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Difference between revisions of "IOC recommended reading"

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{{Mainpage OROBOROS}}
{{Mainpage OROBOROS}}


== [[Image:O2k-Manual.jpg|left|30px|link=http://oroboros.at/?O2k-Manual|O2k-Manual]] General ==
== <big><big>HRR:</big></big> High-resolution respirometry ==


[[Media:MiPNet19.18 O2k-Core Manual.pdf|'''»O2k-Core Manual.pdf''']]
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.


[[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.


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?


[[O2k-Publications|'''»O2k-Publications''']]


[[O2k-Protocols|'''»O2k-Protocols''']]
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


'''» [[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-Publications.jpg|left|50px|link=http://www.bioblast.at/index.php/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]]«
[[Image:O2k-Publications.jpg|left|50px|link=O2k-Publications: Topics|O2k-Publications in the MiPMap]]
** The Blue Book: OXPHOS analysis; CI-linked, CII-linked, CI<small>&</small>II-linked pathways, respiratory states, abbreviations.
== 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.
 


* '''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]]«
» '''[[MitoPedia: Respiratory states]]'''
** Introduction to high-resolution respirometry (HRR), SUIT protocols and flux control ratios.
[[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]]


* '''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: 327-352. »[[Gnaiger 2012 MitoPathways |Bioblast Access]]«
** Methodological introduction to HRR, with focus on Polarographic oxygen sensor and traditional oxygraphy
** Dramatically different: High-resolution respirometry - the 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 (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?


[[Image:O2k-Fluorometer.JPG|60px|left|link=O2k-Fluorometer|O2k-Fluorometer]]
== O2k-Fluorometry ==


== HRR and O2k-Fluorometry ==
* [[MiPNet17.05 O2k-Fluorescence LED2-Module |»Manual: '''O2k-Fluorometry''']]
* [[MiPNet17.05 O2k-Fluorescence LED2-Module |»Manual: '''O2k-Fluo LED2-Module''']]
* Krumschnabel et al (2014) Methods Enzymol. »[[Krumschnabel 2014 Methods Enzymol |Link]]«  
* '''Krumschnabel 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, 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]]«
* '''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]]«
* '''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 Ion Selective Electrodes (ISE) '''[[MiPNet15.03]]'''
 
* 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.
* 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.
** Tissue-OXPHOS capacity and functional diversity.


* '''Gnaiger E (2001)''' Bioenergetics at low oxygen: dependence of respiration and phosphorylation on oxygen and adenosine diphosphate supply. Respir Physiol 128: 277-297. »[[Gnaiger 2001 Respir Physiol |Link]]« – A detailed introduction into high-resolution respirometry with particular emphasis on kinetics and measurements at low oxygen.  
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]]«
** Mitochondrial kinetics measured by high-resolution respirometry
:* Respirometry with permeabilized fibres and isolated mitochondria.
** Calibrations and corrections for response time and instrumental background
:* Convergent CI<small>&</small>II electron input and OXPHOS capacity.
** Steady-state injection respirometry
:* Tissue-OXPHOS capacity in human permeabilized muscle fibres and isolated mitochondria.
** Mitochondrial respiratory control at low oxygen
:* Tissue-OXPHOS capacity and functional diversity.
** 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
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''']]


* '''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: 431-442. [[Gnaiger 2000 Transplant Proc|'''»Abstract''']]
**Isolated mitochondria and permeabilized muscle fibers, MiR05
**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: 115-123. [[Renner 2003 Biochim Biophys Acta|'''»Abstract''']]  
[[Category:OroboPedia]]
**Intact cells
**Cytochrome c oxidase
**Cytochrome c test
**Respiration per million cells, per citrate synthase, per mg protein, or per cytochrome c oxidase activity.

Revision as of 10:23, 11 January 2015

Template:Mainpage OROBOROS

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



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. »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 OXPHOS ROUTINE ETS LEAK ROX


O2k-Fluorometer

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


Publications in the MiPMap

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.


O2k-Manual

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.

» O2k-Publications

» O2k-Protocols