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Mitochondrial Membranes

Mitochondrial Membranes are the intricate lipid bilayer structures that enclose the mitochondria, the powerhouses of eukaryotic cells.
These membranes play a crucial role in cellular respiration, energy production, and various signaling pathways.
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Most cited protocols related to «Mitochondrial Membranes»

Eukaryotic proteins are processed using the general pipeline depicted in Figure 1. The pipeline is organized as a directed rooted computational graph where each node corresponds to the execution of a specific tool. The graph root is the query protein sequence, while leaves correspond to predicted subcellular localizations, here represented as GO terms of the cellular component ontology. A path from the root to one leaf is determined by the outcomes of the different tools. In Figure 1, GO terms and tools highlighted in green are only applied for plant proteins.
At the very first level, the query sequence is scanned for the presence of signal peptide using the DeepSig predictor (4 ). If the signal sequence is found (suggesting the sorting of the protein through the secretory pathway), the mature protein sequence is determined by cleaving the predicted signal peptide. The resulting mature sequence is then analyzed by the subsequent tools. Firstly, PredGPI (6 (link)) determines the presence of GPI-anchors. If an anchor is found, the sequence is classified as Membrane anchored component (GO:0046658). Otherwise, the sequence is filtered for the presence of α-helical TransMembrane (TM) domains using ENSEMBLE3.0 (7 (link)). If at least one TM domain is found, the protein is predicted as membrane protein and passed to MemLoci (10 (link)), which predicts the final membrane protein localization that includes: Endomembrane system (GO:00112505), Plasma membrane (GO:0005886) and Organelle membrane (GO:0031090). If no TM domain is found, the protein is predicted to be localized in the Extracellular space (GO:0005615).
Proteins not directed to the secretory pathway (as predicted with DeepSig) are analyzed for their potential organelle localization using TPpred3 (5 (link)), which predicts the presence of organelle-targeting peptides and distinguishes between mitochondrial and chloroplast sorting for plant proteins.
If no targeting peptide is detected with TPpred3, ENSEMBLE3.0 is used to discriminate membrane from globular proteins: MemLoci or BaCelLo (9 (link)) are hence applied to predict localization of membrane and globular protein, respectively. In particular, BaCelLo is able to distinguish among five different cellular compartments (four in case of animal or fungi proteins): Nucleus (GO:0005634), Cytoplasm (GO:0005737), Extracellular space (GO:0005615), Mitochondrion (GO:0005739) and, for plant proteins, Chloroplast (GO:0009507). Moreover, since BaCelLo adopts different optimized models for animals and fungi, information about the taxonomic origin of the input is also provided as a parameter to the predictor.
When a mitochondrial targeting signal is detected, this is cleaved-off to determine the mature protein sequence. ENSEMBLE3.0 is then used to determine whether the mature protein is localized into a Mitochondrial membrane (GO:0031966) or, more generally, into the Mitochondrion (GO:0005739).
For plant proteins, TPpred3 is also able to distinguish potential chloroplast-targeting peptides. If detected, they are cleaved and the sequence submitted to SChloro (11 (link)) that discriminates six different sub-chloroplast localizations: Outer membrane (GO:0009707), Inner membrane (GO:0009706), Plastoglobule (GO:0010287), Thylakoid lumen (GO:0009543), Thylakoid membrane (GO:0009535) and Stroma (GO:0009570).
Overall BUSCA is able to predict sixteen different compartments for plants and nine for animals and fungi.
Publication 2018
Amino Acid Sequence Animal Model Animals Cell Nucleus Cells Cellular Structures Chloroplasts Cytoplasm Eukaryotic Cells Extracellular Space Eye Fungal Proteins Fungi Helix (Snails) Membrane Proteins Mitochondria Mitochondrial Membranes Organelles Peptides Plant Leaves Plant Proteins Plant Roots Plants Plasma Membrane Proteins Reproduction Secretory Pathway Signal Peptides Strains Thylakoid Membrane Thylakoids Tissue, Membrane
The RoGFP protein contains two engineered cysteine thiols, as first described by Remington et al. (RoGFP2) 11 (link). The cDNA encoding the protein was created by introducing four mutations in the mammalian GFP expression vector (pEGFP-N1) (C48S, Q80R, S147C, and Q204C) using a QuikChange Multi Site-directed mutagenesis kit (Strategene). The RoGFP construct was ligated into the VQ Ad5CMV K-NpA adenoviral shuttle vector between the KpnI and NotI sites; after sequencing and amplification this plasmid was used to generate a recombinant adenovirus to permit widespread expression in our cells (ViraQuest Inc., North Liberty, IA). The resulting redox-sensitive protein has excitation maxima at 400 and 484 nm, with emission at 525 nm. In response to changes in redox conditions, RoGFP exhibits reciprocal changes in intensity at the two excitation maxima 12 (link), and its ratiometric characteristics render it insensitive to expression levels 13 (link)-15 (link). Although RoGFP’s fluorescence behavior is relatively independent of pH and it does not respond to authentic nitric oxide (NO), reduced NADH, or the antioxidant N-acetyl-L-cysteine (NAC), its spectrum is slightly affected by reduced glutathione (GSH) possibly due to thiol-disulfide exchange (Online Figures I and II).
RoGFP was expressed in the mitochondrial matrix (Mito-RoGFP) by appending a 48 bp region encoding the mitochondrial targeting sequence from cytochrome oxidase subunit IV, at the 5′ end of the coding sequence. This construct was then ligated into the VQ Ad5CMV K-NpA plasmid between the KpnI and NotI sites, and used to generate an adenoviral vector. RoGFP was targeted to the mitochondrial inter-membrane space (IMS-RoGFP) by appending it to glycerol phosphate dehydrogenase (GPD). A cDNA construct encoding GPD, an integral protein of the inner mitochondrial membrane whose C-terminus protrudes into the inter-membrane space 17 (link), was ligated in-frame with cDNA encoding RoGFP 17 (link). The corresponding polypeptide includes amino acids 1–626 of GPD, with RoGFP at the carboxy terminus. This method has been used previously to express YFP in the inter-membrane space 18 (link). (See Online Supplemental Material for characterization of the RoGFP sensors and experimental protocols).
Publication 2009
Acetylcysteine Adenoviruses Adenovirus Vaccine Amino Acids Antioxidants Cells Cloning Vectors Cysteine Cytochrome-c Oxidase Subunit IV Disulfides DNA, Complementary Fluorescence glycerol-1-phosphate dehydrogenase Glycerol-3-Phosphate Dehydrogenase Integral Membrane Proteins Mammals Mitochondria Mitochondrial Membrane, Inner Mitochondrial Membranes Mitomycin Mutagenesis, Site-Directed Mutation NADH Open Reading Frames Oxidation-Reduction Oxide, Nitric Plasmids Polypeptides Proteins Reading Frames Reduced Glutathione Shuttle Vectors Sulfhydryl Compounds Tissue, Membrane
High-resolution O2 consumption measurements were conducted in 2 mL of buffer Z using the OROBOROS Oxygraph-2k (OROBOROS INSTRUMENTS, Corp., Innsbruck, AT) with stirring at 750 rpm. Buffer Z contained 20 mM creatine hydrate to saturate creatine kinase, which facilitates mitochondrial ADP transport [4 (link), 10 (link), 23 (link)-25 (link)], with the exception of specific experiments on human PmFBs which were conducted in the presence of 24 mM phosphocreatine and 12 mM creatine hydrate (described below). 5 mM pyruvate and 2 mM malate were added as complex I substrates. ADP was titrated in step-wise increments and all experiments were completed before oxygraph chamber [O2] reached 150 μM. At the conclusion of each experiment, PmFBs were washed in double-distilled H2O to remove salts, frozen at -20°C, and dried via lyophilization (Labconco Corp., Kansas City, MO). Polarographic oxygen measurements were acquired in 2-second intervals, with the rate of respiration derived from 40 data points, and expressed as pmol • s-1 • mg-1 dry weight. Dry and wet bundle weights were consistently between 0.2 - 0.6 mg and ∼1.0 to 2.5 mg, respectively. Cytochrome c was added to test for mitochondrial membrane integrity as partial loss of cytochrome c during sample preparation may limit active respiration. A cytochrome c response was dectected in <5% of all experiments and no response generated >10% increase in respiration. No relationship was observed between the relative cytochrome c response and Km when grouping all human and rodent data (R2 = 0.013, p>0.05). Additionally, no significant relationship was observed in humans when using a paired t-test to compare the Km for those experiments showing 0-5% cytochrome c response relative to those few samples exhibiting a 5-10% cytochrome c response. Four PmFBs from each rat or human were run simultaneously in four separate oxygraph chambers. Two of the chambers contained either 100 μM BTS or 25 μM BLEB. A third chamber contained 1.25% DMSO (vehicle, +V) to match the content of DMSO added in the BTS and BLEB conditions with the remaining chamber serving as the control (minus vehicle) condition.
The Km for ADP was determined through the Michaelis-Menten enzyme kinetics - fitting model (Y = Vmax*X/(Km + X)), where X = [free ADP; ADPf] and Y = JO2 at [ADPf], using Prism (GraphPad Software, Inc., La Jolla, CA). This equation was also used to calculate the fraction of maximal mitochondrial respiration in resting human skeletal muscle in vivo. This calculation was performed using the experimentally determined Km values assuming resting [ADPf] to be ∼14.6 μM in human skeletal muscle [6 (link)].
Publication 2011
Buffers Cell Respiration Creatine Creatine Kinase cytochrome c'' Enzymes Freeze Drying Freezing Homo sapiens Kinetics malate Mitochondria Mitochondrial Membranes NADH Dehydrogenase Complex 1 Oxygen Phosphocreatine Polarography prisma Pyruvates Respiratory Rate Rodent Salts Skeletal Muscles Sulfoxide, Dimethyl
For large scale global analysis, HeLa S3 cells were prefractionated using custom 2D-LE platform, comprised of sIEF coupled to multiplexed GELFrEE12 (link),13 (link). HeLa S3, H1299, B16F10 cells, and mitochondrial membrane proteins were also fractionated using the custom GELFrEE13 (link) device alone (no sIEF). After separation, detergent and salt were removed, and the fractions were injected into nanocapillary RPLC columns for elution into a 12 Tesla LTQ FTMS for online detection and fragmentation14 (link),15 (link). The MS RAW files were processed with in-house software called crawler to assign masses. Using this program, determination of both the intact masses and the corresponding fragment masses were performed and these data were searched against a human proteome database. Extensive statistical workups were also performed using several FDR estimation approaches (with decoy databases both concatenated and not). A final q-value procedure is described in detail (Methods), with the data above reported using a 5% instantaneous FDR (i.e., q-value) cutoff at the protein level (Supplementary Fig. 14).
Publication 2011
Cells Detergents HeLa Cells Homo sapiens Medical Devices Membrane Proteins Mitochondria Mitochondrial Membranes Mitochondrial Proteins Proteins Proteome Sodium Chloride Tissue, Membrane
The technique is partially adapted from previous methods [12 (link), 17 (link)] and has been described previously [18 , 19 (link)]. Briefly, small portions (∼25 mg) of muscle were dissected and placed in ice-cold buffer X, containing (in mM) 50 MES, 7.23 K2EGTA, 2.77 CaK2EGTA, 20 imidazole, 0.5 DTT, 20 taurine, 5.7 ATP, 14.3 PCr, and 6.56 MgCl2-6 H2O (pH 7.1, 290 mOsm). The muscle was trimmed of connective tissue and fat. Four small muscle bundles (∼2-7 mm, 1.0-2.5 mg wet weight) of either red or white gastrocnemius were prepared from each rat. Each bundle was gently separated along the longitudinal axis with a pair of needle-tipped forceps under magnification (MX6 Stereoscope, Leica Microsystems, Inc., Wetzlar, DE). Rat bundles were then treated with 50 μg/ml saponin in ice-cold buffer X, and incubated on a rotor for 30 min at 4°C. Human muscle fibre bundles were treated with 30 μg/ml saponin, as separate experiments determined optimal respiration with this saponin concentration in humans [20 (link)]. Saponin is a mild, cholesterol-specific detergent that selectively permeabilizes the sarcolemmal membranes while keeping mitochondrial membranes, which contain little cholesterol, completely intact [21 (link), 22 (link)]. Following permeabilization, the PmFB were placed in buffer Z containing (in mM) 105 K-MES, 30 KCl, 1 EGTA, 10 K2HPO4, and 5 MgCl2-6 H2O, 0.005 glutamate, and 0.002 malate with 5.0 mg/ml BSA (pH 7.4, 290 mOsm). PmFB remained in buffer Z on a rotator at 4°C until analysis (< 30 min).
Publication 2011
Buffers Cell Respiration Cholesterol Common Cold Connective Tissue Detergents Egtazic Acid Epistropheus Fibrosis Forceps Glutamate Homo sapiens imidazole Magnesium Chloride malate Mitochondrial Membranes Muscle, Gastrocnemius Muscle Tissue Needles potassium phosphate, dibasic Saponin Taurine Tissue, Membrane

Most recents protocols related to «Mitochondrial Membranes»

Mitochondrial membrane potential was measured using JC-1 dye. JC-1 (Thermo Fisher) is a membrane permeable dye which accumulates within mitochondrial membranes in a membrane potential-dependent manner [30 (link)]. JC-1 forms red fluorescent aggregates within the membrane and mitochondrial membrane potential can be measured by determining the ration of red fluorescent aggregates and green, fluorescent monomers [30 (link)]. The mitochondrial membrane potential disruptor Carbonyl cyanide m-chlorophenyl hydrazone (CCCP, Sigma-Aldrich) was used to determine minimal red fluorescence (S2 Fig) [30 (link)]. 24 hours after polarization, hMDMs were washed with DPBS (Gibco) and 4 uM JC-1, 4 uM JC-1 with 100 uM CCCP, or base media were added to wells. Cells were incubated for 30 minutes at 37C, and media was replaced with fresh base media. Cells were incubated for an additional 10 minutes at 37C, and fluorescence was quantified using a CLARIOstar plate reader (BMG Labtech). Data were normalized by subtracting mean base media fluorescence intensity from fluorescence intensity of each well.
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Publication 2023
Carbonyl Cyanide m-Chlorophenyl Hydrazone Cell Membrane Permeability Cells Fluorescence Membrane Potential, Mitochondrial Membrane Potentials Mitochondrial Membranes Tissue, Membrane
To assess the membrane potential of sperm mitochondria, sperm cells from the spermathecae of C. osakensis queens were stained using 40 µL of an MT-1 MitoMP Detection Kit (Dojindo), diluted 1000-fold with 39.44 mM sodium sulfite in PBS (anoxic condition), PBS (aerobic condition) and 10 µM FCCP in PBS (negative control) for 15 min. After the sperm samples were centrifuged at 5000 rpm for 5 min and the supernatants were removed, a further 20 µL of each solution was added. Further, 3 µL of the sperm suspension was placed on a slide, covered with a coverslip, and observed under a fluorescence microscope (Olympus BX53 combined with U-FGW filters). Photomicrographs were captured using a 3CCD digital camera (Olympus DP74).
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Publication 2023
Anoxia Bacteria, Aerobic Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone Fingers Microscopy, Fluorescence Mitochondrial Membranes Photomicrography sodium sulfite Sperm
Mitochondrial membrane depolarization was determined using tetramethylrhodamine methyl ester (TMRM, ThermoFisher Scientific, T668) according to the manufacturer’s protocol. TMRM is a cationic, cell-permeant, red-orange fluorescent dye that accumulates in polarized mitochondria, but it is released after their depolarization. Untreated or treated cells were harvested, centrifuged and resuspended in culture medium containing 50 nM TMRM, and then incubated at 37 °C for 30 min in the dark. Cells were washed twice with PBS and immediately analyzed using flow cytometry.
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Publication 2023
Cations Cells Culture Media Flow Cytometry Fluorescent Dyes Mitochondria Mitochondrial Membranes tetramethylrhodamine methyl ester
The total mitochondrial mass was determined using 10-N-Nonyl acridine orange (NAO, Invitrogen, Waltham, MA, USA), a dye that binds to cardiolipin present specifically on the mitochondrial membrane [63 (link)]. Briefly, wt and cdh1Δ cells were grown to mid-log phase in YPGal medium and incubated in culture medium containing 10 μM NAO for 30 min. Fluorescence intensity measured using the BD Accuri C6 flow cytometer. Data were analysed with FlowJo v10 software version.
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Publication 2023
Cardiolipins Cells Culture Media Fluorescence Mitochondrial Inheritance Mitochondrial Membranes N(10)-nonylacridine orange
Mice were sacrificed 24 h after CLP, and the lung tissues of mice were washed with the prepared low-temperature preservation PBS solution and dried. The chopped mushy lung tissue was transferred to a homogenizer with pipette (avoid left-right rotation to ensure the integrity of mitochondrial membrane). and fully homogenized with centrifugal tubes. The precooled centrifuge was centrifuged 1000× g at 4 °C for 10 min, and the lung tissue was filtered with double-layer gauze, leaving the supernatant. The filtrates were centrifuged again under the same parameters, and the precipitates were used as mitochondria.
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Publication 2023
Biologic Preservation Cold Temperature Lung Mitochondria Mitochondrial Membranes Mus Tissues

Top products related to «Mitochondrial Membranes»

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The FACSCalibur is a flow cytometry system designed for multi-parameter analysis of cells and other particles. It features a blue (488 nm) and a red (635 nm) laser for excitation of fluorescent dyes. The instrument is capable of detecting forward scatter, side scatter, and up to four fluorescent parameters simultaneously.
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JC-1 dye is a fluorescent probe used for measuring mitochondrial membrane potential in cells. It exhibits potential-dependent accumulation in mitochondria, indicated by a fluorescence emission shift from green to red. The dye can be used to detect changes in mitochondrial membrane potential, which is an important indicator of cellular health and function.
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MitraTracker Green is a fluorescent dye used to label and monitor mitochondria in live cells. It passively diffuses across the cell membrane and accumulates in active mitochondria. The dye exhibits enhanced fluorescence upon binding to the mitochondrial membrane potential.
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The MitoProbe JC-1 assay kit is a laboratory reagent used to measure the mitochondrial membrane potential in live cells. It employs the cationic dye JC-1, which exhibits potential-dependent accumulation in mitochondria, indicated by a fluorescence emission shift from green to red. The kit provides the necessary components to perform this assay.
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The Oxygraph-2k is a high-performance respirometer designed for precise measurement of oxygen consumption and production in biological samples. It provides real-time monitoring of oxygen levels, making it a valuable tool for researchers in the fields of cell biology, physiology, and bioenergetics.
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The JC-1 Mitochondrial Membrane Potential Assay Kit is a fluorometric tool used to measure mitochondrial membrane potential in cells. The kit employs the cationic dye JC-1, which accumulates in the mitochondria in a potential-dependent manner.
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DiOC6 is a fluorescent dye used for the detection and analysis of mitochondrial membrane potential in cells. It is a lipophilic cationic dye that accumulates in active mitochondria due to the negative membrane potential. DiOC6 can be used in flow cytometry, fluorescence microscopy, and other fluorescence-based techniques to assess mitochondrial function and health.
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MitraTracker Red CMXRos is a fluorescent dye that can be used to stain mitochondria in live cells. It is a cell-permeant dye that accumulates in active mitochondria, enabling the visualization and analysis of mitochondrial structure and function.
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The Muse Cell Analyzer is a compact, fully automated cell analysis system designed for sample preparation and high-throughput analysis. The instrument utilizes the principles of flow cytometry to provide accurate and reliable cell counts, viability, and cell population analysis.
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MitoTracker Green FM is a fluorescent dye that specifically labels mitochondria in live cells. It passively diffuses across the plasma membrane and accumulates in active mitochondria. The dye exhibits bright green fluorescence upon binding to mitochondrial lipids.

More about "Mitochondrial Membranes"

Mitochondrial Membranes are the intricate lipid bilayer structures that enclose the mitochondria, the powerhouses of eukaryotic cells.
These dynamic and complex organelles play a crucial role in cellular respiration, energy production, and various signaling pathways.
Explore the world of Mitochondrial Membranes with PubCompare.ai's AI-driven platform.
Discover optimized research protocols that ensure reproducibility and accuracy.
Our platform helps you locate the best protocols from literature, pre-prints, and patents, using intelligent comparisons to identify the most reliable and effective approaches.
Unlock the secrets of Mitochondrial Membranes with cutting-edge tools like FACSCalibur, JC-1 dye, MitoTracker Green, MitoProbe JC-1 assay kit, Oxygraph-2k, JC-1 Mitochondrial Membrane Potential Assay Kit, DiOC6, MitoTracker Red CMXRos, and Muse Cell Analyzer.
These technologies enable seamless research and help you understand the intricate workings of these powerhouse organelles.
Expereince seamless research with PubCompare.ai's cutting-edge technology and uncover the full potential of Mitochondrial Membranes.
Discover the best research protocols, optimize your experiments, and unlock the secrets of these dynamic structures.