Difference between revisions of "IOC recommended reading"
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::::* From oxygen concentration to oxygen flux '''••''' Membrane potential: electric and chemical forces '''••''' Coupling and efficiency '''••''' Biochemical thresholds | ::::* From oxygen concentration to oxygen flux '''••''' Membrane potential: electric and chemical forces '''••''' Coupling and efficiency '''••''' Biochemical thresholds | ||
::::* Respiratory states | ::::* Respiratory states | ||
::::* MitoPathways | ::::* MitoPathways - the electron transfer system | ||
::::* Normalization of mitochondrial respiration: coupling control and | ::::* Normalization of mitochondrial respiration: coupling control and pathway control. | ||
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[[Image:O2k-Publications.jpg|left|50px|link=O2k-Publications: Topics|O2k-Publications in the MiPMap]] | |||
== SUIT protocols for high-resolution respirometry == | |||
Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of oxidative phosphorylation by temperature in the heart. bioRxiv doi.org/10.1101/103457. - [[Lemieux 2017 bioRxiv |»Bioblast link«]] | |||
::::* Updated terminology with SUIT protocols - open for discussion. | |||
::::* NADH-linked or N-pathways (CI-entry into Q); succinate-linked or S-pathway (CII-entry into Q); NS-pathway (convergent CI<small>&</small>II-entry into Q). | |||
Gnaiger E (2014) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 4th ed. Mitochondr Physiol Network 19.12. OROBOROS MiPNet Publications, Innsbruck:80 pp. - [[Gnaiger 2014 MitoPathways |»Bioblast link«]] | Gnaiger E (2014) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 4th ed. Mitochondr Physiol Network 19.12. OROBOROS MiPNet Publications, Innsbruck:80 pp. - [[Gnaiger 2014 MitoPathways |»Bioblast link«]] | ||
::::* The Blue Book: OXPHOS analysis; CI-linked, CII-linked, CI<small>&</small>II-linked | ::::* The Blue Book: OXPHOS analysis; CI-linked (= N-pathway), CII-linked (= S-pathway), CI<small>&</small>II-linked (= NS-pathway), respiratory states, abbreviations. | ||
» '''[[MitoPedia: SUIT]]''' | |||
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::::* Tissue-OXPHOS capacity in human permeabilized muscle fibres and isolated mitochondria. | ::::* Tissue-OXPHOS capacity in human permeabilized muscle fibres and isolated mitochondria. | ||
::::* Tissue-OXPHOS capacity and functional diversity. | ::::* Tissue-OXPHOS capacity and functional diversity. | ||
Pesta D, Gnaiger E (2012) High-resolution respirometry. OXPHOS protocols for human cells and permeabilized fibres from small biopisies of human muscle. Methods Mol Biol 810: 25-58. - [[Pesta 2012 Methods Mol Biol |»Bioblast link«]] | |||
::::* Introduction to high-resolution respirometry (HRR), SUIT protocols and flux control ratios. | |||
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::::* Cytochrome ''c'' test. | ::::* Cytochrome ''c'' test. | ||
::::* Respiration per million cells, per citrate synthase, per mg protein, or per cytochrome ''c'' oxidase activity. | ::::* Respiration per million cells, per citrate synthase, per mg protein, or per cytochrome ''c'' oxidase activity. | ||
Gnaiger E (2001) Bioenergetics at low oxygen: dependence of respiration and phosphorylation on oxygen and adenosine diphosphate supply. Respir Physiol 128:277-97. - [[Gnaiger 2001 Respir Physiol |»Bioblast link«]] | |||
::::* A detailed introduction into high-resolution respirometry with particular emphasis on kinetics and measurements at low oxygen | |||
::::* Mitochondrial kinetics measured by high-resolution respirometry | |||
::::* Calibrations and corrections for response time and instrumental background | |||
::::* Steady-state injection respirometry | |||
::::* Mitochondrial respiratory control at low oxygen | |||
::::* Apparent oxygen affinity and catalytic efficiency of mitochondrial respiration | |||
::::* Effect of ADP and oxygen limitation on ADP/O2 flux ratios | |||
::::* The low-oxygen environment of the cell: Mitochondria between hypoxic and oxidative stress | |||
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::::* Deconvolution of the oxygen signal for time resolution required in oxygen kinetics. | ::::* Deconvolution of the oxygen signal for time resolution required in oxygen kinetics. | ||
::::* Quality control of the limit of detection of oxygen flux at ±1 pmol O<sub>2</sub>·s<sup>-1</sup>·ml<sup>-1</sup>. | ::::* Quality control of the limit of detection of oxygen flux at ±1 pmol O<sub>2</sub>·s<sup>-1</sup>·ml<sup>-1</sup>. | ||
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::::» [[Media:MiPNet19.18 O2k-Core Manual.pdf|'''O2k-Core Manual.pdf''']]: O2k-Manual for [[DatLab 6]]. | ::::» [[Media:MiPNet19.18 O2k-Core Manual.pdf|'''O2k-Core Manual.pdf''']]: O2k-Manual for [[DatLab 6]]. | ||
::::» [[MiPNet17.09 IOC Questions | '''Worksheet O2k-Basic''']]: This worksheet contains questions on the O2k and HRR addressed to participants of O2k-Basic Workshops. Answers to these questions are elaborated during the O2k-Workshop. | ::::» [[MiPNet17.09 IOC Questions |'''Worksheet O2k-Basic''']]: This worksheet contains questions on the O2k and HRR addressed to participants of O2k-Basic Workshops. Answers to these questions are elaborated during the O2k-Workshop. | ||
::::» [[O2k-Publications|'''O2k-Publications''']] | ::::» [[O2k-Publications: Topics |'''O2k-Publications''']] | ||
::::» [[O2k-Protocols|'''O2k-Protocols''']] | ::::» [[O2k-Protocols |'''O2k-Protocols''']] | ||
[[Category:OroboPedia]] | [[Category:OroboPedia]] |
Revision as of 14:19, 15 February 2017
IOC recommended reading
HRR: high-resolution respirometry
Recommended reading
Gnaiger E (2014) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 4th ed. Mitochondr Physiol Network 19.12. OROBOROS MiPNet Publications, Innsbruck:80 pp. - »Bioblast link«
- A hard copy of this monograph on mitochondrial physiology will be included in the workshop material. The Blue Book is available on-line free of charge and provides a background on OXPHOS analysis:
- From oxygen concentration to oxygen flux •• Membrane potential: electric and chemical forces •• Coupling and efficiency •• Biochemical thresholds
- Respiratory states
- MitoPathways - the electron transfer system
- Normalization of mitochondrial respiration: coupling control and pathway control.
Gnaiger E (2008) Polarographic oxygen sensors, the oxygraph and high-resolution respirometry to assess mitochondrial function. In: Mitochondrial Dysfunction in Drug-Induced Toxicity (Dykens JA, Will Y, eds) John Wiley:327-52. - »Bioblast link«
- Methodological introduction, comparison of HRR with traditional oxygraphy.
- Dramatically different: high-resolution respirometry - the OROBOROS Oxygraph-2k.
- Calibration of polarographic oxygen sensors and oxygen concentration in respiration media at air saturation.
- From Oxygraph slopes to respiratory flux corrected for background effects.
- Phosphorylation or coupling control protocol (PCP, CCP) with intact cells.
- Titration steps of the CCP.
- Experimental example.
- Flux control ratios from the CCP.
- Intact cells, permeabilized cells and tissue, or isolated mitochondria?
SUIT protocols for high-resolution respirometry
Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of oxidative phosphorylation by temperature in the heart. bioRxiv doi.org/10.1101/103457. - »Bioblast link«
- Updated terminology with SUIT protocols - open for discussion.
- NADH-linked or N-pathways (CI-entry into Q); succinate-linked or S-pathway (CII-entry into Q); NS-pathway (convergent CI&II-entry into Q).
Gnaiger E (2014) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 4th ed. Mitochondr Physiol Network 19.12. OROBOROS MiPNet Publications, Innsbruck:80 pp. - »Bioblast link«
- The Blue Book: OXPHOS analysis; CI-linked (= N-pathway), CII-linked (= S-pathway), CI&II-linked (= NS-pathway), respiratory states, abbreviations.
» MitoPedia: Respiratory states
O2k-Fluorometry
- O2k-Manual: »O2k-Fluo LED2-Module«
- Makrecka-Kuka M, Krumschnabel G, Gnaiger E (2015) High-resolution respirometry for simultaneous measurement of oxygen and hydrogen peroxide fluxes in permeabilized cells, tissue homogenate and isolated mitochondria. Biomolecules 5:1319-38. »Bioblast pdf«
- Krumschnabel G, Eigentler A, Fasching M, Gnaiger E (2014) Use of safranin for the assessment of mitochondrial membrane potential by high-resolution respirometry and fluorometry. Methods Enzymol 542:163-81. - »Bioblast link«
- Krumschnabel G, Fontana-Ayoub M, Sumbalova Z, Heidler J, Gauper K, Fasching M, Gnaiger E (2015) Simultaneous high-resolution measurement of mitochondrial respiration and hydrogen peroxide production. Methods Mol Biol 1264:245-61. - »Bioblast link«
- Eigentler A, Fontana-Ayoub M, Gnaiger E (2013) O2k-Fluorometry: HRR and H2O2 production in mouse cardiac tissue homogenate. Mitochondr Physiol Network 18.05(01):1-6. - »Bioblast link«
TPP/ISE
- O2k-MultiSensor System with ion selective electrodes (ISE) MiPNet15.03
- Determination of membrane potential using TPP+ and an ion selective electrode (ISE) MiPNet14.05
- Rottenberg H (1984) Membrane potential and surface potential in mitochondria: uptake and binding of lipophilic cations. J Membr Biol 81:127-38.
Further reading
Gnaiger E (2009) Capacity of oxidative phosphorylation in human skeletal muscle. New perspectives of mitochondrial physiology. Int J Biochem Cell Biol 41: 1837-1845. - »Bioblast link«
- Respirometry with permeabilized fibres and isolated mitochondria.
- Convergent NS (CI&II) electron input and OXPHOS capacity.
- Tissue-OXPHOS capacity in human permeabilized muscle fibres and isolated mitochondria.
- Tissue-OXPHOS capacity and functional diversity.
Pesta D, Gnaiger E (2012) High-resolution respirometry. OXPHOS protocols for human cells and permeabilized fibres from small biopisies of human muscle. Methods Mol Biol 810: 25-58. - »Bioblast link«
- Introduction to high-resolution respirometry (HRR), SUIT protocols and flux control ratios.
Scandurra FM, Gnaiger E (2010) Cell respiration under hypoxia: Facts and artefacts in mitochondrial oxygen kinetics. Adv Exp Med Biol 662: 7-25. - »Bioblast link«
- Isolated mitochondria and intact cells.
- Nanomolar resolution of oxygen concentration.
- Effects of cell density and activity.
- Closed versus open systems.
- p50 in vivo.
Gnaiger E, Kuznetsov AV, Schneeberger S, Seiler R, Brandacher G, Steurer W, Margreiter R (2000) Mitochondria in the cold. In: Life in the Cold (Heldmaier G, Klingenspor M, eds) Springer, Heidelberg, Berlin, New York:431-42. - »Bioblast link«
- Isolated mitochondria and permeabilized muscle fibers.
- Optimization of mitochondrial cold storage • Mitochondrial respiration medium, MiR05 • Mitochondrial cold ischemia-reperfusion injury.
Renner K, Amberger A, Konwalinka G, Kofler R, Gnaiger E (2003) Changes of mitochondrial respiration, mitochondrial content and cell size after induction of apoptosis in leukemia cells. Biochim Biophys Acta 1642:115-23. - »Bioblast link«
- Intact cells.
- Cytochrome c oxidase.
- Cytochrome c test.
- Respiration per million cells, per citrate synthase, per mg protein, or per cytochrome c oxidase activity.
Gnaiger E (2001) Bioenergetics at low oxygen: dependence of respiration and phosphorylation on oxygen and adenosine diphosphate supply. Respir Physiol 128:277-97. - »Bioblast link«
- A detailed introduction into high-resolution respirometry with particular emphasis on kinetics and measurements at low oxygen
- Mitochondrial kinetics measured by high-resolution respirometry
- Calibrations and corrections for response time and instrumental background
- Steady-state injection respirometry
- Mitochondrial respiratory control at low oxygen
- Apparent oxygen affinity and catalytic efficiency of mitochondrial respiration
- Effect of ADP and oxygen limitation on ADP/O2 flux ratios
- The low-oxygen environment of the cell: Mitochondria between hypoxic and oxidative stress
Gnaiger E, Steinlechner-Maran R, Méndez G, Eberl T, Margreiter R (1995) Control of mitochondrial and cellular respiration by oxygen. J Bioenerg Biomembr 27:583-96. - »Bioblast link«
- First publication to establish high-resolution respirometry, based on the OROBOROS Oxygraph.
- Standardized oxygen calibration (air and internal zero oxygen calibration).
- Automatic instrumental background correction of oxygen flux.
- Deconvolution of the oxygen signal for time resolution required in oxygen kinetics.
- Quality control of the limit of detection of oxygen flux at ±1 pmol O2·s-1·ml-1.
General
- » O2k-Core Manual.pdf: O2k-Manual for DatLab 6.
- » Worksheet O2k-Basic: This worksheet contains questions on the O2k and HRR addressed to participants of O2k-Basic Workshops. Answers to these questions are elaborated during the O2k-Workshop.