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Difference between revisions of "User talk:Tindle Lisa/My sandbox O2k-Procedures"

From Bioblast
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== Redox biology ==
== Redox biology ==
{{#ask:[[Category:Publications]] [[Instrument and method::O2k-Protocol]] [[Additional label::O2k-Demo]] [[Additional label::Redox]]
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==  H<sub>2</sub>O<sub>2</sub> production ==
==  H<sub>2</sub>O<sub>2</sub> production ==
{{#ask:[[Category:Publications]] [[Instrument and method::O2k-Protocol]] [[Additional label::O2k-Demo]] [[Additional label::H2O2]]
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==  mt-Membrane potential ==
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==  ATP production ==
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==  Calcium ==
{{#ask:[[Category:Publications]] [[Instrument and method::O2k-Protocol]] [[Additional label::O2k-Demo]] [[Additional label::calcium]]
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==  Plant physiology ==
{{#ask:[[Category:Publications]] [[Instrument and method::O2k-Protocol]] [[Additional label::O2k-Demo]] [[Additional label::Plant physiology]]
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==  NO concentration ==
{{#ask:[[Category:Publications]] [[Instrument and method::O2k-Protocol]] [[Additional label::O2k-Demo]] [[Additional label::NO]]
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[[Image:Titration-Injection-microPump.jpg|200px|left|link=TIP2k-Module|TIP2k-Module]]
[[Image:Titration-Injection-microPump.jpg|200px|left|link=TIP2k-Module|TIP2k-Module]]
== O2k-Demo TIP2k ==
== O2k-Demo TIP2k ==

Revision as of 12:13, 27 October 2023


                  

O2k-Open Support

User talk:Tindle Lisa/My sandbox O2k-Procedures

O2k-Procedures


O2 consumption

ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
Gnaiger 2020 BEC MitoPathwaysOpen Access pdf published online 2020-12-30

Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. Bioenerg Commun 2020.2. https://doi.org/10.26124/bec:2020-0002Permeabilized cells
Permeabilized tissue
Homogenate
Isolated mitochondria
Intact cells		Heart
Skeletal muscle
Fibroblast		Human
Mouse		2020
MiPNet12.01 Suppl T-issueBioblast pdf »Versions
O2k-Protocols contents
MitoPathways at the Q-junction: mouse skeletal muscle fibers.		Permeabilized tissueSkeletal muscleMouse2018-11-18
MiPNet21.14 Reference sample HRRBioblast pdf »Versions
O2k-Protocols
Development of a reference sample for HRR.		Intact cells
Permeabilized cells		HEKHuman2016-10-19
MiPNet08.09 CellRespirationBioblast pdf  »Versions
O2k-Procedures contents
High-resolution respirometry and coupling-control protocol with living cells: ROUTINE, LEAK, ET-pathway, ROX.		Intact cellsBlood cells
Lymphocyte		Human2016-08-11
MiPNet17.03 Shredder vs FibersBioblast pdf »Versions
O2k-Protocols
Mitochondrial respiration in permeabilized fibers versus homogenate from fish liver and heart. An application study with the PBI-Shredder.		HomogenateHeart
Liver		Fishes2015-06-18
MiPNet12.11 MitoRespirationBioblast pdf »Versions
O2k-Protocols
Flux control ratios in isolated mitochondria. OXPHOS capacity and respiratory control.		Isolated mitochondriaArtemia
Crustaceans		2014-02-20
Pesta 2012 Methods Mol BiolPMID: 22057559
Bioblast pdf
O2k-Protocols
Pesta D, Gnaiger E (2012) High-resolution respirometry. OXPHOS protocols for human cells and permeabilized fibers from small biopsies of human muscle. Methods Mol Biol 810:25-58. https://doi.org/10.1007/978-1-61779-382-0_3Permeabilized cells
Permeabilized tissue
Intact cells		Skeletal muscle
Other cell lines
HEK
Fibroblast
HUVEC		Human2012
MiPNet08.12 IOC22Bioblast pdf
O2k-Protocols
NO effect on mitochondrial oxygen kinetics at low oxygen. O2k workshop Report.		Isolated mitochondriaLiverRat2011-12-11
Gnaiger 2008 POSBioblast pdf
O2k-Protocols contents
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 & Sons, Inc, Hoboken, NJ:327-52.Permeabilized cells
Permeabilized tissue
Intact cells		Blood cellsMouse2008
MiPNet04.05 Titration-InjectionBioblast pdf
O2k-Protocols contents
From step titration to ramp injection: Uncoupling by FCCP with TIP.		Intact cellsEndothelial;epithelial;mesothelial cell
HUVEC		Human1999-01
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Redox biology

ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
Komlodi 2021 BEC QBioenerg Commun 2021.3. Open Access pdf published online 2021-11-11

Komlódi T, Cardoso LHD, Doerrier C, Moore AL, Rich PR, Gnaiger E (2021) Coupling and pathway control of coenzyme Q redox state and respiration in isolated mitochondria. Bioenerg Commun 2021.3. https://doi.org/10.26124/bec:2021-0003Isolated mitochondriaHeart
Nervous system		Mouse2021
Back to top ▲

H2O2 production

ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
Komlodi 2021 BEC AmR-O2Bioenerg Commun 2021.4. Open Access pdf published online 2021-12-21

Komlódi T, Sobotka O, Gnaiger E (2021) Facts and artefacts on the oxygen dependence of hydrogen peroxide production using Amplex UltraRed. Bioenerg Commun 2021.4. https://doi.org/10.26124/bec:2021-0004Intact cellsOther cell linesSaccharomyces cerevisiae2021
MiPNet20.14 AmplexRed H2O2-productionBioblast pdf »Versions
O2k-Protocols
O2k-FluoRespirometry: HRR and simultaneous determination of H2O2 production with Amplex UltraRed.		Isolated mitochondriaHeartMouse2019-06-24
MiPNet18.06 Amplex-YeastBioblast pdf »Versions
O2k-Protocols
O2k-FluoRespirometry: Amplex UltraRed using freeze-dried baker’s yeast. » Update: Komlódi T, Sobotka O, Gnaiger E (2021) Facts and artefacts on the oxygen dependence of hydrogen peroxide production using Amplex UltraRed. MitoFit Preprints 2021.10. doi:10.26124/mitofit:2021-0010		2019-06-24
Komlodi 2018 Methods Mol BiolPMID:29850998Komlodi T, Sobotka O, Krumschnabel G, Bezuidenhout N, Hiller E, Doerrier C, Gnaiger E (2018) Comparison of mitochondrial incubation media for measurement of respiration and hydrogen peroxide production. Methods Mol Biol 1782:137-55.Permeabilized cells
Permeabilized tissue		Skeletal muscle
HEK		Human
Mouse		2018
Krumschnabel 2015 Methods Mol BiolPMID: 25631019Krumschnabel 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.Isolated mitochondriaNervous systemMouse2015
Makrecka-Kuka 2015 BiomoleculesBiomolecules 5:1319-38. PMID: 26131977 Open Access
O2k-Protocols contents
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. https://doi.org/10.3390/biom5031319Permeabilized cells
Homogenate
Isolated mitochondria
Intact cells		Heart
Nervous system
HEK		Human
Mouse		2015
Back to top ▲

mt-Membrane potential

ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
MiPNet20.13 Safranin mt-membranepotentialBioblast pdf »Versions
O2k-Protocols
O2k-FluoRespirometry: HRR and simultaneous determination of mt-membrane potential with safranin or TMRM.		HomogenateNervous systemMouse2019-06-24
MiPNet14.05 TPP-mtMembranePotentialBioblast pdf »Versions
O2k-Protocols contents
TPP+ and mt-membrane potential.		2016-04-01
Krumschnabel 2014 Methods EnzymolPMID: 24862266 »O2k-brief
O2k-Protocols contents
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. https://doi.org/10.1016/B978-0-12-416618-9.00009-1HomogenateNervous systemMouse2014
MiPNet15.08 TPP electrodeBioblast pdf »Versions
O2k-Protocols
Ion selective electrode for TPP+ and high-resolution respirometry.		2011-12-11
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ATP production

ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
Cardoso 2021 BEC MgGBioenerg Commun 2021.1. BEC pdf published online 2021-06-30

Cardoso LHD, Doerrier C, Gnaiger E (2021) Magnesium Green for fluorometric measurement of ATP production does not interfere with mitochondrial respiration. Bioenerg Commun 2021.1. https://doi.org/10.26124/bec:2021-0001Isolated mitochondriaHeartMouse2021
Chinopoulos 2014 Methods EnzymolPMID: 24862274 Open Access»O2k-briefChinopoulos C, Kiss G, Kawamata H, Starkov AA (2014) Measurement of ADP-ATP exchange in relation to mitochondrial transmembrane potential and oxygen consumption. Methods Enzymol 542:333-48. doi:10.1016/B978-0-12-416618-9.00017-0Permeabilized cellsHEKHuman2014
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Calcium

ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
Naszai 2019 Sci RepPMID: 31848391 Open AccessNászai A, Terhes E, Kaszaki J, Boros M, Juhász L (2019) Ca(2+)N it be measured? Detection of extramitochondrial calcium movement with high-resolution FluoRespirometry. Sci Rep 9:19229.Isolated mitochondriaLiverRat2019
Elustondo 2014 Biochim Biophys ActaPMID: 25448536Elustondo PA, Negoda A, Kane CL, Kane DA, Pavlov EV (2014) Spermine selectively inhibits high-conductance, but not low-conductance calcium-induced permeability transition pore. Biochim Biophys Acta 1847:231–40.Isolated mitochondriaLiverRat2014
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Plant physiology

ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
Went 2021 MitoFit PBMitoFit Preprints 2021.05.
MitoFit pdf


Went N, Di Marcello M, Gnaiger E (2021) Oxygen dependence of photosynthesis and light-enhanced dark respiration studied by High-Resolution PhotoRespirometry. MitoFit Preprints 2021.05. https://doi.org/10.26124/mitofit:2021-0005Intact cellsAlgae2021
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NO concentration

ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
Aguirre 2010 Biochim Biophys ActaPMID: 20144583 Open AccessAguirre E, Rodríguez-Juárez F, Bellelli A, Gnaiger E, Cadenas S (2010) Kinetic model of the inhibition of respiration by endogenous nitric oxide in intact cells. Biochim Biophys Acta 1797:557-65. https://doi.org/10.1016/j.bbabio.2010.01.033Intact cells
Enzyme
Oxidase;biochemical oxidation		HEK2010
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TIP2k-Module

O2k-Demo TIP2k

» O2k-Catalogue: TIP2k
» O2k-Publications: TIP2k
ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
Pesta 2012 Methods Mol BiolPMID: 22057559
Bioblast pdf
O2k-Protocols
Pesta D, Gnaiger E (2012) High-resolution respirometry. OXPHOS protocols for human cells and permeabilized fibers from small biopsies of human muscle. Methods Mol Biol 810:25-58. https://doi.org/10.1007/978-1-61779-382-0_3Permeabilized cells
Permeabilized tissue
Intact cells		Skeletal muscle
Other cell lines
HEK
Fibroblast
HUVEC		Human2012
Gnaiger 2008 POSBioblast pdf
O2k-Protocols contents
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 & Sons, Inc, Hoboken, NJ:327-52.Permeabilized cells
Permeabilized tissue
Intact cells		Blood cellsMouse2008
MiPNet04.05 Titration-InjectionBioblast pdf
O2k-Protocols contents
From step titration to ramp injection: Uncoupling by FCCP with TIP.		Intact cellsEndothelial;epithelial;mesothelial cell
HUVEC		Human1999-01

TIP2k Manual

ChapterViewSectionLast update
MiPNet12.10 TIP2k-manualBioblast pdf »Versions
O2k-Manual
Titration-Injection microPump TIP2k manual.		2021-07-08



O2k-FluoRespirometer
link=O2k-TPP%2B_and_Ca2%2B_ISE-Module

O2k-Demo O2k-MultiSensor

» O2k-Catalogue: O2k-MultiSensor
» O2k-Publications: O2k-Fluorometry
ProtocolViewTopicPreparationTissue and cellMammal and modelLast update
Komlodi 2021 BEC AmR-O2Bioenerg Commun 2021.4. Open Access pdf published online 2021-12-21

Komlódi T, Sobotka O, Gnaiger E (2021) Facts and artefacts on the oxygen dependence of hydrogen peroxide production using Amplex UltraRed. Bioenerg Commun 2021.4. https://doi.org/10.26124/bec:2021-0004Intact cellsOther cell linesSaccharomyces cerevisiae2021
MiPNet24.11 mtMP calculationPDF.jpg » Versions
O2k-Protocols
Mitochondrial membrane potential calculation		2019-08-05
MiPNet18.05 Amplex-Mouse-heartBioblast pdf »Versions
O2k-Protocols
O2k-Fluorometry: HRR and H2O2 production in mouse cardiac tissue homogenate.		HomogenateHeartMouse2019-06-24
MiPNet20.14 AmplexRed H2O2-productionBioblast pdf »Versions
O2k-Protocols
O2k-FluoRespirometry: HRR and simultaneous determination of H2O2 production with Amplex UltraRed.		Isolated mitochondriaHeartMouse2019-06-24
MiPNet20.13 Safranin mt-membranepotentialBioblast pdf »Versions
O2k-Protocols
O2k-FluoRespirometry: HRR and simultaneous determination of mt-membrane potential with safranin or TMRM.		HomogenateNervous systemMouse2019-06-24
Makrecka-Kuka 2015 BiomoleculesBiomolecules 5:1319-38. PMID: 26131977 Open Access
O2k-Protocols contents
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. https://doi.org/10.3390/biom5031319Permeabilized cells
Homogenate
Isolated mitochondria
Intact cells		Heart
Nervous system
HEK		Human
Mouse		2015
Krumschnabel 2015 Methods Mol BiolPMID: 25631019Krumschnabel 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.Isolated mitochondriaNervous systemMouse2015
Krumschnabel 2014 Methods EnzymolPMID: 24862266 »O2k-brief
O2k-Protocols contents
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. https://doi.org/10.1016/B978-0-12-416618-9.00009-1HomogenateNervous systemMouse2014
MiPNet08.12 IOC22Bioblast pdf
O2k-Protocols
NO effect on mitochondrial oxygen kinetics at low oxygen. O2k workshop Report.		Isolated mitochondriaLiverRat2011-12-11

O2k-MultiSensor Manual

ChapterViewSectionLast update
MiPNet15.03 O2k-MultiSensor-ISEBioblast pdf »Versions
O2k-Manual
O2k-MultiSensor system with ion selective electrodes (ISE).		2021-08-02
MiPNet15.05 NO-manualBioblast pdf  »Versions
O2k-Manual
O2k-MultiSensor system with amperometric sensors: NO, H2S, H2O2.		2016-04-21
MiPNet17.05 O2k-Fluo LED2-ModuleBioblast pdf »Versions
O2k-Manual
O2k-Fluo LED2-Module.		2021-06-22
MiPNet23.15 O2k-pH ISE-Module
O2k-Manual
Measurement of proton flux with the O2k-pH ISE-Module.		2018-09-08
MiPNet24.12 NextGen-O2k: Q-ModulePDF.jpg » Versions
O2k-Manual
NextGen-O2k: Q-Module manual		2021-10-29
MiPNet26.11 NextGen-O2k: PB-ModulePDF.jpg » Versions
O2k-Manual
NextGen-O2k: PB-Module manual		2021-10-29
MiPNet26.12 NextGen-O2k: NADH-ModulePDF.jpg » Versions
O2k-Manual
NextGen-O2k: NADH-Module manual		2022-05-17
MiPNet28.09 O2k-Fluo Smart-Module manualPDF.jpg » Versions
O2k-Manual
O2k-Fluo Smart-Module manual		2023-09-25


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