Difference between revisions of "IOC recommended reading"
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{{Mainpage OROBOROS}} | {{Mainpage OROBOROS}} | ||
== | == <big><big>HRR:</big></big> 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 |Open Access]]« | ||
:* The Blue Book: Background on OXPHOS analysis. | |||
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 Access]]« | |||
:* 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. »[[Gnaiger 2001 Respir Physiol |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 | |||
[[Image:O2k-Publications.jpg|left|50px|link=O2k-Publications: Topics|O2k-Publications in the MiPMap]] | |||
== 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 |Open Access]]« | |||
:* 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 |Bioblast Access]]« | |||
:* Introduction to high-resolution respirometry (HRR), SUIT protocols and flux control ratios. | |||
» '''[[MitoPedia: Respiratory states]]''' | |||
[[Image:P.jpg|link=OXPHOS capacity|OXPHOS]] [[Image:R.jpg|link=ROUTINE respiration|ROUTINE]] [[Image:E.jpg|link=ETS capacity|ETS]] [[Image:L.jpg|link=LEAK respiration|LEAK]] [[Image:ROX.jpg|link=Residual oxygen consumption|ROX]] | |||
[[Image:O2k-Fluorometer.JPG|60px|left|link=O2k-Fluorometer|O2k-Fluorometer]] | |||
== O2k-Fluorometry == | |||
* [[MiPNet17.05 O2k-Fluorescence LED2-Module |»Manual: '''O2k-Fluorometry''']] | |||
* [[MiPNet17.05 O2k-Fluorescence LED2-Module |»Manual: '''O2k- | * Krumschnabel et al (2014) Methods Enzymol. »[[Krumschnabel 2014 Methods Enzymol |Link]]« | ||
* | * Krumschnabel G, Eigentler A, Fasching M, Gnaiger E (2014) O2k-Fluorometry: HRR and simultaneous determination of mt membrane potential with safranin. Mitochondr Physiol Network 19.19(01):1-5. »[[MiPNet19.19_Safranin_Data_Acquisition_and_Analysis |Open Access]]« | ||
* | * Krumschnabel G, Makrecka-Kuka M, Kumphune S, Fontana-Ayoub M, Fasching M, Gnaiger E (2014) O2k-Fluorometry: HRR and simultaneous determination of H2O2 production with Amplex Red. Mitochondr Physiol Network 19.20(01):1-6. »[[MiPNet19.20_Amplex_Red_Data_Acquisition_and_Analysis |Open Access]]« | ||
* | * 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 |Open Access]]« | ||
* | |||
* '''[[O2k-Publications: O2k-Fluorometry]]''' | * '''[[O2k-Publications: O2k-Fluorometry]]''' | ||
== TPP/ISE == | == TPP/ISE == | ||
* O2k-MultiSensor System with | |||
* O2k-MultiSensor System with ion selective electrodes (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]]''' | ||
* '''[[Calculation of mitochondrial membrane potential from measurements with a TPP electrode]]''' | * '''[[Calculation of mitochondrial membrane potential from measurements with a TPP electrode]]''' | ||
* | * Rottenberg H (1984) Membrane potential and surface potential in mitochondria: uptake and binding of lipophilic cations. J Membr Biol 81:127-38. | ||
[[Image:MiPMap Publication.jpg|left|44px|link=MiPMap|Publications in the MiPMap]] | |||
== 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 |Link]]« | |||
** | :* Respirometry with permeabilized fibres and isolated mitochondria. | ||
* | :* Convergent CI<small>&</small>II electron input and OXPHOS capacity. | ||
** | :* Tissue-OXPHOS capacity in human permeabilized muscle fibres and isolated mitochondria. | ||
** Mitochondrial | :* 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. »[[Scandurra 2010 Adv Exp Med Biol |Open Access]]« | ||
:* 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 |Open Access]]« | |||
:* 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 |'''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, 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 |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>. | |||
[[Image:O2k-Manual.jpg|left|30px|link=O2k-Manual|O2k-Manual]] | |||
== General == | |||
» [[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|'''O2k-Publications''']] | |||
» [[O2k-Protocols|'''O2k-Protocols''']] | |||
[[Category:OroboPedia]] | |||
Revision as of 10:23, 11 January 2015
HRR: 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. »Open Access«
- The Blue Book: Background on OXPHOS analysis.
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 Access«
- 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. »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
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. »Open Access«
- 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. »Bioblast Access«
- Introduction to high-resolution respirometry (HRR), SUIT protocols and flux control ratios.
» MitoPedia: Respiratory states
O2k-Fluorometry
- »Manual: O2k-Fluorometry
- Krumschnabel et al (2014) Methods Enzymol. »Link«
- Krumschnabel G, Eigentler A, Fasching M, Gnaiger E (2014) O2k-Fluorometry: HRR and simultaneous determination of mt membrane potential with safranin. Mitochondr Physiol Network 19.19(01):1-5. »Open Access«
- Krumschnabel G, Makrecka-Kuka M, Kumphune S, Fontana-Ayoub M, Fasching M, Gnaiger E (2014) O2k-Fluorometry: HRR and simultaneous determination of H2O2 production with Amplex Red. Mitochondr Physiol Network 19.20(01):1-6. »Open Access«
- 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. »Open Access«
- 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
- Calculation of mitochondrial membrane potential from measurements with a TPP electrode
- 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. »Link«
- 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. »Open Access«
- 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. »Open Access«
- 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. »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, Steinlechner-Maran R, Méndez G, Eberl T, Margreiter R (1995) Control of mitochondrial and cellular respiration by oxygen. J Bioenerg Biomembr 27:583-96. »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.