Gnaiger 2021 MitoFit BCA: Difference between revisions
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|title=Gnaiger E (2021) Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.#. [[doi:10.26124/mitofit:2021-000#]] (in preparation) | |title=Gnaiger E (2021) Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.#. [[doi:10.26124/mitofit:2021-000#]] (in preparation) | ||
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|mipnetlab=AT Innsbruck Oroboros | |mipnetlab=AT Innsbruck Oroboros | ||
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ORC'''ID''': [[File:ORCID.png|20px|link=https://orcid.org/0000-0003-3647-5895]] Gnaiger Erich | ORC'''ID''': [[File:ORCID.png|20px|link=https://orcid.org/0000-0003-3647-5895]] Gnaiger Erich | ||
= References = | = References = | ||
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[[File:Template NextGen-O2k.jpg|right|400px|link=NextGen-O2k]] | [[File:Template NextGen-O2k.jpg|right|400px|link=NextGen-O2k]] | ||
:::: Supported by project NextGen-O2k which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 859770. | :::: Supported by project NextGen-O2k which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 859770. | ||
{{Labeling | |||
|area=Respiration, Instruments;methods | |||
|diseases=Aging;senescence | |||
|organism=Human | |||
|tissues=Fibroblast | |||
|preparations=Intact cells | |||
|topics=Coupling efficiency;uncoupling | |||
|couplingstates=LEAK, OXPHOS, ET | |||
|pathways=ROX | |||
|instruments=Oxygraph-2k | |||
|additional=SUIT-003, MitoEAGLEPublication, MitoFit 2021 ace-sce | |||
}} |
Revision as of 11:53, 25 August 2021
Gnaiger 2021 MitoFit BCA
Gnaiger E (2021) Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.#. doi:10.26124/mitofit:2021-000# (in preparation) |
»
Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts
Gnaiger Erich (2021-##-##) MitoFit Preprints
Abstract: Cell respiration reflects mitochondrial fitness and plays a pivotal role in health and disease. Despite the rapidly increasing number of applications of cell respirometry to address current challenges in biomedical research, cross-references are rare between respirometric projects and platforms. Evaluation of accuracy and reproducibility between laboratories requires presentation of results in a common format independent of the applied method. When cell respiration is expressed as oxygen consumption rate in an experimental chamber, normalization is mandatory for comparability of results. Concept-driven normalization and regression analysis are key towards bioenergetic cluster analysis presented as a graphical tool to identify discrete data populations.
In a meta-analysis of human skin fibroblasts, high-resolution respirometry and polarography covering cell senescence and the human age range are compared with multiwell respirometry. The common coupling control protocol measures ROUTINE respiration of living cells followed by sequential titrations of oligomycin, uncoupler, and inhibitors of electron transfer.
Bioenergetic cluster analysis increases the resolution of outliers within and differences between groups. An outlier-skewness index is introduced as a guide towards logarithmic transformation for statistical analysis. Isolinear clusters are separated by variations in the extent of a quantity that correlates with the rate, whereas heterolinear clusters fall on different regression lines. Dispersed clusters are clouds of data separated by a critical threshold value. Bioenergetic cluster analysis provides new insights into mitochondrial respiratory control and a guideline for establishing a quality control paradigm for bioenergetics and databases in mitochondrial physiology. • Keywords: human dermal fibroblasts HDF, living cells ce, cell respiration, coupling control, oxidative phosphorylation OXPHOS, age, senescence, bioenergetic cluster analysis BCA, meta-analysis, normalization, high-resolution respirometry HRR, Oroboros O2k, Seahorse XF Analyzer, outlier-skewness index OSI, regression analysis • Bioblast editor: Gnaiger E • O2k-Network Lab: AT Innsbruck Oroboros
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Keywords
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Support
- Supported by project NextGen-O2k which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 859770.
Labels: MiParea: Respiration, Instruments;methods
Pathology: Aging;senescence
Organism: Human Tissue;cell: Fibroblast Preparation: Intact cells
Regulation: Coupling efficiency;uncoupling Coupling state: LEAK, OXPHOS, ET Pathway: ROX HRR: Oxygraph-2k
SUIT-003, MitoEAGLEPublication, MitoFit 2021 ace-sce
Term | Link to MitoPedia term | Symbol | Unit | Links and comments |
---|---|---|---|---|
catabolic rate of respiration | Cell respiration | JkO2; IkO2 | varies | flux J versus flow I |
catabolic reaction | Cell respiration | k | - | |
cell count | Count | Nce | [x] | see number of cells; countable object s=ce |
cell-count concentration | Concentration | Cce | [x∙L-1] | Cce = Nce∙V-1; count concentration C versus amount concentration c; subscript ce indicates the entity type: concentration of ce. But it does not signal 'per entity', which would be written as 'per cell' Xce. |
cell mass | Body mass | mce | [kg] | mass of cells m versus mass per cell (per single entity cell) MXce |
cell mass, mass per cell | Body mass | MXce | [kg∙x-1] | mass per single cell MXce; upper case M and subscript X signal 'per count', subscript ce signals the entity s=ce; in a context restricted to cells or molecules or a particular organism such as humans, the abbreviated symbol M [kg∙x-1] provides a sufficiently informative signal, particularly in combination with the explicit unit. |
cell-mass concentration in chamber | Concentration | Cmce | [kg∙L-1] | see Cms: Cmce = mce∙V-1; upper case C alone would signal 'count concentration' (CN is more explicit), whereas the signal for 'mass concentration' is in the combination Cm. |
concentration of O2, amount | Concentration | cO2 = nO2∙V-1 | [mol∙L-1] | [O2] |
concentration of s, count | Concentration | Cs = Ns∙V-1 | [x∙L-1] (number concentration Cohen 2008 IUPAC Green Book); the signal for count concentration is given by the upper case C in contrast to c for amount concentration. In both cases, the subscript X indicates the entity type, not to be confused with a number of entities. | |
count of Xs | Count | Ns | [x] | SI; see number of entities Xs |
coupling control | Coupling-control ratio | CCR | - | |
coupling control state | Coupling control state | CCS | - | |
electron transfer pathway | Electron transfer pathway | ET pathway | - | |
electron transfer, state | Electron transfer pathway | ET | - | (State 3u) |
electron transfer system | Electron transfer pathway | ETS | - | (electron transport chain) |
elementary entity | Entity | Xs | [x] | single countable object of sample type s |
ET capacity | ET capacity | E | varies | rate |
flow, for O2 | Flow | IO2 | [mol∙s-1] | system-related extensive quantity |
flux, for O2 | Flux | JO2 | varies | size-specific quantity |
flux control ratio | Flux control ratio | FCR | 1 | background/reference flux |
International System of Units | International System of Units | SI | - | Cohen 2008 IUPAC Green Book |
LEAK state | LEAK respiration | LEAK | - | (compare State 4) |
LEAK respiration | LEAK respiration | L | varies | rate |
living cells | Living cells | ce | - | (intact cells) |
mass concentration of sample s in chamber | Concentration | Cms | [kg∙L-1] | |
mass of sample s in a mixture | Mass | ms | [kg] | SI: mass of pure sample mS |
mass per single object | Body mass | MNX | [kg∙x1] | SI: m(X); compare molar mass M(X) |
mitochondria or mitochondrial | Mitochondria | mt | - | |
mitochondrial concentration | Mitochondrial marker, Concentration | CmtE = mtE∙V-1 | [mtEU∙L-1] | |
mitochondrial content per X | Mitochondrial marker | mtENX | [mtEU∙x-1] | mtENX = mtE∙NX-1 |
mitochondrial elementary marker | Mitochondria | mtE | [mtEU] | quantity of mt-marker |
mitochondrial elementary unit | Mitochondria | mtEU | varies | specific units for mt-marker |
MitoPedia | MitoPedia, MitoPedia: Respiratory states | |||
normalization of rate | Normalization of rate | - | - | |
number of cells | Count | Nce | [x] | total cell count of living cells, Nce = Nvce + Ndce |
oxidative phosphorylation | Oxidative phosphorylation | OXPHOS | - | |
OXPHOS-capacity | OXPHOS-capacity | P | varies | rate |
OXPHOS state | OXPHOS-capacity | OXPHOS | - | OXPHOS-state distinguished from the process OXPHOS (State 3 at kinetically-saturating [ADP] and [Pi]) |
oxygen concentration | Oxygen concentration | cO2 = nO2∙V-1 | [mol∙L-1] | [O2] |
oxygen solubility | Oxygen solubility | SO2 | [µmol·kPa-1] | |
oxygen flux, in reaction r | Oxygen flux | JrO2 | varies | |
quantities, symbols, and units | Quantities, symbols, and units | - | - | An explanation of symbols and unit [x] |
rate in ET state | Electron transfer pathway | E | varies | ET capacity |
rate in LEAK state | LEAK respiration | L | varies | L(Omy) |
rate in ROX state | Residual oxygen consumption | Rox | varies | |
residual oxygen consumption | Residual oxygen consumption | ROX; Rox | - | state ROX; rate Rox |
respiration | Respirometry | JrO2 | varies | rate of reaction r |
respiratory state | MitoPedia: Respiratory states | - | - | |
steay state | Steady state | - | - | |
substrate-uncoupler-inhibitor-titration | Substrate-uncoupler-inhibitor titration | SUIT | - | |
system | System | - | - | |
unit elementary entity | Entity | UX | [x] | single countable object |
uncoupling | Uncoupler titrations | - | - | |
volume of experimental chamber | Volume | V | [L] | liquid volume V including the sample s |