastic syndrome receiving lenalidomide

Mitochondria are the most complex and the most important organelles of eukaryotic cells, which are involved in many cellular processes, including energy metabolism, apoptosis, and aging. And mitochondria have been identified as the "hot spot" by researchers for exploring relevant associated dysfunctions in many fields. The emergence of comparative proteomics enables us to have a close look at the mitochondrial proteome in a comprehensive and effective manner under various conditions and cellular circumstances. Two-dimensional electrophoresis combined with mass spectrometry is still the most popular techniques to study comparative mitochondrial proteomics. Furthermore, many new techniques, such as ICAT, MudPIT, and SILAC, equip researchers with more flexibilities inselecting proper methods. This article also reviews the recent development of comparative mitochondrial proteomics on diverse human diseases. And the results of mitochondrial proteomics enhance a better understanding of the pathogenesis associated with mitochondria and provide promising therapeutic targets.     

Functional characterization of the creatine phosphokinase reactions in heart mitochondria and myofibrils]

The kinetic properties of MM-isozyme of creatine phosphokinase (CPK) bound to heart myofibrils have been determined experimentally. It has been shown that CPK isozymes bound to the heart myofibrils and mitochondria are electrophoretically different, but have very similar kinetic properties. For both isozymes the ATP formation reaction is preferable. However, in heart mitochondria the kinetic properties of CPK are compensated for by a tight functional coupling with ATP-ADP translocase. Due to this coupling the ATP formed in the course of oxidative phosphorylation can be used completely for creatine phosphate production in mitochondria. On the other hand, the kinetic properties of myofibrillar CPK isozyme are such that they provide for the effective utilization of creatine phosphate produced in mitochondria for rephosphorylation of AKP formed in the myofibrils during contraction. It is concluded that in the heart cells energy can be transferred from the mitochondria to the myofibrils by creatine phosphate molecules.     

Method: automatic segmentation of mitochondria utilizing patch classification,contour pair classification,and automatically seeded level sets

Background  

While progress has been made to develop automatic segmentation techniques for mitochondria, there remains a need for more accurate and robust techniques to delineate mitochondria in serial blockface scanning electron microscopic data. Previously developed texture based methods are limited for solving this problem because texture alone is often not sufficient to identify mitochondria. This paper presents a new three-step method, the Cytoseg process, for automated segmentation of mitochondria contained in 3D electron microscopic volumes generated through serial block face scanning electron microscopic imaging. The method consists of three steps. The first is a random forest patch classification step operating directly on 2D image patches. The second step consists of contour-pair classification. At the final step, we introduce a method to automatically seed a level set operation with output from previous steps.     

Sequence and codon recognition of bean mitochondria and chloroplast tRNAsTrp: evidence for a high degree of homology.

Bean mitochondria and chloroplast tRNAsTrp, purified by RPC-5 chromatography and two-dimensional gel electrophoresis, have been sequenced using post-labeling techniques. The high degree of sequence homology between bean mitochondria and chloroplast tRNAsTrp shows that these two tRNAs are coded for by closely related genes which have probably evolved from a common ancestor gene. The anticodon of bean mitochondria tRNATrp is CmCA, which can recognize UGG (the codon for tryptophan in the universal code) and is complementary neither to UGA (which codes for tryptophan in mammalian and yeast mitochondria) nor to CGG (which could be a tryptophan codeword in plant mitochondria).     

Permeabilized cell and skinned fiber techniques in studies of mitochondrial function in vitro

In this chapter we describe in details the permeabilized cell and skinned fiber techniques and their applications for studies of mitochondrial function in vivo. The experience of more than 10 years of research in four countries is summarized. The use of saponin in very low concentration (50-100 g/ml) for permeabilisation of the sarcolemma leaves all intracellular structures, including mitochondria, completely intact. The intactness of mitochondrial function in these skinned muscle fibers is demonstrated in this work by multiple methods, such as NADH and flavoprotein fluorescence studies, fluorescence imaging, confocal immunofluorescence microscopy and respiratory analysis. Permeabilized cell and skinned fiber techniques have several very significant advantages for studies of mitochondrial function, in comparison with the traditional methods of use of isolated mitochondria: (1) very small tissue samples are required; (2) all cellular population of mitochondria can be investigated; (3) most important, however, is that mitochondria are studied in their natural surrounding. The results of research by using this method show the existence of several new phenomenon - tissue dependence of the mechanism of regulation of mitochondrial respiration, and activation of respiration by selective proteolysis. These phenomena are explained by interaction of mitochondria with other cellular structures in vivo. The details of experimental studies with use of these techniques and problems of kinetic analysis of the results are discussed. Examples of large-scale clinical application of these methods are given.     

Identification and morphometric evaluation of the synapses of optic nerve afferents in the optic tectum of the axolotl (Ambystoma mexicanum)

Summary The terminals of retinal afferents in the tectum of the axolotl have been identified ultrastructurally using techniques of horseradish peroxidase-filling and degeneration. The mitochondria in filled structures show a characteristic electron-lucent matrix. After both eyes have been removed, terminals with light mitochondria disappear from the area known to receive an optic input. In this area the presence of light mitochondria is almost always diagnostic of the retinal origin of a bouton. The synapses are similar to those assumed to be of retinal origin in other vertebrates. Detailed morphometric analysis has been carried out on identified optic synapses in the optic tectum of the axolotl.     

Large-scale purification and some properties of the mitochondrial aspartate aminotransferase from pig heart.

A method has been developed which allows isolation of 0.3--0.5 g of mitochondrial aspartate aminotransferase in five days starting from 10 pig hearts; the method does not involve initial preparation of mitochondria. Mitochondrial malate dehydrogenase and the cytoplasmic aspartate aminotransferase may conveniently be recovered from side fractions. The product mitochondrial aspartate aminotransferase is homogeneous as judged by various electrophoretic techniques and by N-terminal analysis. Crystals of the enzyme have been obtained both from concentrated, essentially salt-free, solutions and from solutions of ammonium sulphate. The amino acid composition, N and C-terminal amino acid sequences and subunit molecular weight have been determined; these characteristic properties are compared with those of the cytoplasmic isozyme from the same source.     

Light microscopic methods to visualize mitochondria on tissue sections

Mitochondria are cytoplasmic, double-membrane organelles, a main role of which is to synthesize ATP, the universal energy ‘supply’ of cells. In the last three decades, molecular genetic, biochemical, immunological and cell biological techniques have been applied in a coordinated fashion to unveil the pathogenesis of known mitochondrial disorders, as well as to explore the role of mitochondria in aging and neurodegenerative diseases. Once to be thought to be rare, it is now clear that mitochondrial dysfunction is an important cause of neurological and cardiac diseases, and age-related disorders such as cancer. Here, we review, illustrate, and provide updated protocols of two histochemical, and three immunohistochemical methods that in our opinion are the most reliable tools to visualize mitochondria on tissue sections from normal and disease specimens.     

Genetic Control of Mitochondria in Paramecium

Mitochondrial mutations for resistance to various antibiotics (erythromycin, chloramphenicol, spiramycin, mikamycin) have been obtained in Paramecium aurelia and their properties are reviewed. Using these mitochondrial markers, the interactions between nucleus and mitochondria have been studied in two ways: by microinjection of mitochondria from one stock or species into other stocks and species of P. aurelia and by a genetic study of a nuclear mutation affecting mitochondrial multiplication. Both types of experiments show: (1) that there may exist incompatibility between a given type of mitochondria and the cell into which they are introduced and (2) that through multiplication in the host cell, mitochondrial properties can be modified. The possible basis for incompatibility and host-induced modifications is discussed.     

THE DISTRIBUTION OF SOLUBLE AND MEMBRANE-BOUND FORMS OF GLUTAMINASE IN PIG BRAIN

Abstract— About 10% of the glutaminase activity associated with pig brain mitochondria was readily extractable by a variety of techniques but the remainder was very resistant to extraction. These two forms, which have been termed the soluble and membrane-bound forms respectively, have been shown to differ in their responses to activation by phosphate and phosphate-borate containing buffers. Submitochondrial fractionation studies indicated that the soluble form was located in the mitochondrial inner matrix whereas the membrane-bound form was associated with the inner membrane. The mitochondria associated with the synaptosomes were found to contain only the membrane-bound form of the enzyme whereas both forms were present in the free brain mitochondria.     

A method for isolating intact mitochondria and nuclei from the same homogenate,and the influence of mitochondrial destruction on the properties of cell nuclei

1. An improved type of ground glass homogenizer for soft tissues has been described which brings about a high degree of cell disruption and liberation of nuclei without causing appreciable damage to mitochondria. The gentleness and effectiveness of the new homogenizer in respect to isolation of mitochondria have been ascertained by comparing the ATP-ase activities of mitochondria isolated in 0.25 M sucrose solution without pH adjustment using a previous type of homogenizer with those of mitochondria isolated under the same conditions with the aid of the new homogenizer. In these experiments sucrose of 0.25 molarity without pH adjustment has been used in order to maintain the mitochondria in a rather sensitive state so as to make slightly deleterious effects of homogenization readily apparent. 2. A new method is described for the isolation of morphologically intact mitochondria and cell nuclei from the same homogenate. In this procedure the pH of the homogenate in 0.44 M sucrose is maintained at 6.0-6.2 with citric acid during the homogenization. An alternative method employing 0.44 M sucrose plus 0.005 M CaCl(2) is given for the isolation of nuclei from tumor cells. However, the latter method does not produce unaltered mitochondria. 3. The alpha-ketoglutarate, malate, succinate, and hexanoate oxidases of the "intact" mitochondria isolated in 0.44 M sucrose adjusted to pH 6.0-6.2 with very dilute citric acid as described in this paper have been investigated, and it has been shown that the mitochondria compare favorably to those isolated in 0.25 M sucrose by a previously described method. 4. Mitochondria have been found to contain an enzyme which causes nuclei to lose their ability to form gels in dilute alkali. This enzyme is released from the mitochondria when the latter are disrupted. 5. Some properties of nuclei isolated by the new method have been briefly discussed.     

Imaging in five dimensions: time-dependent membrane potentials in individual mitochondria.

Because of its importance in the chemiosmotic theory, mitochondrial membrane potential has been the object of many investigations. Significantly, however, quantitative data on how energy transduction might be regulated or perturbed by the physiological state of the cell has only been gathered via indirect studies on isolated mitochondrial suspensions; quantitative studies on individual mitochondria in situ have not been possible because of their small size, their intrinsic motility, and the absence of appropriate analytical reagents. In this article, we combine techniques for rapid, high resolution, quantitative three-dimensional imaging microscopy and mathematical modeling to determine accurate distributions of a potentiometric fluorescent probe between the cytosol and individual mitochondria inside a living cell. Analysis of this distribution via the Nernst equation permits assignment of potentials to each of the imaged mitochondrial membranes. The mitochondrial membrane potentials are distributed over a narrow range centered at -150 mV within the neurites of differentiated neuroblastoma cells. We find that the membrane potential of a single mitochondrion is generally remarkably stable over times of 40-80 s, but significant fluctuations can occasionally be seen. The motility of individual mitochondria is not directly correlated to membrane potential, but mitochondria do become immobile after prolonged treatment with respiratory inhibitors or uncouplers. Thus, three spatial dimensions, a key physiological parameter, and their changes over time are all quantitated for objects at the resolution limit of light microscopy. The methods described may be readily extended to permit investigations of how mitochondrial function is integrated with other processes in the intact cell.     

Physicochemical properties of flavodoxin from Desulfovibrio vulgaris

Various physicochemical and biochemical properties of the most potent uncoupler of oxidative phosphorylation known to date 3,5-di-tert-butyl-4-hydroxybenzylidenemalononitrile (SF 6847), such as pH dependence of the uncoupling activity and binding to mitochondria, spectral properties in the presence of different types of liposomes, biopolymers and mitochondria, and effects on model membrane systems have been investigated. From the results, it is concluded that the uncoupler most likely is localized in the phospholipid part of the membrane.     

High resolution imaging of live mitochondria

Classically, mitochondria have been studied by biochemical, genetic and electron microscopic approaches. In the last two decades, it became evident that mitochondria are highly dynamic organelles that are frequently dividing and fusing, changing size and shape and traveling long distances throughout the life of a cell. The study of the complex structural changes of mitochondria in vivo became possible with the advent of fluorescent labeling techniques in combination with live cell imaging microscopy. This review aims to provide an overview on novel fluorescent markers that are used in combination with mitochondrial fusion assays and various live cell microscopy techniques to study mitochondrial dynamics. In particular, approaches to study the movement of mitochondrial proteins and novel imaging techniques (FRET imaging-, 4Pi- and STED-microscopy) that provide high spatial resolution are considered.     

Flow Cytometric Analysis of Rhodamine 123 Fluorescence during Modulation of the Membrane Potential in Plant Mitochondria

The fluorescent dye rhodamine 123, which selectively accumulates in mitochondria based on the membrane potential, was used with flow cytometry to evaluate variations in activity of mitochondria isolated from plant tissues. In the presence of succinate and ATP, potato (Solanum tuberosum L.) tuber mitochondrial activity was affected by metabolic inhibitors and compounds that modify the membrane potential. The more uniform the mitochondrial population, the higher the observed membrane potential. The reactive population corresponds to the proportion of intact mitochondria (94-97%) defined by classic methods. Changes in the light-scattering properties are more related to internal modifications affecting the inner membrane-matrix system of the mitochondria during metabolic modulation than to specific volume change or outer membrane surface modifications. We tested our approach using an Arum maculatum preparation that contains three different types of mitochondria and demonstrated the validity of the light-scatter measurements to distinguish the α, β, and [ill] mitochondria and to measure their ability to built up a membrane potential in the presence of succinate. These results demonstrate clearly that flow cytometric techniques using rhodamine 123 can be employed to study the activity in isolated plant mitochondria.     

Imaging mitochondrial reactive oxygen species with fluorescent probes: Current applications and challenges

Abstract

Mitochondrial reactive oxygen species (ROS) is a key element in the regulation of several physiological functions and in the development or progression of multiple pathological events. A key task in the study of mitochondrial ROS is to establish reliable methods for measuring the ROS level in mitochondria with high selectivity, sensitivity, and spatiotemporal resolution. Over the last decade, imaging tools with fluorescent indicators from either small-molecule dyes or genetically encoded probes that can be targeted to mitochondria have been developed, which provide a powerful method to visualize and even quantify mitochondrial ROS level not only in live cells, but also in live animals. These innovative tools that have bestowed exciting new insights in mitochondrial ROS biology have been further promoted with the invention of new techniques in indicator design and fluorescent detection. However, these probes present some limitations in terms of specificity, sensitivity, and kinetics; failure to recognize these limitations often results in inappropriate interpretations of data. This review evaluates the recent advances in mitochondrial ROS imaging approaches with emphasis on their proper application and limitations, and highlights the future perspectives in the development of novel fluorescent probes for visualizing all species of ROS.     

The Km of NADH dehydrogenase is decreased in mitochondria of cystic fibrosis cells

The kinetic properties of the NADH dehydrogenase of the mitochondrial respiratory chain, assayed as NADH-dependent rotenone-sensitive cytochrome c reductase have been studied in mitochondria isolated from mononuclear white blood cells in patients affected by cystic fibrosis. Data reported here show that the apparent Km of the enzyme for NADH is significantly decreased in cystic fibrosis mitochondria. These findings are independent of the age or the clinical state of the disease and have also been obtained with mitochondria isolated from cultured skin fibroblasts. These observations support the notion that cystic fibrosis is possibly accompanied by alterations of intracellular membranes and these are evident also in circulating cells and cultured fibroblasts.