SUIT protocol library: Difference between revisions

From Bioblast
No edit summary
No edit summary
Line 8: Line 8:
== List of SUIT protocol D-numbers ==
== List of SUIT protocol D-numbers ==


:::# [[D01_1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd]]
== Library of SUIT protocols: SUIT A ==
:::# [[D02_1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd]]
{{#ask:[[MitoPedia concept::SUIT A]]
:::# [[D03_ce1;1Dig;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd]]
| ?Has SUIT number=SUIT technical name
:::# [[D04_ce1;1Dig;1PM;2D;2c;3U;4G;5S;6Rot;7Gp;8Ama;9AsTm;10Azd]]
| mainlabel=SUIT code
:::# [[D05_1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd]]
| format=broadtable
:::# [[D06_1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd]]
| limit=5000
:::# [[D07_ce1;1Dig;1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd]]
| order=ascending
:::#
}}
:::# [[D09_ce1;ce2Omy;ce3U;ce4Rot;ce5Ama]]
:::# [[D10_1PM;2D;3U;4S;5Rot]]
:::# [[D11_1OctM;2D;3P;4S;5U;6Rot]]
:::# [[D12_ce1;ce2P;ce3Omy;ce4U;ce5Rot;ce6Ama]]
:::# [[D13_ce1;ce2P;ce3Omy;ce4U;ce5Glc;ce6M;ce7Rot;ce8S;1Dig;1U;1c;2Ama;3AsTm;4Azd]]
:::# [[D14_1PM;2D;2c;3G;4S;4D;5U;6Rot;7Ama;8AsTm;9Azd]]
:::# [[SUIT-9 O2 mt D15]]
:::# [[SUIT-9 O2 pce D16]]
:::# [[D17_ce1;ce2P;ce3Omy;ce4U;ce5Rot;ce6S;ce7Ama]]
:::# [[SUIT-9 AmR mt D18]]
:::# [[SUIT-9 AmR pce D19]]
 
 




Revision as of 12:36, 22 August 2018


high-resolution terminology - matching measurements at high-resolution


SUIT protocol library

Description

[[Description::The Substrate-uncoupler-inhibitor titration (SUIT) protocol library contains a sequential list of SUIT protocols (D01, D02, ..) with links to the specific SUIT pages. Classes of SUIT protocols are explained with coupling and substrate control defined for mitochondrial preparations.]]

Abbreviation: SUITs

Reference: [[Info::MitoPedia: SUIT]]

List of SUIT protocol D-numbers

Library of SUIT protocols: SUIT A

SUIT codeSUIT technical name
SUIT-001 O2 ce-pce D003D003_ce1;1Dig;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd
SUIT-001 O2 ce-pce D004D004_ce1;1Dig;1PM;2D;2c;3U;4G;5S;(6Oct);7Rot;8Gp;9Ama;10AsTm;11Azd
SUIT-001 O2 mt D001D001_mt;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd
SUIT-001 O2 pfi D002D002_pfi;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd
SUIT-002 O2 ce-pce D007D007_ce1;1Dig;1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd
SUIT-002 O2 ce-pce D007aD007a_ce1;1Dig;1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd
SUIT-002 O2 mt D005D005_mt;1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd
SUIT-002 O2 pfi D006D006_pfi;1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd
SUIT-003 AmR ce D058D058_ce1;ce1SOD;ce1HRP;ce1AmR;ce2Omy;ce3U;ce4Rot;ce5Ama
SUIT-003 O2 ce D009D009_ce1;ce2Omy;ce3U;ce4Ama
SUIT-003 O2 ce D037D037_ce1;ce1Glc;(ce2Omy);ce3U;ce4Ama
SUIT-003 O2 ce D038D038_ce1;(ce2Omy);ce3U;ce3Glc;ce3'U;ce4Ama
SUIT-003 O2 ce D039D039_ce1;(ce2Omy);ce3U;ce4Rot;ce5Ama
SUIT-003 O2 ce D050D050_ce1;ce1Snv;(ce2Omy);ce3U;ce4Rot;ce5Ama
SUIT-003 O2 ce-pce D020D020_ce1;ce1P;ce2Omy;ce3U;ce4Rot;ce5S;1Dig;1c;2Ama;3AsTm;4Azd
SUIT-003 pH ce D067D067_ce1;ce1Glc;ce2Omy;ce3DG;ce4Ama
SUIT-004 O2 pfi D010D010_1PM;2D;2c;3U;4S;5Rot;6Ama;7AsTm;8Azd
SUIT-005 O2 pfi D011D011_1OctM;2D;2c;3P;4S;5U;6Rot;7Ama;8AsTm;9Azd
SUIT-006 AmR mt D048D048_1PM;2D;3Omy;4U;5Ama
SUIT-006 Fluo mt D034D034_1PM;2D;3Omy;4U;5Ama
SUIT-006 MgG ce-pce D085D085_ce1;1Dig;1PM;2D;3Cat;4U;5Ama
SUIT-006 MgG mt D055D055_1PM;2D;3Cat;4U;5Ama
SUIT-006 O2 ce-pce D029D029_ce1;1Dig;1PM;2D;2c;3Omy;4U;5Ama
SUIT-006 O2 mt D022D022_1SRot;2D;2c;(3Omy);4U;5Ama
SUIT-006 O2 mt D047D047_1PM;2D;2c;3Omy;4U;5Ama
SUIT-006 Q ce-pce D073D073_ce1;1Dig;1Q2;1Rot;1S;2D;(3Omy);4U;5Anox;6Ama.png
SUIT-006 Q mt D071D071_mt;1Q2;1Rot;1S;2D;(3Omy);4U;5Anox;6Ama.png
SUIT-007 O2 ce-pce D030D030_ce1;1Dig;1G;2D;2c;3M;4U;5Ama
SUIT-008 O2 ce-pce D025D025_ce1;1Dig;1PM;2D;2c;3G;4S;5U;6Rot;7Ama;8AsTm;9Azd
SUIT-008 O2 mt D026D026_1PM;2D;2c;3G;4S;4D;5U;6Rot;7Ama;8AsTm;9Azd
SUIT-008 O2 pfi D014D014_1PM;2D;2c;3G;4S;4D;5U;6Rot;7Ama;8AsTm;9Azd
SUIT-010 O2 ce-pce D008D008_ce1;ce2Rot;ce3S;ce4D;1Dig;1c
SUIT-011 O2 pfi D024D024_1GM;2D;2c;3S;4U;5Rot;6Ama
SUIT-012 O2 ce-pce D052D052_ce1;1Dig;1PM;2D;2c;3G;4U;5Ama
SUIT-012 O2 mt D027D027_1PM;2D;2c;3G;4U;5Ama
SUIT-013 AmR ce D023D023_ce1
SUIT-014 O2 pfi D042D042_1GM;2D;2c;3P;4S;5U;6Rot;7Ama
SUIT-015 O2 pti D043D043_1OctM;2D;2c;3G;4P;5S;6U;7Rot;8Ama
SUIT-016 O2 pfi D044D044_1OctM;2D;3G;4S;5Rot;6Omy;7U;8Ama
SUIT-017 O2 mt D046D046_1OctM;2D;2c;3G;3c;4S;5U;6Rot;7Ama
SUIT-017 O2 pfi D049D049_1OctM;2D;2c;3G;4S;5U;6Rot;7Ama
SUIT-018 AmR ce-pce D068D068_ce1;1Dig;1GMS;2D;3Ama
SUIT-018 AmR mt D031D031_mt;1GMS;2D;3Ama
SUIT-018 AmR mt D040D040_mt;1GMS;2D;3Ama
SUIT-018 AmR mt D041D041_mt;1GMS;2D;3Ama
SUIT-019 O2 pfi D045D045_1PalM;2D;2c;3Oct;4P;5G;6U;7S;8Rot;9Ama
SUIT-020 Fluo mt D033D033_1PM;2D;3G;4S;5Rot;6Omy;7U;8Ama
SUIT-020 O2 mt D032D032_1PM;2D;2c;3G;4S;5Rot;6Omy;7U;8Ama
SUIT-021 Fluo mt D036D036_1GM;2D;3S;4Rot;5Omy;6U;7Ama
SUIT-021 O2 mt D035D035_1GM;2D;2c;3S;4Rot;5Omy;6U;7Ama
SUIT-022 O2 ce D051D051_ce1;ce2KCN;ce3SHAM
SUIT-023 O2 ce D053D053_ce1;ce2SHAM;ce3KCN
SUIT-024 O2 ce-pce D056D056_ce1;1Dig;1PM;2T;2D;3Omy;4Ama
SUIT-025 O2 mt D057D057_1D;2M;3Oct;3c;4M;5P;6G;7S;8Rot;9Ama
SUIT-026 AmR ce-pce D087D087_ce1;1Dig;1S;2Rot;3D;4Ama
SUIT-026 AmR mt D064D064_1S;2Rot;3D;4Ama
SUIT-026 AmR mt D077D077_1S;2Rot;3D;4Ama
SUIT-027 O2 ce-pce D065D065_ce1;1Dig;1M;2D;3M;4P;5G
SUIT-029 O2 mt D066D066_mt;1PM;2T;2D;2c;3Omy;4U;5G;6S;6U;7Rot;8Ama
SUIT-031 O2 ce-pce D079D079_ce1;1Dig;1PM;2D;2c;3S;4Rot;5U;6Ama
SUIT-031 O2 mt D075D075_1mt;1PM;2D;2c;3S;4Rot;5U;6Ama
SUIT-031 Q ce-pce D074D074_ce1;1Dig;1Q2;1PM;2D;3S;4Rot;5U;6Anoxia;7Ama
SUIT-031 Q mt D072D072_mt;1Q2;1PM;2D;3S;4Rot;5U;6Anox;7Ama


Strategy

  1. Define substrates and inhibitors for each pathway state.
  2. 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 pathway states

Pathway control states are defined for many substrate-inhibitor combinations in SUIT protocols, particularly: (N-pathway control state, S-pathway control state, NS-pathway control state). Titrations may performed in a single step, or in multiple steps for sequential analyis of different pathway control states.
  • N: PM, GM, PGM, M, ..
  • S: S(Rot), S, SM, ..
  • NS: PS, GS, PMS, GMS, PGMS, ..
  • CIV: AsTM
  • F: Oct, Pal, ...
  • Gp


Define coupling states

The coupling control states require a complementary definition of an ET-pathway competent state.

Coupling states: LEAK OXPHOS ET-capacity


Define residual oxygen consumption

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

ROX


Categories of SUIT protocols

» Categories of SUIT protocols
» Talk:SUIT protocol library

SUIT protocol patterns

» SUIT protocol pattern


Examples of SUIT protocols

N; NS; S diametral

Old nomenclature: CI + CI&II + CII diametral
Respiratory states: NL -> NP -> NSP -> NSE -> SE -> 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: PGM;D;c;S;U;Rot::ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the NS-OXPHOS state (NSP) is saturating (Sumbalova 2011 Abstract Bordeaux); ROX: Mna&Ama; Myx


N; N; NS; S diamteral

Old nomenclature: 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


F; FN; FNS; S diametral

Old nomenclature: FAO + CI + CI&II + CII diametral
Respiratory states: FL -> FP -> FNP -> FNSP -> FNSE -> SE -> ROX


Respiratory states: FL -> FP -> FNP -> FNSP -> SP -> SL -> SE -> 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


MitoPedia concepts: MiP concept, SUIT concept 






Retrieved from "https://wiki.oroboros.at/index.php?title=SUIT_protocol_library&oldid=161363"
Cookies help us deliver our services. By using our services, you agree to our use of cookies.
More information
Powered by MediaWiki
Powered by Semantic MediaWiki