WG1 MitoEAGLE protocols, terminology, documentation: Difference between revisions
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:::: '''Standard operating procedures and user requirement document: Protocols, terminology, documentation''' | :::: '''Standard operating procedures and user requirement document: Protocols, terminology, documentation''' | ||
</big></big></big> | </big></big></big> | ||
::::» [[ | ::::» [[MitoEAGLE protocols, terminology, documentation |WG1 Project application]] | ||
[[File:MITOEAGLE Working groups.jpg|right|400px|MitoEAGLE Working Groups]] | [[File:MITOEAGLE Working groups.jpg|right|400px|MitoEAGLE Working Groups]] | ||
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::::[[ | ::::[[File:Vendelin Marko.jpg|left|90px]] | ||
:::::: '''[[ | :::::: '''[[Vendelin M|Marko Vendelin]]''', Dr. - [mailto:markov@sysbio.ioc.ee markov@sysbio.ioc.ee] | ||
<br> | <br> | ||
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== WG Co-Leader == | == WG Co-Leader == | ||
::::[[File: | ::::[[File:Pesta d.jpg|left|90px]] | ||
::::: '''[[ | ::::: '''[[Pesta D|Dominik Pesta]]''', Mag. Dr. - [Dominik.Pesta@DDZ.uni-duesseldorf.de Dominik.Pesta@DDZ.uni-duesseldorf.de] | ||
<br> | <br> | ||
<br> | <br> | ||
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==Participants and discussion== | ==Participants and discussion== | ||
:::: » [[Talk: | :::: » [[Talk:MitoEAGLE protocols, terminology, documentation|Talk:WG1 MitoEAGLE protocols, terminology, documentation]] | ||
= Task groups = | = Task groups = | ||
:: ''TG leaders: suggestions discussed at the [[MitoFit Science Camp 2016 Kuehtai AT]], and updated according to the [[ | :: ''TG leaders: suggestions discussed at the [[MitoFit Science Camp 2016 Kuehtai AT]], and updated according to the [[MitoEAGLE_MC_Meeting_2016_Brussels_BE]].'' | ||
:: ''TG participants: please send us an '''Email to join: [email protected]''' '' | :: ''TG participants: please send us an '''Email to join: [email protected]''' '' | ||
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=== Task group 1.1 === | === Task group 1.1 === | ||
:::: Coupling states and coupling control ratios: consensus statements''' | :::: Coupling states and coupling control ratios: consensus statements''' | ||
:::: ''TG leaders:'' | :::: ''TG leaders:'' [[Gnaiger Erich]] AT / [[Hoppel Charles L]] US | ||
::::» [[ | ::::» Gnaiger E, Aasander Frostner E, Abdul Karim N, Abumrad NA, Acuna-Castroviejo D, Adiele RC et al (2019) Mitochondrial respiratory states and rates. MitoFit Preprint Arch doi:10.26124/mitofit:190001. - [[Gnaiger 2019 MitoFit Preprint Arch |»Bioblast link«]] | ||
=== Task group 1.2 === | === Task group 1.2 === | ||
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::::» [[MitoPedia: Media for respirometry]] | ::::» [[MitoPedia: Media for respirometry]] | ||
::::» [[MitoPedia: Substrates and metabolites]] | ::::» [[MitoPedia: Substrates and metabolites]] | ||
::::» [[MiPNet21.06 SUIT | ::::» [[MiPNet21.06 SUIT RP]] | ||
::: '''References''' | ::: '''References''' | ||
::::# Gnaiger E (2017) Quality first: a paradigm shift in mt-respiratory control towards global connection. Abstract MitoEAGLE Barcelona 2017. [[Gnaiger 2017 Abstract MITOEAGLE Barcelona |»Bioblast link«]] | ::::# Doerrier C, Garcia-Souza LF, Krumschnabel G, Wohlfarter Y, Mészáros AT, Gnaiger E (2018) High-Resolution FluoRespirometry and OXPHOS protocols for human cells, permeabilized fibers from small biopsies of muscle, and isolated mitochondria. Methods Mol Biol 1782:31-70. - [[Doerrier 2018 Methods Mol Biol |»Bioblast link«]] | ||
::::# Gnaiger E (2017) Quality first: a paradigm shift in mt-respiratory control towards global connection. Abstract MitoEAGLE Barcelona 2017. - [[Gnaiger 2017 Abstract MITOEAGLE Barcelona |»Bioblast link«]] | |||
::::# Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of mitochondrial respiratory capacity by temperature in mouse heart: electron flow through the Q-junction in permeabilized fibers. Sci Rep 7:2840, DOI:10.1038/s41598-017-02789-8. - [[Lemieux 2017 Sci Rep |»Bioblast link«]] | ::::# Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of mitochondrial respiratory capacity by temperature in mouse heart: electron flow through the Q-junction in permeabilized fibers. Sci Rep 7:2840, DOI:10.1038/s41598-017-02789-8. - [[Lemieux 2017 Sci Rep |»Bioblast link«]] | ||
::::# Ost M, Doerrier C, Gama-Perez P, Moreno-Gomez S (2018) Analysis of mitochondrial respiratory function in tissue biopsies and blood cells. Curr Opin Clin Nutr Metab Care 21:336-42. - [[Ost 2018 Curr Opin Clin Nutr Metab Care |»Bioblast link«]] | |||
== Instrumental platforms: comparisons == | == Instrumental platforms: comparisons == | ||
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=== Task group 1.5 === | === Task group 1.5 === | ||
:::: Knowledge management system | :::: Knowledge management system | ||
:::: ''TG participants:'' [[Vendelin Marko]] EE, [[Garcia-Roves PM |Garcia-Roves Pablo]] ES | :::: ''TG participants:'' [[Vendelin Marko]] EE, [[Garcia-Roves PM |Garcia-Roves Pablo]] ES | ||
::::* Towards and beyond a mitochondrial physiology database: filter and amplify more signals from this data, making them more meaningful and valuable for research and medicine. | ::::* Towards and beyond a mitochondrial physiology database: filter and amplify more signals from this data, making them more meaningful and valuable for research and medicine. | ||
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::::» [[MitoFit Quality Control System]] | ::::» [[MitoFit Quality Control System]] | ||
::::» [[MiPMap]] | ::::» [[MiPMap]] | ||
::::» [[MitoFit proficiency test]] | ::::» [[Development MitoFit proficiency test|MitoFit proficiency test]] | ||
::::» [[MiPNet21.07 MitoFit DatLab PT]] | ::::» [[MiPNet21.07 MitoFit DatLab PT]] | ||
Line 117: | Line 119: | ||
:::: '''Preprints for MitoEAGLE ''' | :::: '''Preprints for MitoEAGLE ''' | ||
:::::# Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of oxidative phosphorylation by temperature in the heart. bioRxiv doi10.1101/103457. - [[Lemieux 2017 bioRxiv |»Bioblast link«]] | :::::# Gnaiger E, Aasander Frostner E, Abdul Karim N, Abumrad NA, Acuna-Castroviejo D, Adiele RC et al (2019) Mitochondrial respiratory states and rates. MitoFit Preprint Arch doi:10.26124/mitofit:190001. - [[Gnaiger 2019 MitoFit Preprint Arch |»Bioblast link«]] | ||
:::::# Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of oxidative phosphorylation by temperature in the heart. bioRxiv doi10.1101/103457. - [[Lemieux 2017 bioRxiv 103457 |»Bioblast link«]] | |||
:::::# Lemieux H, Subarsky P, Doblander C, Wurm M, Troppmair J, Gnaiger E (2017) Impairment of mitochondrial respiratory function as an early biomarker of apoptosis induced by growth factor removal. bioRxiv doi: https://doi.org/10.1101/151480. - [[Lemieux 2017 bioRxiv 151480 |»Bioblast link«]] | |||
:::: '''Cores of reproducibility, data availability''' | :::: '''Cores of reproducibility, data availability''' | ||
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:::: ''TG leaders:'' [[Makrecka-Kuka Marina]] LV / [[Gnaiger Erich]] AT | :::: ''TG leaders:'' [[Makrecka-Kuka Marina]] LV / [[Gnaiger Erich]] AT | ||
:::: ''TG participants:'' [[Ali Sameh S]] EG, [[Cervinkova Zuzana]] CZ, [[Chicco Adam J]] US, [[Coen Paul M]] US, [[Eide Lars]] NO, [[Garcia-Roves Pablo M]] ES, [[Gasparre Giuseppe]] IT, [[Genova Maria Luisa]] IT, [[Haendeler Judith]] DE, [[Iyer Shilpa]] US, [[Krako Nina]] RS, [[Laner Verena]] AT, [[Mayan Maria D]] ES, [[Mishmar Dan]] IL, [[Nehlin Jan]] DK, [[Palmeira Carlos]] PT, [[Paterlini Serena]] IT, [[Porcelli Anna Maria]] IT, [[Rao Raj]] US, [[Schaefer Patrick]] DE, [[Tronstad Karl Johan]] NO, [[Trougakos Ioannis]] GR, [[Volani Chiara]] AT, [[Votion Dominique-Marie]] BE | :::: ''TG participants:'' [[Ali Sameh S]] EG, [[Cervinkova Zuzana]] CZ, [[Chicco Adam J]] US, [[Coen Paul M]] US, [[Eide Lars]] NO, [[Garcia-Roves Pablo M]] ES, [[Gasparre Giuseppe]] IT, [[Genova Maria Luisa]] IT, [[Haendeler Judith]] DE, [[Iyer Shilpa]] US, [[Krako Nina]] RS, [[Laner Verena]] AT, [[Mayan Maria D]] ES, [[Mishmar Dan]] IL, [[Nehlin Jan]] DK, [[Palmeira Carlos]] PT, [[Paterlini Serena]] IT, [[Porcelli Anna Maria]] IT, [[Rao Raj]] US, [[Schaefer Patrick]] DE, [[Tronstad Karl Johan]] NO, [[Trougakos Ioannis]] GR, [[Volani Chiara]] AT, [[Votion Dominique-Marie]] BE | ||
::: '''The Project Repository Journal''' - https://www.europeandissemination.eu/the-project-repository-journal | |||
:::: In February 2019 the first edition of '''The Project Repository Journal''' will be launched. Fully open access and dedicated to EU funded projects it will become the first point of call for project dissemination. Containing information on future funding calls and open access guidelines it will '''feature projects from across all different funding mechanisms and allow them to publish results, annual reports or general updates about the progress of the project'''. | |||
=== Task group 1.10 === | === Task group 1.10 === | ||
Line 144: | Line 151: | ||
::: '''Action''' | ::: '''Action''' | ||
::::» STSM cooperation [[NeuroVive]] and [[Oroboros Instruments]] [http://www.neurovive.com/wp-content/uploads/2018/11/NVP_newsletter_2018-11_EN_final.pdf '''Eleonor Åsander Frostner – guest tutor at international workshop'''] | |||
::::» [https://www.facebook.com/costmitoeagle/ '''MitoEAGLE on Facebook'''] | ::::» [https://www.facebook.com/costmitoeagle/ '''MitoEAGLE on Facebook'''] | ||
::::» [[Media:Dissemination plan MITOEAGLE.docx]] | ::::» [[Media:Dissemination plan MITOEAGLE.docx]] | ||
::::» [[ | ::::» [[Short-Term Scientific Missions MitoEAGLE]] | ||
= Progress = | = Progress = | ||
::::» | ::::» [https://sysbio.ioc.ee/software/iocbio-webdb/ Database] | ||
::::» | ::::» [[MiP2019/MitoEAGLE_Belgrade_RS#Working_Groups|WG1 summary - Belgrade]] | ||
::::» | ::::» [[MitoEAGLE WG1 Coimbra 2019]] - WG1 and WG3 protocol development and liver | ||
::::» | ::::» [[COST Connect workshop on Data Sharing Brussel 2019]] - “COST Connect” workshop on the topic of Data Sharing | ||
::::» [[MitoEAGLE Innsbruck 2018-11-19|WG1 Q Meeting]] | |||
::::» [[MiP2018/MitoEAGLE_Jurmala_LV#Working_Groups |WG1 summary - Jurmala]] | |||
::: [[MitoEAGLE protocols, terminology, documentation |WG1: MitoEAGLE protocols, terminology, documentation]] | |||
::::* Final discussion of [[Gnaiger 2019 MitoFit Preprint Arch |'''MitoFit Preprint Arch doi:10.26124/mitofit:190001. - [[Gnaiger 2019 MitoFit Preprint Arch |»Bioblast link«]]''']] - ''All participants are invited to submit comments and improvements, and those who are not yet included as co-authors are invited to join.'' | |||
::::* [[Gnaiger 2018 MiP2018 |Mitochondrial respiratory control by fuel substrates and specific inhibitors of respiratory enzymes: Building blocks of mitochondrial physiology Part 2]] | |||
::::* Training and knowledge management concept - [[MiPschool Tromso-Bergen 2018]] | |||
::::* Towards a MitoEAGLE proficiency training workshop | |||
::::* [[Krako Jakovljevic 2018 MiP2018 |Report on ECI, ITC and gender balance in COST Action MitoEAGLE]] | |||
::::* Gnaiger E, Aasander Frostner E, Abdul Karim N, Abumrad NA, Acuna-Castroviejo D, Adiele RC et al (2019) Mitochondrial respiratory states and rates. MitoFit Preprint Arch doi:10.26124/mitofit:190001. - [[Gnaiger 2019 MitoFit Preprint Arch |»Bioblast link«]] | |||
::::» [[MiP2017/MitoEAGLE_Hradec_Kralove_CZ#Programme|WG1 summary - Hradec Kralove]] | |||
::::» [[MiPschool_Obergurgl_2017#Programme_MitoEAGLE_Working_Groups_Workshop|WG1 summary - Obergurgl]] | |||
::::» [[MitoEAGLE_Barcelona_2017#Minutes_MitoEAGLE_Barcelona_2017|Minutes with WG1 summary - Barcelona]] | |||
::::» [[MitoEAGLE_Verona_2016#Minutes|Minutes with WG1 summary - Verona]] | |||
== Open call== | |||
::::» [[Talk:WG1 MitoEAGLE protocols, terminology, documentation|Network discussion forum WG1: cytochrome c effect]] | |||
== Next steps == | == Next steps == |
Latest revision as of 04:59, 19 July 2022
News and Events | Working Groups | Short-Term Scientific Missions | Management Committee | Members |
COST Action CA15203 (2016-2021): MitoEAGLE
Evolution-Age-Gender-Lifestyle-Environment: mitochondrial fitness mapping
WG1 MitoEAGLE protocols, terminology, documentation
WG1 Action
- Standard operating procedures and user requirement document: Protocols, terminology, documentation
- Many analyses lack statistical power within a single study. Statistical combination of different studies is often difficult due to lack of methodological standardization and harmonization.
WG1 Action
WG Leader
- Marko Vendelin, Dr. - [email protected]
WG Co-Leader
- Dominik Pesta, Mag. Dr. - [[email protected] [email protected]]
Participants and discussion
Task groups
- TG leaders: suggestions discussed at the MitoFit Science Camp 2016 Kuehtai AT, and updated according to the MitoEAGLE_MC_Meeting_2016_Brussels_BE.
- TG participants: please send us an Email to join: [email protected]
SUIT protocols and terminology
Task group 1.1
- Coupling states and coupling control ratios: consensus statements
- TG leaders: Gnaiger Erich AT / Hoppel Charles L US
- » Gnaiger E, Aasander Frostner E, Abdul Karim N, Abumrad NA, Acuna-Castroviejo D, Adiele RC et al (2019) Mitochondrial respiratory states and rates. MitoFit Preprint Arch doi:10.26124/mitofit:190001. - »Bioblast link«
Task group 1.2
- SUIT protocols: nomenclature consistent with concept of database
- TG leader: Doerrier Velasco Carolina A AT, Gnaiger Erich AT
- TG participants: Attimonelli Marcella IT, Krako Nina RS, Vendelin Marko EE
Task group 1.3
- Experimental details in SUIT
- TG leaders: Chicco Adam J US/ Hickey Anthony J NZ/ Doerrier Velasco Carolina A AT
- TG participants: Casado Pinna Marta ES, Endlicher Rene CZ, Krako Nina RS, Kucera Otto CZ, Sobotka Ondrej CZ, Stankova Pavla CZ
- » MitoPedia: Sample preparations
- References
- Doerrier C, Garcia-Souza LF, Krumschnabel G, Wohlfarter Y, Mészáros AT, Gnaiger E (2018) High-Resolution FluoRespirometry and OXPHOS protocols for human cells, permeabilized fibers from small biopsies of muscle, and isolated mitochondria. Methods Mol Biol 1782:31-70. - »Bioblast link«
- Gnaiger E (2017) Quality first: a paradigm shift in mt-respiratory control towards global connection. Abstract MitoEAGLE Barcelona 2017. - »Bioblast link«
- Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of mitochondrial respiratory capacity by temperature in mouse heart: electron flow through the Q-junction in permeabilized fibers. Sci Rep 7:2840, DOI:10.1038/s41598-017-02789-8. - »Bioblast link«
- Ost M, Doerrier C, Gama-Perez P, Moreno-Gomez S (2018) Analysis of mitochondrial respiratory function in tissue biopsies and blood cells. Curr Opin Clin Nutr Metab Care 21:336-42. - »Bioblast link«
- References
Instrumental platforms: comparisons
Task group 1.4
- Instrumental platforms: comparisons
- TG leaders: Molina Anthony JA US
- TG participants: Canto Carles CH (suggested), Genova Maria Luisa IT, Tronstad Karl Johan NO (suggested), Vendelin Marko EE, Zorzano Antonio ES (suggested)
Knowledge management system and proficiency test
Task group 1.5
- Knowledge management system
- TG participants: Vendelin Marko EE, Garcia-Roves Pablo ES
- Towards and beyond a mitochondrial physiology database: filter and amplify more signals from this data, making them more meaningful and valuable for research and medicine.
Task group 1.6
- Proficiency test
- TG leaders: Gnaiger Erich AT/ Doerrier Velasco Carolina A AT
- TG participants: Genova Maria Luisa IT
- References
Documentation
Task group 1.7
- Documentation
- TG leaders: Arnould Thierry BE / Votion Dominique-Marie BE
- TG participants: Gnaiger Erich AT
- Preprints for MitoEAGLE
- Gnaiger E, Aasander Frostner E, Abdul Karim N, Abumrad NA, Acuna-Castroviejo D, Adiele RC et al (2019) Mitochondrial respiratory states and rates. MitoFit Preprint Arch doi:10.26124/mitofit:190001. - »Bioblast link«
- Lemieux H, Blier PU, Gnaiger E (2017) Remodeling pathway control of oxidative phosphorylation by temperature in the heart. bioRxiv doi10.1101/103457. - »Bioblast link«
- Lemieux H, Subarsky P, Doblander C, Wurm M, Troppmair J, Gnaiger E (2017) Impairment of mitochondrial respiratory function as an early biomarker of apoptosis induced by growth factor removal. bioRxiv doi: https://doi.org/10.1101/151480. - »Bioblast link«
- Preprints for MitoEAGLE
- Cores of reproducibility, data availability
- » Wagner P (2017) Cores of reproducibility in physiology (CORP): Advancing the corpus of physiological knowledge. J Appl Physiol 122:89-90.
- » Curran-Everett D (2017) CORP: Minimizing the chances of false positives and false negatives. J Appl Physiol 122:91-5.
- Think less about a simple P value and more about the scientific importance of the confidence interval bounds for some experimental result. Even a convincing P value of 0.005 can be associated with a confidence interval whose bounds indicate an effect that is scientifically inconsequential.
- Rely on repeated studies to accumulate evidence for some biological phenomenon.
- » Data availability statements in PLOS journals
- Cores of reproducibility, data availability
Dissemination and training
Task group 1.8
- Translation to community in general
- TG leader: Makrecka-Kuka Marina LV (Dissemination Coordinator), Rattan Suresh DK
- TG participants: Krako Nina RS, Irving Brian A US
Task group 1.9
- Dissemination Scientific community
- TG leaders: Makrecka-Kuka Marina LV / Gnaiger Erich AT
- TG participants: Ali Sameh S EG, Cervinkova Zuzana CZ, Chicco Adam J US, Coen Paul M US, Eide Lars NO, Garcia-Roves Pablo M ES, Gasparre Giuseppe IT, Genova Maria Luisa IT, Haendeler Judith DE, Iyer Shilpa US, Krako Nina RS, Laner Verena AT, Mayan Maria D ES, Mishmar Dan IL, Nehlin Jan DK, Palmeira Carlos PT, Paterlini Serena IT, Porcelli Anna Maria IT, Rao Raj US, Schaefer Patrick DE, Tronstad Karl Johan NO, Trougakos Ioannis GR, Volani Chiara AT, Votion Dominique-Marie BE
- The Project Repository Journal - https://www.europeandissemination.eu/the-project-repository-journal
- In February 2019 the first edition of The Project Repository Journal will be launched. Fully open access and dedicated to EU funded projects it will become the first point of call for project dissemination. Containing information on future funding calls and open access guidelines it will feature projects from across all different funding mechanisms and allow them to publish results, annual reports or general updates about the progress of the project.
- The Project Repository Journal - https://www.europeandissemination.eu/the-project-repository-journal
Task group 1.10
- Training, Short Term Scientific Missions
- TG leader: Labieniec-Watala Magdalena PL, Klaus Susanne DE
- TG participants: Ali Sameh S EG, Cervinkova Zuzana CZ, Chicco Adam J US, Coen Paul M US, Eide Lars NO, Garcia-Roves Pablo M ES, Gasparre Giuseppe IT, Genova Maria Luisa IT, Haendeler Judith DE, Iyer Shilpa US, Krako Nina RS, Mayan Maria D ES, Mishmar Dan IL, Nehlin Jan DK, Palmeira Carlos PT, Paterlini Serena IT, Porcelli Anna Maria IT, Rao Raj US, Schaefer Patrick DE, Tronstad Karl Johan NO, Trougakos Ioannis GR, Volani Chiara AT, Votion Dominique-Marie BE
Progress
- » Database
- » WG1 summary - Belgrade
- » MitoEAGLE WG1 Coimbra 2019 - WG1 and WG3 protocol development and liver
- » COST Connect workshop on Data Sharing Brussel 2019 - “COST Connect” workshop on the topic of Data Sharing
- » WG1 Q Meeting
- » WG1 summary - Jurmala
- WG1: MitoEAGLE protocols, terminology, documentation
- Final discussion of [[Gnaiger 2019 MitoFit Preprint Arch |MitoFit Preprint Arch doi:10.26124/mitofit:190001. - »Bioblast link«]] - All participants are invited to submit comments and improvements, and those who are not yet included as co-authors are invited to join.
- Mitochondrial respiratory control by fuel substrates and specific inhibitors of respiratory enzymes: Building blocks of mitochondrial physiology Part 2
- Training and knowledge management concept - MiPschool Tromso-Bergen 2018
- Towards a MitoEAGLE proficiency training workshop
- Report on ECI, ITC and gender balance in COST Action MitoEAGLE
- Gnaiger E, Aasander Frostner E, Abdul Karim N, Abumrad NA, Acuna-Castroviejo D, Adiele RC et al (2019) Mitochondrial respiratory states and rates. MitoFit Preprint Arch doi:10.26124/mitofit:190001. - »Bioblast link«
- » WG1 summary - Hradec Kralove
- » WG1 summary - Obergurgl
- » Minutes with WG1 summary - Barcelona
- » Minutes with WG1 summary - Verona
Open call
Next steps
References
- General requirements for the competence of testing and calibration laboratories » ISO/IEC 17025:2005