Difference between revisions of "IOC recommended reading"
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[[File:MITOEAGLE-representation.jpg|right|180px|link=http://www.mitoglobal.org/index.php/COST Action MitoEAGLE|COST Action MitoEAGLE]] | |||
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Gnaiger | == MitoEAGLE 'Mitochondrial physiology' BEC 2020.1 == | ||
:::* <big>Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1. - [[BEC_2020.1_doi10.26124bec2020-0001.v1 |»Bioblast link«]]</big> | |||
<br /> | |||
[[Image:O2k-Workshops.png|right|180px|link=OROBOROS_Events]] | |||
[[Image:O2k-Publications.jpg|left|80px|link=O2k-Publications: Topics|O2k-Publications in the MiPMap]] | |||
== Workshop material== | |||
Gnaiger E ( | :::* Doerrier C, Garcia-Souza LF, Krumschnabel G, Wohlfarter Y, Mészáros AT, Gnaiger E (2018) High-Resolution FluoRespirometry and OXPHOS protocols for human cells, permeabilized fibres from small biopsies of muscle, and isolated mitochondria. Methods Mol Biol 1782 (Palmeira CM, Moreno AJ, eds): Mitochondrial Bioenergetics, 978-1-4939-7830-4. - [[Doerrier 2018 Methods Mol Biol |»Bioblast link«]] | ||
:* | :::* Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. Bioenerg Commun 2020.2. - [[Gnaiger 2020 BEC MitoPathways |»Bioblast link«]] - ''A new edition with updated terminology and more ..'' | ||
:::* 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. [[Makrecka-Kuka 2015 Biomolecules|»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. - [[Krumschnabel 2014 Methods Enzymol |»Bioblast link«]] | ||
: | :::* [[Media:MiPNet22.11_O2k-FluoRespirometer-manual.pdf|'''O2k-Manual.pdf''']]: O2k-Manual for [[DatLab 7]]. | ||
:* | |||
:* | |||
: | |||
== HRR: high-resolution respirometry and SUIT protocols == | |||
:::* <big>Doerrier C, Garcia-Souza LF, Krumschnabel G, Wohlfarter Y, Mészáros AT, Gnaiger E (2018) High-Resolution FluoRespirometry and OXPHOS protocols for human cells, permeabilized fibres from small biopsies of muscle, and isolated mitochondria. Methods Mol Biol 1782 (Palmeira CM, Moreno AJ, eds): Mitochondrial Bioenergetics, 978-1-4939-7830-4. - [[Doerrier 2018 Methods Mol Biol |»Bioblast link«]]</big> | |||
Gnaiger E ( | :::* <big>Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of mitochondrial respiratory capacity by temperature in mouse heart: electron flow through the Q-junction in permeabilized fibers. Sci Rep 7:2840, DOI:10.1038/s41598-017-02789-8. - [[Lemieux 2017 Sci Rep |»Bioblast link«]]</big> | ||
: | ::::» Updated terminology with SUIT protocols. | ||
::::» 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). | |||
:::* <big>Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. BEC 2020.2. - [[Gnaiger 2020 BEC MitoPathways |»Bioblast link«]]</big> | |||
::::» ''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-pathway | |||
::::» Normalization of mitochondrial respiration: coupling control and pathway control. | |||
:::* <big>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. - [[Gnaiger_2008_POS |»Bioblast link«]]</big> | |||
::::» Methodological introduction, comparison of HRR with traditional oxygraphy. | |||
::::» Dramatically different: high-resolution respirometry - the [[Oroboros O2k]]. | |||
::::» 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. | |||
::::» Living cells, permeabilized cells and tissue, or isolated mitochondria? | |||
* [[ | :::* '''[[MitoPedia: SUIT]]''' | ||
* Krumschnabel | |||
* Krumschnabel G, Eigentler A, Fasching M, Gnaiger E (2014) | |||
* Krumschnabel G, | :::* '''[[MitoPedia: Respiratory states]]''' | ||
* Eigentler A, Fontana-Ayoub M, Gnaiger E (2013) O2k-Fluorometry: HRR and H<sub>2</sub>O<sub>2</Sub> production in mouse cardiac tissue homogenate. Mitochondr Physiol Network 18.05(01): 1-6. | [[Image:P.jpg|link=OXPHOS capacity|OXPHOS]] [[Image:R.jpg|link=ROUTINE respiration|ROUTINE]] [[Image:E.jpg|link=ET capacity|ETS]] [[Image:L.jpg|link=LEAK respiration|LEAK]] [[Image:ROX.jpg|link=Residual oxygen consumption|ROX]] | ||
* '''[[O2k-Publications: O2k-Fluorometry]]''' | |||
[[Image:O2k-Fluorometer.JPG|60px|left|link=O2k-Fluorometer|O2k-FluoRespirometer]] | |||
== O2k-FluoRespirometry == | |||
:::* 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. [[Makrecka-Kuka 2015 Biomolecules|»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. - [[Krumschnabel 2014 Methods Enzymol |»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. - [[Krumschnabel 2015 Methods Mol Biol |»Bioblast link«]] | |||
:::* Eigentler A, Fontana-Ayoub M, Gnaiger E (2013) O2k-Fluorometry: HRR and H<sub>2</sub>O<sub>2</Sub> production in mouse cardiac tissue homogenate. Mitochondr Physiol Network 18.05(01):1-6. - [[MiPNet18.05 Amplex-Mouse-heart |»Bioblast link«]] | |||
:::* '''[[O2k-Publications: O2k-Fluorometry]]''' | |||
== TPP/ISE == | == TPP/ISE == | ||
* O2k-MultiSensor System with ion selective electrodes (ISE) '''[[MiPNet15.03]]''' | :::* O2k-MultiSensor System with ion selective electrodes (ISE) '''[[MiPNet15.03 O2k-MultiSensor-ISE |MiPNet15.03]]''' | ||
* Determination of membrane potential using TPP+ and an ion selective electrode (ISE) '''[[MiPNet14.05]]''' | |||
:::* 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. | |||
:::* Rottenberg H (1984) Membrane potential and surface potential in mitochondria: uptake and binding of lipophilic cations. J Membr Biol 81:127-38. | |||
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== Further reading == | == 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- | :::* Gnaiger E (2009) Capacity of oxidative phosphorylation in human skeletal muscle. New perspectives of mitochondrial physiology. Int J Biochem Cell Biol 41:1837-45. - [[Gnaiger 2009 Int J Biochem Cell Biol |»Bioblast link«]] | ||
: | ::::» Respirometry with permeabilized fibres and isolated mitochondria. | ||
: | ::::» Convergent NS (CI<small>&</small>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 biopsies 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. | |||
:::* Scandurra FM, Gnaiger E (2010) Cell respiration under hypoxia: Facts and artefacts in mitochondrial oxygen kinetics. Adv Exp Med Biol 662:7-25. - [[Scandurra 2010 Adv Exp Med Biol |»Bioblast link«]] | |||
::::» Isolated mitochondria and intact cells. | |||
::::» Nanomolar resolution of oxygen concentration. | |||
::::» Effects of cell density and activity. | |||
::::» Closed versus open systems. | |||
::::» ''p''<sub>50</sub> 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. - [[Gnaiger 2000 Life in the Cold |»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. - [[Renner 2003 Biochim Biophys Acta |»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. - [[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 | |||
:::* 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. - [[Gnaiger 1995 J Bioenerg Biomembr |»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 O<sub>2</sub>·s<sup>-1</sup>·ml<sup>-1</sup>. | |||
Line 109: | Line 140: | ||
:::* [[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. | |||
:::* [[O2k-Publications: Topics |'''O2k-Publications''']] | |||
:::* [[O2k-Protocols |'''O2k-Protocols''']] | |||
[[Category:OroboPedia]] | [[Category:OroboPedia]] |
Revision as of 01:23, 31 December 2020
IOC recommended reading
MitoEAGLE 'Mitochondrial physiology' BEC 2020.1
- Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1. - »Bioblast link«
Workshop material
- Doerrier C, Garcia-Souza LF, Krumschnabel G, Wohlfarter Y, Mészáros AT, Gnaiger E (2018) High-Resolution FluoRespirometry and OXPHOS protocols for human cells, permeabilized fibres from small biopsies of muscle, and isolated mitochondria. Methods Mol Biol 1782 (Palmeira CM, Moreno AJ, eds): Mitochondrial Bioenergetics, 978-1-4939-7830-4. - »Bioblast link«
- Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. Bioenerg Commun 2020.2. - »Bioblast link« - A new edition with updated terminology and more ..
- 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«
- O2k-Manual.pdf: O2k-Manual for DatLab 7.
HRR: high-resolution respirometry and SUIT protocols
- Doerrier C, Garcia-Souza LF, Krumschnabel G, Wohlfarter Y, Mészáros AT, Gnaiger E (2018) High-Resolution FluoRespirometry and OXPHOS protocols for human cells, permeabilized fibres from small biopsies of muscle, and isolated mitochondria. Methods Mol Biol 1782 (Palmeira CM, Moreno AJ, eds): Mitochondrial Bioenergetics, 978-1-4939-7830-4. - »Bioblast link«
- Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of mitochondrial respiratory capacity by temperature in mouse heart: electron flow through the Q-junction in permeabilized fibers. Sci Rep 7:2840, DOI:10.1038/s41598-017-02789-8. - »Bioblast link«
- » Updated terminology with SUIT protocols.
- » 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 (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. BEC 2020.2. - »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-pathway
- » 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 O2k.
- » 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.
- » Living cells, permeabilized cells and tissue, or isolated mitochondria?
O2k-FluoRespirometry
- 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 41:1837-45. - »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 biopsies 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.