Difference between revisions of "SUIT protocol library"

Revision as of 09:05, 15 May 2016

high-resolution terminology - matching measurements at high-resolution

SUIT protocol library

Description

The Substrate-uncoupler-inhibitor titration (SUIT) protocol library contains classes of SUIT protocols with coupling and substrate control defined for mitochondrial preparations.

Abbreviation: SUITs

Reference: MitoPedia: SUIT

MitoPedia concepts: MiP concept, SUIT concept

This page is in preparation (intern wiki: [1])

Strategy

Select a pathway control state.
Select a control pattern.
Define substrates for each pathway state.
Define coupling states.

Definition of states

Experimental conditions

Temp
O2
Medium
Oxygen level
ADP kinetics
Substrate kinetics

O2k configuration

Amp: Amplex Red, TMRM, Ca Green, ...
Pot
Spectrophotometry

Define substrates

Substrate control states are defined for each pathway control state (CI-linked, CII-linked, CI&II-linked) is defined by a specific substrate or substrate combination. These substrates may be added in a single step, or in multiple steps for analyis of the effect of different substrate combinations within a pathway control state.

CI: PM, GM, PGM, M, ..
CII: S(Rot), S, SM, ..
CI&II: PS, GS, PMS, GMS, PGMS, ..
CIV: AsTM
FAO: Oct, Pal, ...
CGpDH:
c

Define coupling states

The coupling control states require a complementary definition of an ETS-competent substrate state.

L, P, E (Uncouplers, U: FCCP, CCCP, DNP)

Coupling states:

Define residual oxygen consumption

ROX: Rot&Ama, Rot&Mna&Ama, Myx, Cn, Az, ..

Categories of SUIT protocols

» Categories of SUIT protocols

» Talk:SUIT protocol library

SUIT protocol patterns

» SUIT protocol pattern

SUIT library

Work in progress

» MitoPedia: SUIT

CI + CI&II + CII diametral

Respiratory states: CI_L -> CI_P -> CI&II_P -> CI&II_E -> CII_E -> ROX

GM+D+S+U+Rot Innsbruck-Copenhagen protocol: GM+D+c+S+U+Rot ::Cyt c: added after ADP; cyt c added after S; ADP conc: _ _; ROX: Ama (Boushel 2007 Diabetologia)

PMG+D+S+U+Rot Brain protocol: PMG+D+c+S+U+Rot::ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the OXPHOS state (CI&II) is saturating (Sumbalova 2011 Abstract Bordeaux); ROX: Mna&Ama; Myx

CI + CI + CI&II + CII diamteral

GM+D+P+S+U+Rot Innsbruck-Liege protocol 1: GM+D+c+P+S+U+Rot::Cytochrome c: early addition of c ensures comparability of all states in case of any c effect.

PM+D+G+S+U+Rot Innsbruck-Liege protocol 2: PM+D+c+G+S+U+Rot

FAO + CI + CI&II + CII diametral

Respiratory states: FAO_L -> FAO_P -> CI&FAO_P -> CI&II&FAO_P -> CI&II&FAO_E -> CII_E -> ROX

OctM+D+G+S+U+Rot Innsbruck training protocol: OctM+D+G+c+S+U+Rot::Pesta 2012 Methods Mol Biol, Pesta 2011 Am J Physiol Regul Integr Comp Physiol

Respiratory states: FAO_L -> FAO_P -> CI&FAO_P -> CI&II&FAO_P -> CII_P -> CII_L -> CII_E -> ROX

OctM+D+G+S+Rot+Omy+U Greenland-Monte Rosa protocol: OctM+D+G+S+Rot+Omy+U+c::Cyt c: added after U. The absence of a significant c-effect shows the integrity of the outer mitochondrial membrane after fibre preparation and also shows the preservation of integrity over a 90-100 min incubation in the O2k (MiR05); Oxygen: oxygen limitation of flux was preventd by maintaining oxygen levels in the respirometer above air saturation (Pesta 2012 Methods Mol Biol); ROX: Mna+Ama

References and notes

@@ Line 2: / Line 2: @@
 |abbr=SUITs
 |description=The '''Substrate-uncoupler-inhibitor titration (SUIT) protocol library''' contains classes of [[SUIT protocols]] with coupling and substrate control defined for [[mitochondrial preparations]].
+|info=[[MitoPedia: SUIT]]
 }}
 {{MitoPedia concepts
-|mitopedia concept=MitoFit Quality Control System
+|mitopedia concept=MiP concept, SUIT concept
 }}
 {{MitoPedia methods}}
-{{MitoPedia O2k and high-resolution respirometry
+{{MitoPedia O2k and high-resolution respirometry}}
-|mitopedia O2k and high-resolution respirometry=SUIT protocol
-}}
 {{MitoPedia topics}}
 '''''This page is in preparation''''' (intern wiki: [http://www.intern.oroboros.at/index.php/Protocol_development])
@@ Line 16: / Line 15: @@
 == Strategy ==
-# Select a [[#Pathway control states |pathway control state]].
+:::# Select a [[#Pathway control states |pathway control state]].
-# Select a [[#Control patterns |control pattern]].
+:::# Select a [[#Control patterns |control pattern]].
-# [[#Define substrates |Define substrates]] for each pathway state.
+:::# [[#Define substrates |Define substrates]] for each pathway state.
-# [[#Define coupling states |Define coupling states]].
+:::# [[#Define coupling states |Define coupling states]].
@@ Line 25: / Line 24: @@
 === Experimental conditions ===
-* Temp
+:::* Temp
-* O2
+:::* O2
-* Medium
+:::* Medium
-* Oxygen level
+:::* Oxygen level
-* ADP kinetics
+:::* ADP kinetics
-* Substrate kinetics
+:::* Substrate kinetics
 === O2k configuration ===
-* Amp: Amplex Red, TMRM, Ca Green, ...
+:::* Amp: Amplex Red, TMRM, Ca Green, ...
-* Pot
+:::* Pot
-* Spectrophotometry
+:::* Spectrophotometry
 === Define substrates ===
-[[Substrate control state]]s are defined for each pathway control state ([[Complex I-linked substrate state |CI-linked]], [[Complex II-linked substrate state |CII-linked]], [[Complex I&II-linked substrate state |CI<small>&</small>II-linked]]) is defined by a specific substrate or substrate combination. These substrates may be added in a single step, or in multiple steps for analyis of the effect of different substrate combinations within a pathway control state.
+:::: [[Substrate control state]]s are defined for each pathway control state ([[Complex I-linked substrate state |CI-linked]], [[Complex II-linked substrate state |CII-linked]], [[Complex I&II-linked substrate state |CI<small>&</small>II-linked]]) is defined by a specific substrate or substrate combination. These substrates may be added in a single step, or in multiple steps for analyis of the effect of different substrate combinations within a pathway control state.
-* CI: PM, GM, PGM, M, ..
-* CII: S(Rot), S, SM, ..
+:::* CI: PM, GM, PGM, M, ..
-* CI<small>&</small>II: PS, GS, PMS, GMS, PGMS, ..
+:::* CII: S(Rot), S, SM, ..
-* CIV: AsTM
+:::* CI<small>&</small>II: PS, GS, PMS, GMS, PGMS, ..
-* FAO: Oct, Pal, ...
+:::* CIV: AsTM
-* CGpDH:
+:::* FAO: Oct, Pal, ...
-* c
+:::* CGpDH:
+:::* c
 === Define coupling states ===
-The [[coupling control state]]s require a complementary definition of an [[ETS-competent substrate state]].
+:::: The [[coupling control state]]s require a complementary definition of an [[ETS-competent substrate state]].
-* ''L'', ''P'', ''E'' ([[Uncoupler]]s, U: FCCP, CCCP, DNP)
+:::* ''L'', ''P'', ''E'' ([[Uncoupler]]s, U: FCCP, CCCP, DNP)
 Coupling states: [[Image:L.jpg|link=LEAK respiration|LEAK]] [[Image:P.jpg|link=OXPHOS capacity|OXPHOS]] [[Image:E.jpg|link=ETS capacity|ETS]]
 === Define residual oxygen consumption ===
-* ROX: Rot&Ama, Rot&Mna&Ama, Myx, Cn, Az, ..
+:::* ROX: Rot&Ama, Rot&Mna&Ama, Myx, Cn, Az, ..
 [[Image:ROX.jpg|link=Residual oxygen consumption|ROX]]
 == Categories of SUIT protocols  ==
-:» [[Categories of SUIT protocols]]
+:::» [[Categories of SUIT protocols]]
-:» [[Talk:SUIT protocol library]]
+:::» [[Talk:SUIT protocol library]]
 == SUIT protocol patterns ==
-:» [[SUIT protocol pattern]]
+:::» [[SUIT protocol pattern]]
 == SUIT library ==
   ''Work in progress''
+:::» [[MitoPedia: SUIT]]
 === CI + CI<small>&</small>II + CII diametral ===
-Respiratory states: CI<sub>''L''</sub> -> CI<sub>''P''</sub> -> CI<small>&</small>II<sub>''P''</sub> -> CI<small>&</small>II<sub>''E''</sub> -> CII<sub>''E''</sub> -> ROX
+:::: Respiratory states: CI<sub>''L''</sub> -> CI<sub>''P''</sub> -> CI<small>&</small>II<sub>''P''</sub> -> CI<small>&</small>II<sub>''E''</sub> -> CII<sub>''E''</sub> -> ROX
-* '''GM+D+S+U+Rot''' ''Innsbruck-Copenhagen protocol'': GM+D+c+S+U+Rot ::Cyt c: added after ADP; cyt c added after S; ADP conc: _ _; ROX: Ama ([[Boushel 2007 Diabetologia]])
+::::* '''GM+D+S+U+Rot''' ''Innsbruck-Copenhagen protocol'': GM+D+c+S+U+Rot ::Cyt c: added after ADP; cyt c added after S; ADP conc: _ _; ROX: Ama ([[Boushel 2007 Diabetologia]])
-* '''PMG+D+S+U+Rot''' ''Brain protocol'': PMG+D+c+S+U+Rot::ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the [[OXPHOS]] state (CI<small>&</small>II) is saturating ([[Sumbalova 2011 Abstract Bordeaux]]); [[ROX]]: Mna&Ama; Myx
+::::* '''PMG+D+S+U+Rot''' ''Brain protocol'': PMG+D+c+S+U+Rot::ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the [[OXPHOS]] state (CI<small>&</small>II) is saturating ([[Sumbalova 2011 Abstract Bordeaux]]); [[ROX]]: Mna&Ama; Myx
 === CI + CI + CI<small>&</small>II + CII diamteral ===
-* '''GM+D+P+S+U+Rot''' ''Innsbruck-Liege protocol 1'': GM+D+c+P+S+U+Rot::[[Cytochrome c]]: early addition of ''c'' ensures comparability of all states in case of any ''c'' effect.
+::::* '''GM+D+P+S+U+Rot''' ''Innsbruck-Liege protocol 1'': GM+D+c+P+S+U+Rot::[[Cytochrome c]]: early addition of ''c'' ensures comparability of all states in case of any ''c'' effect.
-* '''PM+D+G+S+U+Rot''' ''Innsbruck-Liege protocol 2'': PM+D+c+G+S+U+Rot
+::::* '''PM+D+G+S+U+Rot''' ''Innsbruck-Liege protocol 2'': PM+D+c+G+S+U+Rot
 === FAO + CI + CI<small>&</small>II + CII diametral ===
-Respiratory states: FAO<sub>''L''</sub> -> FAO<sub>''P''</sub> -> CI<small>&</small>FAO<sub>''P''</sub> -> CI<small>&</small>II<small>&</small>FAO<sub>''P''</sub> -> CI<small>&</small>II<small>&</small>FAO<sub>''E''</sub> -> CII<sub>''E''</sub> -> ROX
+:::: Respiratory states: FAO<sub>''L''</sub> -> FAO<sub>''P''</sub> -> CI<small>&</small>FAO<sub>''P''</sub> -> CI<small>&</small>II<small>&</small>FAO<sub>''P''</sub> -> CI<small>&</small>II<small>&</small>FAO<sub>''E''</sub> -> CII<sub>''E''</sub> -> ROX
-* '''OctM+D+G+S+U+Rot''' ''Innsbruck training protocol'': OctM+D+G+c+S+U+Rot::[[Pesta 2012 Methods Mol Biol]], [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]]
+::::* '''OctM+D+G+S+U+Rot''' ''Innsbruck training protocol'': OctM+D+G+c+S+U+Rot::[[Pesta 2012 Methods Mol Biol]], [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]]
-Respiratory states: FAO<sub>''L''</sub> -> FAO<sub>''P''</sub> -> CI<small>&</small>FAO<sub>''P''</sub> -> CI<small>&</small>II<small>&</small>FAO<sub>''P''</sub> -> CII<sub>''P''</sub> -> CII<sub>''L''</sub> -> CII<sub>''E''</sub> -> ROX
+:::: Respiratory states: FAO<sub>''L''</sub> -> FAO<sub>''P''</sub> -> CI<small>&</small>FAO<sub>''P''</sub> -> CI<small>&</small>II<small>&</small>FAO<sub>''P''</sub> -> CII<sub>''P''</sub> -> CII<sub>''L''</sub> -> CII<sub>''E''</sub> -> ROX
-* '''OctM+D+G+S+Rot+Omy+U''' ''Greenland-Monte Rosa protocol'': OctM+D+G+S+Rot+Omy+U+c::[[Cytochrome c|Cyt ''c'']]: added after U. The absence of a significant ''c''-effect shows the integrity of the outer mitochondrial membrane after fibre preparation and also shows the preservation of integrity over a 90-100 min incubation in the O2k ([[MiR05]]); Oxygen: oxygen limitation of flux was preventd by maintaining oxygen levels in the respirometer above air saturation ([[Pesta 2012 Methods Mol Biol]]); [[ROX]]: Mna+Ama
+::::* '''OctM+D+G+S+Rot+Omy+U''' ''Greenland-Monte Rosa protocol'': OctM+D+G+S+Rot+Omy+U+c::[[Cytochrome c|Cyt ''c'']]: added after U. The absence of a significant ''c''-effect shows the integrity of the outer mitochondrial membrane after fibre preparation and also shows the preservation of integrity over a 90-100 min incubation in the O2k ([[MiR05]]); Oxygen: oxygen limitation of flux was preventd by maintaining oxygen levels in the respirometer above air saturation ([[Pesta 2012 Methods Mol Biol]]); [[ROX]]: Mna+Ama
 == References and notes ==
-* [[MitoPedia: Respiratory states]]
+:::* [[MitoPedia: Respiratory states]]
-* [[MitoPedia: Terms and abbreviations]]
+:::* [[MitoPedia: Terms and abbreviations]]
-* [[Gnaiger_2014_MitoPathways]]
+::::* [[Gnaiger_2014_MitoPathways]]
-* [[Gnaiger_2009_Int J Biochem Cell Biol]]
+::::* [[Gnaiger_2009_Int J Biochem Cell Biol]]
-* [[Pesta 2012 Methods Mol Biol]]
+::::* [[Pesta 2012 Methods Mol Biol]]
-* [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]]
+::::* [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]]
-* [[Sumbalova 2011 Abstract Bordeaux]]
+::::* [[Sumbalova 2011 Abstract Bordeaux]]