Difference between revisions of "Sample"
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{{MitoPedia | {{MitoPedia | ||
|abbr=s, S | |abbr=s, S | ||
|description=A '''sample''' is one or more parts taken from an ensemble that is studied. A sample is either stored for later quantification or prepared and possibly separated into subsamples, which are enclosed in a system for qualitative or quantitative investigation. A pure sample S is a pure gas, pure liquid or pure solid of a defined elementary [[entity]]-type. Then the system used to investigate sample S contains only entities of entity-type S, and the [[volume]] ''V''<sub>S</sub> [L] and [[mass]] ''m''<sub>S</sub> [kg] of the (sub)sample S are identical to the volume ''V'' and mass ''m'' of the experimental [[system]]. A pure sample S may be mixed with other components to be investigated as a mixture, | |description=A '''sample''' is one or more parts taken from an ensemble that is studied. A sample is either stored for later quantification or prepared and possibly separated into subsamples, which are enclosed in a system for qualitative or quantitative investigation. A pure sample S is a pure gas, pure liquid or pure solid of a defined elementary [[entity]]-type. A pure biological sample is a cell type, tissue, or organism without its solid, liquid or gaseous environment. Then the system used to investigate sample S contains only entities of entity-type S, and the [[volume]] ''V''<sub>S</sub> [L] and [[mass]] ''m''<sub>S</sub> [kg] of the pure (sub)sample S are identical to the volume ''V'' and mass ''m'' of the experimental [[system]]. A pure sample S may be mixed with other components to be investigated as a solution, mixture, or suspension, indicated by the symbol s in contrast to the pure sample S. A sample s is obtained in combination with other components, such that the [[volume]] ''V''<sub>s</sub> [L] and [[mass]] ''m''<sub>s</sub> [kg] of the sample s are larger than the volume ''V''<sub>S</sub> and mass ''m''<sub>S</sub> of the pure sample S. For example, the number of cells ''N''<sub>ce</sub> [Mx] can be counted in a sample s of a cell suspension, whereas the mass ''m''<sub>ce</sub> [mg] of cells requires a pure sample S of cells to be measured on a mass-balance. Clarity of statistical representation is improved, if the symbol ''N'' is used for the number of [[primary sample]]s taken from a study group, and the symbol ''n'' is used for the number of subsamples studied as technical repeats. | ||
|info=[[BEC 2020.1]] | |info=[[BEC 2020.1]] | ||
}} | }} | ||
__TOC__ | __TOC__ | ||
Communicated by [[Gnaiger Erich]] last update 2020- | Communicated by [[Gnaiger Erich]] last update 2020-10-24 | ||
== Sample type, sample and subsample == | == Sample type, sample and subsample == | ||
:::: A sample of a defined '''[[sample type]]''' subjected to a specific sample preparation (see [[MitoPedia: Sample preparations]]) may be, ''e.g.'', a mitochondrial preparation obtained from an organ, cells suspended from a cell culture dish, a tissue biopsy, an organ, an individual organism, or a group of organisms (e.g. a number of nematodes studied collectively in an experimental chamber). | :::: A sample of a defined '''[[sample type]]''' subjected to a specific sample preparation (see [[MitoPedia: Sample preparations]]) may be, ''e.g.'', a mitochondrial preparation obtained from an organ, cells suspended from a cell culture dish, a tissue biopsy, an organ, an individual organism, or a group of organisms (''e.g.'', a number of nematodes studied collectively in an experimental chamber). | ||
::: '''''Example'': Sample and subsample''' | ::: '''''Example'': Sample and subsample''' | ||
:::: A blood '''sample''' or a biopsy taken from an individual organism. The '''[[sample size]]''', ''N'', corresponds to the number of [[replica]], ''e.g.'', ''N'' organisms in a study group (arm). A sample may be processed and split into a number of '''[[subsample]]s''' (''e.g.'', smaller volumes of blood taken from a larger volume of blood) for (i) application of different types of [[assay]], and (ii) a number of [[repetitions]], ''n'', of the same assay, using subsamples of the same sample. | :::: A blood '''sample''' or a biopsy taken from an individual organism. The '''[[sample size]]''', ''N'', corresponds to the number of [[replica]], ''e.g.'', ''N''<sub>org</sub> organisms in a study group (arm). A sample may be processed and split into a number of '''[[subsample]]s''' (''e.g.'', smaller volumes of blood taken from a larger volume of blood) for (i) application of different types of [[assay]], and (ii) a number of [[repetitions]] or technical repeats, ''n'', of the same assay, using subsamples of the same sample. | ||
== ISO 15189:2012 == | == ISO 15189:2012 == | ||
| Line 21: | Line 21: | ||
== Application in [[HRR]] == | == Application in [[HRR]] == | ||
::: The amount of tissue used for high-resolution respirometry strongly depends on the sample preparation: For permeabilized fibers, usually 0. | ::: The amount of tissue used for high-resolution respirometry strongly depends on the sample preparation: For permeabilized fibers, usually 0.7 mg tissue; for many cell types, 1 Mill cells per mL, however for some cell types it can be less. With the [https://www.oroboros.at/index.php/product/o2k-sv-module/ O2k-sV-Module] (included in all [https://www.oroboros.at/index.php/o2k-products/packages/ O2k-packages]), the amount of tissue required can be decreased by a factor of 4. | ||
'''Addition of sample to the respirometer chamber''' | '''Addition of sample to the respirometer chamber''' | ||
:::'''[[Isolated_mitochondria|Isolated mitochondria]] (imt):''' Imt are typically added with a Hamilton syringe. Care should be taken to not exert damaging low | :::'''[[Isolated_mitochondria|Isolated mitochondria]] (imt):''' Imt are typically added with a Hamilton syringe. Care should be taken to not exert damaging low pressure during aspiration of the sample into the syringe or exerting high pressure during injection into the chamber. | ||
:::'''[[Living cells]] (ce)''' are typically added with a pipette. Care should be taken to not exert damaging low pressure during aspiration of the sample into the pipette or exerting high pressure during injection into the chamber. | :::'''[[Living cells]] (ce)''' are typically added with a pipette. Care should be taken to not exert damaging low pressure during aspiration of the sample into the pipette or exerting high pressure during injection into the chamber. | ||
:::'''Very large and/or fragile [[living cells]] (ce):''' Some cell types may be easily damaged when injected with a syringe. For these we recommend: remove the | :::'''Very large and/or fragile [[living cells]] (ce):''' Some cell types may be easily damaged when injected with a syringe. For these we recommend: remove the stopper, replace a defined volume of the respiration medium with cell suspension, close the chamber again. Sometimes (i.e. [[microalgal]] cells) the whole volume of the chamber (2 mL) is replaced by the cells suspension with the cell concentration adjusted to the desired value. ''Further details'': »[[Cell count and normalization in HRR]]. | ||
:::'''[[PBMC]]s and [[Platelet]]s''': We recommend adding for PBMC 2·10<sup>6</sup> x/mL; for PLT 200·10<sup>6</sup> x/mL. | :::'''[[PBMC]]s and [[Platelet]]s''': We recommend adding for PBMC 2·10<sup>6</sup> x/mL; for PLT 200·10<sup>6</sup> x/mL. | ||
:::'''[[Permeabilized tissue]] (pti)''': For permeabilized tissue, remove the Stopper, add the permeabilized tissue into the O2k-chamber, close the chamber again. | :::'''[[Permeabilized tissue]] (pti)''': For permeabilized tissue, remove the Stopper, add the permeabilized tissue into the O2k-chamber, close the chamber again. | ||
Revision as of 16:40, 24 October 2020
- high-resolution terminology - matching measurements at high-resolution
Sample
Description
A sample is one or more parts taken from an ensemble that is studied. A sample is either stored for later quantification or prepared and possibly separated into subsamples, which are enclosed in a system for qualitative or quantitative investigation. A pure sample S is a pure gas, pure liquid or pure solid of a defined elementary entity-type. A pure biological sample is a cell type, tissue, or organism without its solid, liquid or gaseous environment. Then the system used to investigate sample S contains only entities of entity-type S, and the volume VS [L] and mass mS [kg] of the pure (sub)sample S are identical to the volume V and mass m of the experimental system. A pure sample S may be mixed with other components to be investigated as a solution, mixture, or suspension, indicated by the symbol s in contrast to the pure sample S. A sample s is obtained in combination with other components, such that the volume Vs [L] and mass ms [kg] of the sample s are larger than the volume VS and mass mS of the pure sample S. For example, the number of cells Nce [Mx] can be counted in a sample s of a cell suspension, whereas the mass mce [mg] of cells requires a pure sample S of cells to be measured on a mass-balance. Clarity of statistical representation is improved, if the symbol N is used for the number of primary samples taken from a study group, and the symbol n is used for the number of subsamples studied as technical repeats.
Abbreviation: s, S
Reference: BEC 2020.1
Communicated by Gnaiger Erich last update 2020-10-24
Sample type, sample and subsample
- A sample of a defined sample type subjected to a specific sample preparation (see MitoPedia: Sample preparations) may be, e.g., a mitochondrial preparation obtained from an organ, cells suspended from a cell culture dish, a tissue biopsy, an organ, an individual organism, or a group of organisms (e.g., a number of nematodes studied collectively in an experimental chamber).
- Example: Sample and subsample
- A blood sample or a biopsy taken from an individual organism. The sample size, N, corresponds to the number of replica, e.g., Norg organisms in a study group (arm). A sample may be processed and split into a number of subsamples (e.g., smaller volumes of blood taken from a larger volume of blood) for (i) application of different types of assay, and (ii) a number of repetitions or technical repeats, n, of the same assay, using subsamples of the same sample.
ISO 15189:2012
- A sample is one or more parts taken from a system and intended to provide information on the system, often to serve as a basis for evaluation of the system (diagnosis) or for a decision on intervention (therapy, production process) (ISO 15189:2012 Medical laboratories — Particular requirements for quality and competence).
- The term 'system' is used in this context with reference to a 'study system', distinguished from the 'system' in the context of thermodynamics (open, closed, isolated systems; instrumental chamber).
- Compare: Primary sample.
Application in HRR
- The amount of tissue used for high-resolution respirometry strongly depends on the sample preparation: For permeabilized fibers, usually 0.7 mg tissue; for many cell types, 1 Mill cells per mL, however for some cell types it can be less. With the O2k-sV-Module (included in all O2k-packages), the amount of tissue required can be decreased by a factor of 4.
Addition of sample to the respirometer chamber
- Isolated mitochondria (imt): Imt are typically added with a Hamilton syringe. Care should be taken to not exert damaging low pressure during aspiration of the sample into the syringe or exerting high pressure during injection into the chamber.
- Living cells (ce) are typically added with a pipette. Care should be taken to not exert damaging low pressure during aspiration of the sample into the pipette or exerting high pressure during injection into the chamber.
- Very large and/or fragile living cells (ce): Some cell types may be easily damaged when injected with a syringe. For these we recommend: remove the stopper, replace a defined volume of the respiration medium with cell suspension, close the chamber again. Sometimes (i.e. microalgal cells) the whole volume of the chamber (2 mL) is replaced by the cells suspension with the cell concentration adjusted to the desired value. Further details: »Cell count and normalization in HRR.
- PBMCs and Platelets: We recommend adding for PBMC 2·106 x/mL; for PLT 200·106 x/mL.
- Permeabilized tissue (pti): For permeabilized tissue, remove the Stopper, add the permeabilized tissue into the O2k-chamber, close the chamber again.
- Permeabilized muscle fibers (pfi): Remove the Stopper, add the permeabilized fibers into the O2k-chamber, close the chamber again.
- Permeabilized cells (pce): If the cells can be loaded into a syringe, they may be injected with a Hamilton syringe. If the cells are rather fragile, remove the Stopper, replace a defined volume of the respiration medium with cell suspension, close the chamber again.
References
| Bioblast link | Reference | Year |
|---|---|---|
| Gnaiger 2020 BEC MitoPathways | 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:2020-0002 | 2020 |
| BEC 2020.1 doi10.26124bec2020-0001.v1 | Gnaiger E et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. https://doi.org/10.26124/bec:2020-0001.v1 | 2020 |
MitoPedia concepts: "MitoFit Quality Control System" is not in the list (MiP concept, Respiratory state, Respiratory control ratio, SUIT concept, SUIT protocol, SUIT A, SUIT B, SUIT C, SUIT state, Recommended, ...) of allowed values for the "MitoPedia concept" property.
MitoFit Quality Control System"MitoFit Quality Control System" is not in the list (Enzyme, Medium, Inhibitor, Substrate and metabolite, Uncoupler, Sample preparation, Permeabilization agent, EAGLE, MitoGlobal Organizations, MitoGlobal Centres, ...) of allowed values for the "MitoPedia topic" property.
MitoPedia topics:
Sample preparation
