Difference between revisions of "IOC recommended reading"
From Bioblast
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== Recommended reading == | == Recommended reading == | ||
<big>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. | <big>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 |Ā»Bioblast linkĀ«]]</big> | ||
:* ''A hard copy of this | :* ''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 '''ā¢ā¢''' Membrane potential: electric and chemical forces '''ā¢ā¢''' Coupling and efficiency '''ā¢ā¢''' Biochemical thresholds | :* From oxygen concentration to oxygen flux '''ā¢ā¢''' Membrane potential: electric and chemical forces '''ā¢ā¢''' Coupling and efficiency '''ā¢ā¢''' Biochemical thresholds | ||
:* Respiratory states | :* Respiratory states | ||
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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 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 |Ā»Bioblast linkĀ«]] | ||
:* Methodological introduction, comparison of HRR with traditional oxygraphy. | :* Methodological introduction, comparison of HRR with traditional oxygraphy. | ||
:* Dramatically different: high-resolution respirometry - the OROBOROS [[Oxygraph-2k]]. | :* Dramatically different: high-resolution respirometry - the OROBOROS [[Oxygraph-2k]]. | ||
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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 |Ā»Bioblast | 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 |Ā»Bioblast linkĀ«]] ā A detailed introduction into high-resolution respirometry with particular emphasis on kinetics and measurements at low oxygen. Ā | ||
:* Mitochondrial kinetics measured by high-resolution respirometry Ā | :* Mitochondrial kinetics measured by high-resolution respirometry Ā | ||
:* Calibrations and corrections for response time and instrumental background Ā | :* Calibrations and corrections for response time and instrumental background Ā | ||
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== SUIT protocols for high-resolution respirometry == | == SUIT protocols for high-resolution respirometry == | ||
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 | | 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 |Ā»Bioblast linkĀ«]] | ||
:* The Blue Book: OXPHOS analysis; CI-linked, CII-linked, CI<small>&</small>II-linked pathways, respiratory states, abbreviations. | :* The Blue Book: OXPHOS analysis; CI-linked, CII-linked, CI<small>&</small>II-linked pathways, respiratory states, abbreviations. | ||
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 |Ā»Bioblast | 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 |Ā»Bioblast linkĀ«]] | ||
:* Introduction to high-resolution respirometry (HRR), SUIT protocols and flux control ratios. | :* Introduction to high-resolution respirometry (HRR), SUIT protocols and flux control ratios. | ||
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* '''O2k-Manual''': [[MiPNet17.05 O2k-Fluo LED2-Module|Ā»O2k-Fluo LED2-ModuleĀ«]] | * '''O2k-Manual''': [[MiPNet17.05 O2k-Fluo LED2-Module|Ā»O2k-Fluo LED2-ModuleĀ«]] | ||
* 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 |Ā»Bioblast | * 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 |Ā»Bioblast linkĀ«]] | ||
* 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 |Ā»Bioblast | * 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 |Ā»Bioblast linkĀ«]] | ||
* 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 |Ā»Bioblast | * 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 |Ā»Bioblast linkĀ«]] | ||
* '''[[O2k-Publications: O2k-Fluorometry]]''' | * '''[[O2k-Publications: O2k-Fluorometry]]''' | ||
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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: 1837-1845. [[Gnaiger 2009 Int J Biochem Cell Biol |Ā»Bioblast | Gnaiger E (2009) Capacity of oxidative phosphorylation in human skeletal muscle. New perspectives of mitochondrial physiology. Int J Biochem Cell Biol 41: 1837-1845. - [[Gnaiger 2009 Int J Biochem Cell Biol |Ā»Bioblast linkĀ«]] | ||
:* Respirometry with permeabilized fibres and isolated mitochondria. | :* Respirometry with permeabilized fibres and isolated mitochondria. | ||
:* Convergent CI<small>&</small>II electron input and OXPHOS capacity. | :* Convergent CI<small>&</small>II electron input and OXPHOS capacity. | ||
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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 |Ā»Bioblast | 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 |Ā»Bioblast linkĀ«]] | ||
:* Isolated mitochondria and intact cells. Ā | :* Isolated mitochondria and intact cells. Ā | ||
:* Nanomolar resolution of oxygen concentration. Ā | :* Nanomolar resolution of oxygen concentration. Ā | ||
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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 |Ā»Bioblast | 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 |Ā»Bioblast linkĀ«]] | ||
:* Isolated mitochondria and permeabilized muscle fibers. | :* Isolated mitochondria and permeabilized muscle fibers. | ||
:* Optimization of mitochondrial cold storage ā¢ Mitochondrial respiration medium, [[MiR05]] ā¢ Mitochondrial cold ischemia-reperfusion injury. | :* Optimization of mitochondrial cold storage ā¢ Mitochondrial respiration medium, [[MiR05]] ā¢ 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 |Ā»Bioblast | 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 |Ā»Bioblast linkĀ«]] Ā | ||
:* Intact cells. Ā | :* Intact cells. Ā | ||
:* Cytochrome ''c'' oxidase. | :* Cytochrome ''c'' oxidase. | ||
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Gnaiger E, Steinlechner-Maran R, MĆ©ndez 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 |Ā»Bioblast | Gnaiger E, Steinlechner-Maran R, MĆ©ndez 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 |Ā»Bioblast linkĀ«]] | ||
:* First publication to establish high-resolution respirometry, based on the OROBOROS Oxygraph. | :* First publication to establish high-resolution respirometry, based on the OROBOROS Oxygraph. | ||
:* Standardized oxygen calibration (air and internal zero oxygen calibration). | :* Standardized oxygen calibration (air and internal zero oxygen calibration). | ||
Revision as of 16:12, 26 August 2015
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. - Ā»Bioblast linkĀ«
- 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 ā¢ā¢ Membrane potential: electric and chemical forces ā¢ā¢ Coupling and efficiency ā¢ā¢ Biochemical thresholds
- Respiratory states
- MitoPathways to electron transfer complexes
- Normalization of mitochondrial respiration: coupling control and substrate 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. - Ā»Bioblast linkĀ«
- 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?
Gnaiger E (2001) Bioenergetics at low oxygen: dependence of respiration and phosphorylation on oxygen and adenosine diphosphate supply. Respir Physiol 128:277-97. - Ā»Bioblast linkĀ« ā 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
SUIT protocols for high-resolution respirometry
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. - Ā»Bioblast linkĀ«
- The Blue Book: OXPHOS analysis; CI-linked, CII-linked, CI&II-linked pathways, respiratory states, abbreviations.
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. - Ā»Bioblast linkĀ«
- Introduction to high-resolution respirometry (HRR), SUIT protocols and flux control ratios.
Ā» MitoPedia: Respiratory states
O2k-Fluorometry
- O2k-Manual: Ā»O2k-Fluo LED2-ModuleĀ«
- 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. - Ā»Bioblast linkĀ«
- 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. - Ā»Bioblast linkĀ«
- 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. - Ā»Bioblast linkĀ«
- O2k-Publications: O2k-Fluorometry
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. - Ā»Bioblast linkĀ«
- Respirometry with permeabilized fibres and isolated mitochondria.
- Convergent CI&II electron input and OXPHOS capacity.
- Tissue-OXPHOS capacity in human permeabilized muscle fibres and isolated mitochondria.
- Tissue-OXPHOS capacity and functional diversity.
Scandurra FM, Gnaiger E (2010) Cell respiration under hypoxia: Facts and artefacts in mitochondrial oxygen kinetics. Adv Exp Med Biol 662: 7-25. - Ā»Bioblast linkĀ«
- 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. - Ā»Bioblast linkĀ«
- Isolated mitochondria and permeabilized muscle fibers.
- Optimization of mitochondrial cold storage ā¢ Mitochondrial respiration medium, MiR05 ā¢ 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. - Ā»Bioblast linkĀ«
- 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, Steinlechner-Maran R, MĆ©ndez G, Eberl T, Margreiter R (1995) Control of mitochondrial and cellular respiration by oxygen. J Bioenerg Biomembr 27:583-96. - Ā»Bioblast linkĀ«
- 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 Ā±1 pmol O2Ā·s-1Ā·ml-1.
General
Ā» O2k-Core Manual.pdf: O2k-Manual for DatLab 6.
Ā» 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.
