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Difference between revisions of "MitoPedia"

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::::<big><big> Development of a consistent nomenclature in mitochondrial physiology, in the spirit of Gentle Science</big></big>
::::<big><big> Development of a consistent nomenclature in mitochondrial physiology, in the spirit of Gentle Science</big></big>
 
[[File:MitoPedia.jpg|left|200px|MitoPedia]]
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:::: '''High-resolution terminology - matching measurements at high-resolution'''
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'''High-resolution terminology - matching measurements at high-resolution'''
:::: '''» [[MitoPedia: Terms and abbreviations]]''' - IUPAC guidelines are followed for general terms of physical chemistry<ref>Cohen ER, Cvitas T, Frey JG, Holmström B, Kuchitsu K, Marquardt R, Mills I, Pavese F, Quack M, Stohner J, Strauss HL, Takami M, Thor HL (2008) Quantities, Units and Symbols in Physical Chemistry, IUPAC Green Book, 3rd Edition, 2nd Printing, IUPAC & RSC Publishing, Cambridge. - [[Cohen 2008 IUPAC Green Book |»Bioblast link«]]</ref><sup>,</sup><ref>International Union of Biochemistry and Molecular Biology: Recommendations for terminology and databases for biochemical thermodynamics. - [http://www.chem.qmul.ac.uk/iubmb/thermod2/ »Open Access«]</ref><sup>,</sup><ref>International Union of Biochemistry (1981) Symbolism and terminology in enzyme kinetics. - [http://www.chem.qmul.ac.uk/iubmb/kinetics/ »Open Access«]</ref>, extended by concepts of mitochondrial physiology<ref name="MitoPathways"> Gnaiger E (2014) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 4th ed. Mitochondr Physiol Network 19.12. Oroboros MiPNet Publications, Innsbruck:80 pp. - [[Gnaiger 2014 MitoPathways |»Bioblast link«]]</ref> and nonequilibrium thermodynamics<ref>Gnaiger E (1993) Nonequilibrium thermodynamics of energy transformations. Pure Appl Chem 65:1983-2002. - [[Gnaiger 1993 Pure Appl Chem |»Bioblast link«]]</ref>.
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'''»[[MitoPedia: Terms and abbreviations]]''' - IUPAC guidelines are followed for general terms of physical chemistry<ref>Cohen ER, Cvitas T, Frey JG, Holmström B, Kuchitsu K, Marquardt R, Mills I, Pavese F, Quack M, Stohner J, Strauss HL, Takami M, Thor HL (2008) Quantities, Units and Symbols in Physical Chemistry, IUPAC Green Book, 3rd Edition, 2nd Printing, IUPAC & RSC Publishing, Cambridge. - [[Cohen 2008 IUPAC Green Book |»Bioblast Access«]]</ref>,<ref>International Union of Biochemistry and Molecular Biology: Recommendations for terminology and databases for biochemical thermodynamics. - [http://www.chem.qmul.ac.uk/iubmb/thermod2/ »Open Access«]</ref>,<ref>International Union of Biochemistry (1981) Symbolism and terminology in enzyme kinetics. - [http://www.chem.qmul.ac.uk/iubmb/kinetics/ »Open Access«]</ref>, extended by concepts of nonequilibrium thermodynamics.<ref>Gnaiger E (1993) Nonequilibrium thermodynamics of energy transformations. Pure Appl Chem 65:1983-2002. - [[Gnaiger 1993 Pure Appl Chem |»Bioblast Access«]]</ref>.
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=== MitoPedia: Concepts ===
=== MitoPedia: Concepts ===
: »[[MitoPedia: Respiratory states]]<ref> Gnaiger E (2014) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 4th ed. Mitochondr Physiol Network 19.12. OROBOROS MiPNet Publications, Innsbruck:80 pp. - [[Gnaiger 2014 MitoPathways |»Bioblast Access«]]</ref>
::::» [[MitoPedia: MiP concepts]]
: »[[MitoPedia: Respiratory control ratios]]
::::» [[MitoPedia: Respiratory states]]<ref name="MitoPathways"/>
: »[[Mitochondria and bioblasts: Made history]]
::::» [[MitoPedia: Respiratory control ratios]]<ref name="MitoPathways"/>
::::» [[MitoPedia: SUIT]]
::::» [[MitoPedia: Ergodynamics]]
::::» [[MitoFit Quality Control System]]


=== MitoPedia: Methods ===
=== MitoPedia: Methods ===
: »[[MitoPedia: Respirometry]]
::::» [[MitoPedia: Respirometry]]
: »[[MitoPedia: Fluorometry]]
::::» [[MitoPedia: Fluorometry]]
: »[[MitoPedia: Spectrophotometry]]  
::::» [[MitoPedia: Spectrophotometry]]  
 
=== MitoPedia: O2k and high-resolution respirometry ===
::::» [[MitoPedia: O2k hardware]]
::::» [[MitoPedia: DatLab]]
::::» [[MitoPedia: SUIT]]
 
=== MitoPedia: MiP and biochemistry ===
::::» [[MitoPedia: Substrates and metabolites]]
::::» [[MitoPedia: Uncouplers]]
::::» [[MitoPedia: Inhibitors]]
::::» [[MitoPedia: Sample preparations]]
::::» [[MitoPedia: Permeabilization agents]]
::::» [[MitoPedia: Media for respirometry]]
::::» [[MitoPedia: Enzymes]]<ref>International Union of Biochemistry (1991) Nomenclature of electron-transfer proteins. Biochim Biophys Acta 1060. - [http://www.chem.qmul.ac.uk/iubmb/etp/ »Open Access«]</ref>


=== MitoPedia: Biochemistry ===
=== MitoPedia: Preprints and history ===
: »[[MitoPedia: Substrates and metabolites]]<ref> Pesta D, Gnaiger E (2012) High-resolution respirometry. OXPHOS protocols for human cells and permeabilized fibres from small biopisies of human muscle. Methods Mol Biol 810:25-58. - [[Pesta 2012 Methods Mol Biol |»Bioblast Access«]]</ref>
::::» [[MitoPedia: Preprints]] - '''''New:''''' 2019-02-19
: »[[MitoPedia: Uncouplers]]
::::» [[Mitochondria and bioblasts: Made history]]
: »[[MitoPedia: Inhibitors]]
: »[[MitoPedia: Permeabilization agents]]
: »[[MitoPedia: Media for respirometry]]
: »[[MitoPedia: Enzymes]]<ref>International Union of Biochemistry (1991) Nomenclature of electron-transfer proteins. Biochim Biophys Acta 1060. - [http://www.chem.qmul.ac.uk/iubmb/etp/ »Open Access«]</ref>


=== MitoPedia: Links ===  
=== MitoPedia: Links ===  
: »[[List of Links - Mitochondria: Structure and Function]]
::::» [[List of Links - Mitochondria: Structure and Function]]
: »[[MitoGlobal_Organizations|Mitochondrial Global Network: List of MitoGlobal Organizations]]
::::» [[MitoGlobal Societies |Mitochondrial Global Network: List of MitoGlobal Societies]]


'''OROBOROS'''
'''Oroboros'''
: » [[O2k-Protocols]]
::::» [[O2k-Protocols]]
: » [[O2k-Publications: Topics]]
::::» [[O2k-Publications: Topics]]


[[Image:MitoPedia.jpg|left|80px|link=http://www.bioblast.at/index.php/MitoPedia |MitoPedia]]  
[[Image:MitoPedia.jpg|left|80px|link=http://www.bioblast.at/index.php/MitoPedia |MitoPedia]]  
[[Image:BB-Bioblast.jpg|right|80px|link=http://www.bioblast.at/index.php/Bioblast:About |Bioblast wiki]]
 
[[Image:BB-Bioblast.jpg|left|80px|link=http://www.bioblast.at/index.php/Bioblast:About |Bioblast wiki]]
 
 
== MitoPedia and Bioblast ==
== MitoPedia and Bioblast ==


The term '''MitoPedia''' expresses the link to [https://www.wikipedia.org/ '''Wikipedia''']. We use the [http://www.mediawiki.org/wiki/MediaWiki MediaWiki] software for generating a bottom-up database and glossaries. The 'Bioblast community' of mitochondrial experts is cordially invited to active participation - a vision that may develop further in the future. To make this possible, the OROBOROS-Team continues to work on the '''Bioblast''' website as an ''information synthase'' - in the spirit of [[Gentle Science]]. --[[Gnaiger_E|Gnaiger Erich]] 09:20, 18 May 2014 (CEST)
:::: The term '''MitoPedia''' expresses the link to [https://www.wikipedia.org/ '''Wikipedia''']. We use the [http://www.mediawiki.org/wiki/MediaWiki MediaWiki] software for generating a bottom-up database and glossaries. The 'Bioblast community' of mitochondrial experts is cordially invited to active participation - a vision that may develop further in the future. To make this possible, the Oroboros-team continues to work on the '''Bioblast''' website as an ''information synthase'' - in the spirit of [[Gentle Science]]. ~ [[Gnaiger_E|Gnaiger Erich]] 09:20, 18 May 2014 (CEST)
 
[[File:EPL-free and excess.jpg|right|300px|thumb|[[Gnaiger 2014 MitoPathways |The Blue Book 2014: Fig. 2.4.]]]]
[[File:EPL-free and excess.jpg|thumb|right|300px|[[Gnaiger 2014 MitoPathways |The Blue Book 2014: Fig. 2.4.]]]]





Revision as of 06:21, 29 May 2019


high-resolution terminology - matching measurements at high-resolution


MitoPedia

Development of a consistent nomenclature in mitochondrial physiology, in the spirit of Gentle Science
MitoPedia


High-resolution terminology - matching measurements at high-resolution



» MitoPedia: Terms and abbreviations - IUPAC guidelines are followed for general terms of physical chemistry[1],[2],[3], extended by concepts of mitochondrial physiology[4] and nonequilibrium thermodynamics[5].



MitoFit

MitoFit news                    

MitoFit Preprints.png



MitoFit Preprints - the Open Access preprint server for mitochondrial physiology and bioenergetics

» MitoPedia alert - MitoPedia terms presented in the Oroboros Ecosystem Agenda
BioTechniques welcomes preprints
» .. preprints are a vital step towards a more open and transparent science — a step that brings great benefits for both the broader scientific community and individual authors.
Open Science - from Preprints to open peer review
» Peer Review in Service of Open Science, by Veronique Kiemer



MitoPedia: Concepts

» MitoPedia: MiP concepts
» MitoPedia: Respiratory states[4]
» MitoPedia: Respiratory control ratios[4]
» MitoPedia: SUIT
» MitoPedia: Ergodynamics
» MitoFit Quality Control System

MitoPedia: Methods

» MitoPedia: Respirometry
» MitoPedia: Fluorometry
» MitoPedia: Spectrophotometry

MitoPedia: O2k and high-resolution respirometry

» MitoPedia: O2k hardware
» MitoPedia: DatLab
» MitoPedia: SUIT

MitoPedia: MiP and biochemistry

» MitoPedia: Substrates and metabolites
» MitoPedia: Uncouplers
» MitoPedia: Inhibitors
» MitoPedia: Sample preparations
» MitoPedia: Permeabilization agents
» MitoPedia: Media for respirometry
» MitoPedia: Enzymes[6]

MitoPedia: Preprints and history

» MitoPedia: Preprints - New: 2019-02-19
» Mitochondria and bioblasts: Made history

MitoPedia: Links

» List of Links - Mitochondria: Structure and Function
» Mitochondrial Global Network: List of MitoGlobal Societies

Oroboros

» O2k-Protocols
» O2k-Publications: Topics
MitoPedia
Bioblast wiki


MitoPedia and Bioblast

The term MitoPedia expresses the link to Wikipedia. We use the MediaWiki software for generating a bottom-up database and glossaries. The 'Bioblast community' of mitochondrial experts is cordially invited to active participation - a vision that may develop further in the future. To make this possible, the Oroboros-team continues to work on the Bioblast website as an information synthase - in the spirit of Gentle Science. ~ Gnaiger Erich 09:20, 18 May 2014 (CEST)


MitoPedia - high-resolution terminology, matching measurements at high-resolution



MitoPedia term: Dihydro-orotate dehydrogenase - another respiratory Complex at the Q-junction.


» Respiratory control ratios beyond the RCR - coupling:

P-L control efficiency P-L control efficiency,

R-L control efficiency R-L control efficiency,

E-L coupling efficiency E-L coupling efficiency.


MitoPathways 2020

MitoPathways - The Blue Book


» HRR - high-resolution respirometry was established in 1995. This is the first comprehensive methodological summary: Control of mitochondrial and cellular respiration by oxygen. J Bioenerg Biomembr (1995)


References

  1. Cohen ER, Cvitas T, Frey JG, Holmström B, Kuchitsu K, Marquardt R, Mills I, Pavese F, Quack M, Stohner J, Strauss HL, Takami M, Thor HL (2008) Quantities, Units and Symbols in Physical Chemistry, IUPAC Green Book, 3rd Edition, 2nd Printing, IUPAC & RSC Publishing, Cambridge. - »Bioblast link«
  2. International Union of Biochemistry and Molecular Biology: Recommendations for terminology and databases for biochemical thermodynamics. - »Open Access«
  3. International Union of Biochemistry (1981) Symbolism and terminology in enzyme kinetics. - »Open Access«
  4. 4.0 4.1 4.2 Gnaiger E (2014) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 4th ed. Mitochondr Physiol Network 19.12. Oroboros MiPNet Publications, Innsbruck:80 pp. - »Bioblast link«
  5. Gnaiger E (1993) Nonequilibrium thermodynamics of energy transformations. Pure Appl Chem 65:1983-2002. - »Bioblast link«
  6. International Union of Biochemistry (1991) Nomenclature of electron-transfer proteins. Biochim Biophys Acta 1060. - »Open Access«