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Difference between revisions of "MiPMap"

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{{MitoPedia
{{MitoPedia
|abbr=MiPMap
|abbr=MiPMap
|description='''Mitochondrial Physiology Map (MiPMap): ''A comparative database of mitochondrial physiology may provide the key for understanding the functional implications of mitochondrial diversity from mouse to man, and evaluation of altered mitochondrial respiratory control patterns in health and disease.'' ([[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]).
|description=[[File:MiPMap Publication.jpg|left|240px|MiPMap]]
|info=[[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger E (2009) Capacity of oxidative phosphorylation in human skeletal muscle. New perspectives of mitochondrial physiology. Int J Biochem Cell Biol 41: 1837-1845.]]
The project '''Mitochondrial Physiology Map''' (MiPMap) is initiated to provide an overview of mitochondrial properties in cell types, tissues and species. As part of Bioblast, '''MiPMap''' may be considered as an ''information synthase'' for '''Comparative Mitochondrial Physiology'''. Establishing a comprehensive database will require global input and cooperation.
Β 
''A comparative database of mitochondrial physiology may provide the key for understanding the functional implications of mitochondrial diversity from mouse to man, and evaluation of altered mitochondrial respiratory control patterns in health and disease'' ([[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]).
|info=[[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger E (2009) Capacity of oxidative phosphorylation in human skeletal muscle. New perspectives of mitochondrial physiology. Int J Biochem Cell Biol 41:1837-45.]]
}}
}}
{{MitoPedia methods
{{MitoPedia concepts
|mitopedia method=Respirometry, Fluorometry, Spectrophotometry
|mitopedia concept=MiP concept
}}
}}
{{MitoPedia topics
|mitopedia topic=Respiratory state, Enzyme, Medium, Inhibitor, Substrate and metabolite, Uncoupler, Permeabilization agent
}}
= Mitochondrial Physiology Map - MiPMap =


The project '''Mitochondrial Physiology Map''' is initiated to create a list of mitochondrial properties in cell types, tissues and species. As part of MitoPedia, '''MiPMap''' will provide an ''information synthase'' for '''Comparative Mitochondrial Physiology'''. This project will require global input to establish a comprehensive database.
__TOC__
== MiPMap labels ==
:::: '''MiPMap labels''' provide the backbone of the MiPMap project. The MiPMap labels can be considered as keywords which can be attached to various sources of information (publications). With proper labelling, multidimensional maps of information can be constructed, filtering the sources through various grids.
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:::: The MiPMap labels (filters) are grouped into various topics (properties).
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=== MiP areas ===
::: [[Property:MiP area]]
:::: β€’β€’ Respiration β€’β€’ Instruments;methods β€’β€’ mt-Biogenesis;mt-density β€’β€’ mt-Structure;fission;fusion β€’β€’ mt-Membrane β€’β€’ mtDNA;mt-genetics β€’β€’ nDNA;cell genetics β€’β€’ Genetic knockout;overexpression β€’β€’ Comparative MiP;environmental MiP β€’β€’ Gender β€’β€’ Developmental biology β€’β€’ Exercise physiology;nutrition;life style β€’β€’ mt-Medicine β€’β€’ Patients β€’β€’ Pharmacology;toxicology β€’β€’ mt-Awareness


::::* Patients: when there is real information about patients, not just whenever a pathology is dealt with


=== Organism ===
::: [[Property:Mammal and model]]
::::: β€’β€’ Human β€’β€’ Pig β€’β€’ Mouse β€’β€’ Rat β€’β€’ Guinea pig β€’β€’ Bovines β€’β€’ Horse β€’β€’ Dog β€’β€’ Rabbit β€’β€’ Cat β€’β€’ Other mammals β€’β€’ Chicken β€’β€’ Zebrafish β€’β€’ Drosophila β€’β€’ Artemia β€’β€’ Caenorhabditis elegans β€’β€’ Saccharomyces cerevisiae β€’β€’ Birds β€’β€’ Reptiles β€’β€’ Amphibians β€’β€’ Fishes β€’β€’ Chelicerates β€’β€’ Crustaceans β€’β€’ Hexapods β€’β€’ Myriapods β€’β€’ Annelids β€’β€’ Molluscs β€’β€’ Nematodes β€’β€’ Other invertebrates β€’β€’ Fungi β€’β€’ Plants β€’β€’ Protists β€’β€’ β€’β€’ Eubacteria β€’β€’ Archea


== MiPMap list of mitochondrial properties in organisms (species), and cell types and tissues ==
=== Tissues;cellsΒ  ===
::: [[Property:Tissue and cell]]
:::: β€’β€’ Heart β€’β€’ Skeletal muscle β€’β€’ Nervous system β€’β€’ Liver β€’β€’ Kidney β€’β€’ Lung;gill β€’β€’ Islet Cell; Pancreas; Thymus β€’β€’ Endothelial; Epithelial; Mesothelial Cell β€’β€’ Blood cells β€’β€’ Fat β€’β€’ Genital β€’β€’Β  Other cell lines β€’β€’ CHO β€’β€’ HEK β€’β€’ HeLa β€’β€’ Neuroblastoma β€’β€’ Fibroblast β€’β€’ HUVEC β€’β€’ Macrophage-derived stem cells β€’β€’ Lymphocyte β€’β€’ Platelet β€’β€’ Stem cells


=== 1. Human and model organisms, taxonomic groups ===
=== Preparations ===
''Work in progress''
::: [[Property:Preparation]]
As a test case, O2k-Publications are listed according to organisms:
:::: β€’β€’ Intact Organism β€’β€’ Intact Organ β€’β€’ Intact cells β€’β€’ Permeabilized cells β€’β€’ Permeabilized tissue β€’β€’ Homogenate β€’β€’ Isolated Mitochondria β€’β€’ SMP β€’β€’ Chloroplasts β€’β€’ Enzyme β€’β€’ Oxidase; Biochemical Oxidation
:: >> [[O2k-Publications:_Specific_topics#Organisms|Organisms]]


: For example, in this list you may find information on '''mouse''' cell lines and tissues, e.g. '''mouse kidney mitochondria''':
=== Enzymes ===
:: * Is malic enzyme present?
::: [[Property:Enzyme]]
:: * Is the ''P/E''<1.0 like in mouse brain but different from mouse skeletal muscle?
:::: β€’β€’ Adenine Nucleotide Translocase β€’β€’ Complex I β€’β€’ Complex II; Succinate Dehydrogenase β€’β€’ Complex III β€’β€’ Complex IV; Cytochrome c Oxidase β€’β€’ Complex V; ATP Synthase β€’β€’ Inner mtMembrane Transporter β€’β€’ Marker Enzyme β€’β€’ Supercomplex β€’β€’ TCA Cycle and Matrix Dehydrogenases β€’β€’ Uncoupling protein
:: * Which UCPs are present?
:: * Preparation of isolated mitochondria, permeabilized tissuem, homogenate.
:: * Which respiration medium is recommended? ->> Do not use media with high K<sup>+</sup>, which inhibits kidney mitochondrial respiration.
>> Is this a general issue for the organ, or is it in addition also a species issue? (according to [[Calzia E]] MiR05 works fine with kidney tissue from pig, but not in mouse).
>> [[MiPNet14.13_Medium-MiR06#Limitations_of_using_MiR05_to_MiR06Cr|Limitations of using MiR05 to MiR06Cr]]


=== 2. Cell types and Tissues ===
=== Stress conditions ===
: Or you may find '''Skeletal muscle mitochondria''' studied across species:
::: [[Property:Stress]]
:: * '''Skeletal muscle''' - '''Human'''
:::: β€’β€’ Cell death β€’β€’ Cryopreservation β€’β€’ Ischemia-reperfusion β€’β€’ Permeability transition β€’β€’ Oxidative stress;RONS β€’β€’ Hypothermia; hyperthermia β€’β€’ Mitochondrial desease
::: ->> [[O2k-Publications: Human_-_Skeletal_muscle]]


=== Pathological states ===
::: [[Property:Diseases]]
:::: β€’β€’ Aging; senescence β€’β€’ Alzheimer's β€’β€’ Autism β€’β€’ Cancer β€’β€’ Cardiovascular β€’β€’ COPD β€’β€’ Diabetes β€’β€’ Inherited β€’β€’ Infectious β€’β€’ Myopathy β€’β€’ Neurodegenerative β€’β€’ Obesity β€’β€’ Parkinson's β€’β€’ Sepsis β€’β€’ OtherΒ  Β 


=== 3. Diseases ===
=== Regulation;kinetics ===
::: [[Property:Respiration and regulation]]
:::: β€’β€’ Aerobic glycolysis β€’β€’ ADP β€’β€’ ATP β€’β€’ ATP production β€’β€’ Calcium β€’β€’ Coupling efficiency;uncoupling β€’β€’ Cyt c β€’β€’ Flux control β€’β€’ Inhibitor β€’β€’ Ion;substrate transport β€’β€’ mt-Membrane potential β€’β€’ Oxygen kinetics β€’β€’ PCr;Cr β€’β€’ pH β€’β€’ Phosphate β€’β€’ Redox state β€’β€’ Substrate β€’β€’ Temperature β€’β€’ Threshold;excess capacity β€’β€’ Uncoupler β€’β€’ Fatty acid β€’β€’ Amino acid


''Work in progress''
::::* Oxygen: Oxygen kinetics, oxygen dependence of respiration and mitochondrial processes


[[O2k-Publications:_Specific_topics#Medical_and_pharmacological_applications|Medical and Pharmacological]]
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=== Coupling control states ===
::: [[Property:Coupling states]]
:::: β€’β€’ LEAK β€’β€’ ROUTINE β€’β€’ OXPHOS β€’β€’ ET-pathway


== Initiation ==
=== Pathway control states ===
* Presented at [[Bioblast 2012]].
::: [[Property:Pathways]]
* Focus for [http://www.mitophysiology.org/?mip2013 MiP''conference'' on Comparative Mitochondrial Physiology].
:::: β€’β€’ F β€’β€’ N β€’β€’ S β€’β€’ Gp β€’β€’ DQ β€’β€’ CIV β€’β€’ NS β€’β€’ Other combinations β€’β€’ ROXΒ  Β 
* Link to [[Mitochondrial Global Network]]
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=== High-resolution respirometry - HRR ===
::: [[Property:Instrument and method]]
:::: β€’β€’ High-resolution respirometry: Oxygraph-2k β€’β€’ TIP2k β€’β€’ O2k-Fluorometer β€’β€’ pH β€’β€’ NO β€’β€’ TPP β€’β€’ Ca β€’β€’ O2k-Spectrophotometer β€’β€’ O2k-Manual β€’β€’ O2k-Protocol β€’β€’ Theory
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=== Additional labels ===
::: β€’β€’
::::* Made history: [[Mitochondria and bioblasts: Made history]].
:::* Labels: indicates that publication has been entered but not yet labelled or that labelling might need revision.
::::* noPDF: no PDF was available for the implementation of this publication; labelling is merely based on the abstract.
::::* [Epub ahead of print] helps in finding and complementing references with no available issue and page numbers at the time of implementation.
::::* MitoFitPublication: To label publications affiliated with the MitoFit project.
::::* Date in the format yyyy-mm, e.g. 2015-12: indicates the year and month the publication was implemented and helps in creating the table of recently added Publications.
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[[File:Bioblast-publications.jpg|left|80px]]
== Publications in the MiPMap ==
=== Mitochondrial properties in organisms (species), cell types and tissues ===
::::* [[Special:BrowseData/Publications|Browse publications using MiPMap filters]]
::::* [[O2k-Publications: Topics]]


=== Journals ===
::::* [[Journals in Bioblast]]




== References and notes ==
== Initiation ==
::::* Presented at [[Bioblast 2012]].
::::* Focus for [[MiP2013|MiP''conference'' on Comparative Mitochondrial Physiology]]
::::* [[MiP2013 Abstracts]]
::::* Link to [[MitoGlobal]]






[[Category:MitoPedia]]
[[Category:MitoPedia]]
[[Category:All]]
[[Category:MitoFit]]
[[Category:Mitochondrial Global Network]]
[[Category:EAGLE]]
{{Gentle Science}}
{{Gentle Science}}

Latest revision as of 11:14, 20 October 2017


high-resolution terminology - matching measurements at high-resolution


MiPMap

Description

MiPMap

The project Mitochondrial Physiology Map (MiPMap) is initiated to provide an overview of mitochondrial properties in cell types, tissues and species. As part of Bioblast, MiPMap may be considered as an information synthase for Comparative Mitochondrial Physiology. Establishing a comprehensive database will require global input and cooperation.

A comparative database of mitochondrial physiology may provide the key for understanding the functional implications of mitochondrial diversity from mouse to man, and evaluation of altered mitochondrial respiratory control patterns in health and disease (Gnaiger 2009).

Abbreviation: MiPMap

Reference: Gnaiger E (2009) Capacity of oxidative phosphorylation in human skeletal muscle. New perspectives of mitochondrial physiology. Int J Biochem Cell Biol 41:1837-45.


MitoPedia concepts: MiP concept 


MiPMap labels

MiPMap labels provide the backbone of the MiPMap project. The MiPMap labels can be considered as keywords which can be attached to various sources of information (publications). With proper labelling, multidimensional maps of information can be constructed, filtering the sources through various grids.
The MiPMap labels (filters) are grouped into various topics (properties).


MiP areas

Property:MiP area
β€’β€’ Respiration β€’β€’ Instruments;methods β€’β€’ mt-Biogenesis;mt-density β€’β€’ mt-Structure;fission;fusion β€’β€’ mt-Membrane β€’β€’ mtDNA;mt-genetics β€’β€’ nDNA;cell genetics β€’β€’ Genetic knockout;overexpression β€’β€’ Comparative MiP;environmental MiP β€’β€’ Gender β€’β€’ Developmental biology β€’β€’ Exercise physiology;nutrition;life style β€’β€’ mt-Medicine β€’β€’ Patients β€’β€’ Pharmacology;toxicology β€’β€’ mt-Awareness
  • Patients: when there is real information about patients, not just whenever a pathology is dealt with

Organism

Property:Mammal and model
β€’β€’ Human β€’β€’ Pig β€’β€’ Mouse β€’β€’ Rat β€’β€’ Guinea pig β€’β€’ Bovines β€’β€’ Horse β€’β€’ Dog β€’β€’ Rabbit β€’β€’ Cat β€’β€’ Other mammals β€’β€’ Chicken β€’β€’ Zebrafish β€’β€’ Drosophila β€’β€’ Artemia β€’β€’ Caenorhabditis elegans β€’β€’ Saccharomyces cerevisiae β€’β€’ Birds β€’β€’ Reptiles β€’β€’ Amphibians β€’β€’ Fishes β€’β€’ Chelicerates β€’β€’ Crustaceans β€’β€’ Hexapods β€’β€’ Myriapods β€’β€’ Annelids β€’β€’ Molluscs β€’β€’ Nematodes β€’β€’ Other invertebrates β€’β€’ Fungi β€’β€’ Plants β€’β€’ Protists β€’β€’ β€’β€’ Eubacteria β€’β€’ Archea

Tissues;cells

Property:Tissue and cell
β€’β€’ Heart β€’β€’ Skeletal muscle β€’β€’ Nervous system β€’β€’ Liver β€’β€’ Kidney β€’β€’ Lung;gill β€’β€’ Islet Cell; Pancreas; Thymus β€’β€’ Endothelial; Epithelial; Mesothelial Cell β€’β€’ Blood cells β€’β€’ Fat β€’β€’ Genital β€’β€’ Other cell lines β€’β€’ CHO β€’β€’ HEK β€’β€’ HeLa β€’β€’ Neuroblastoma β€’β€’ Fibroblast β€’β€’ HUVEC β€’β€’ Macrophage-derived stem cells β€’β€’ Lymphocyte β€’β€’ Platelet β€’β€’ Stem cells

Preparations

Property:Preparation
β€’β€’ Intact Organism β€’β€’ Intact Organ β€’β€’ Intact cells β€’β€’ Permeabilized cells β€’β€’ Permeabilized tissue β€’β€’ Homogenate β€’β€’ Isolated Mitochondria β€’β€’ SMP β€’β€’ Chloroplasts β€’β€’ Enzyme β€’β€’ Oxidase; Biochemical Oxidation

Enzymes

Property:Enzyme
β€’β€’ Adenine Nucleotide Translocase β€’β€’ Complex I β€’β€’ Complex II; Succinate Dehydrogenase β€’β€’ Complex III β€’β€’ Complex IV; Cytochrome c Oxidase β€’β€’ Complex V; ATP Synthase β€’β€’ Inner mtMembrane Transporter β€’β€’ Marker Enzyme β€’β€’ Supercomplex β€’β€’ TCA Cycle and Matrix Dehydrogenases β€’β€’ Uncoupling protein

Stress conditions

Property:Stress
β€’β€’ Cell death β€’β€’ Cryopreservation β€’β€’ Ischemia-reperfusion β€’β€’ Permeability transition β€’β€’ Oxidative stress;RONS β€’β€’ Hypothermia; hyperthermia β€’β€’ Mitochondrial desease

Pathological states

Property:Diseases
β€’β€’ Aging; senescence β€’β€’ Alzheimer's β€’β€’ Autism β€’β€’ Cancer β€’β€’ Cardiovascular β€’β€’ COPD β€’β€’ Diabetes β€’β€’ Inherited β€’β€’ Infectious β€’β€’ Myopathy β€’β€’ Neurodegenerative β€’β€’ Obesity β€’β€’ Parkinson's β€’β€’ Sepsis β€’β€’ Other

Regulation;kinetics

Property:Respiration and regulation
β€’β€’ Aerobic glycolysis β€’β€’ ADP β€’β€’ ATP β€’β€’ ATP production β€’β€’ Calcium β€’β€’ Coupling efficiency;uncoupling β€’β€’ Cyt c β€’β€’ Flux control β€’β€’ Inhibitor β€’β€’ Ion;substrate transport β€’β€’ mt-Membrane potential β€’β€’ Oxygen kinetics β€’β€’ PCr;Cr β€’β€’ pH β€’β€’ Phosphate β€’β€’ Redox state β€’β€’ Substrate β€’β€’ Temperature β€’β€’ Threshold;excess capacity β€’β€’ Uncoupler β€’β€’ Fatty acid β€’β€’ Amino acid
  • Oxygen: Oxygen kinetics, oxygen dependence of respiration and mitochondrial processes


Coupling control states

Property:Coupling states
β€’β€’ LEAK β€’β€’ ROUTINE β€’β€’ OXPHOS β€’β€’ ET-pathway

Pathway control states

Property:Pathways
β€’β€’ F β€’β€’ N β€’β€’ S β€’β€’ Gp β€’β€’ DQ β€’β€’ CIV β€’β€’ NS β€’β€’ Other combinations β€’β€’ ROX

High-resolution respirometry - HRR

Property:Instrument and method
β€’β€’ High-resolution respirometry: Oxygraph-2k β€’β€’ TIP2k β€’β€’ O2k-Fluorometer β€’β€’ pH β€’β€’ NO β€’β€’ TPP β€’β€’ Ca β€’β€’ O2k-Spectrophotometer β€’β€’ O2k-Manual β€’β€’ O2k-Protocol β€’β€’ Theory

Additional labels

β€’β€’
  • Labels: indicates that publication has been entered but not yet labelled or that labelling might need revision.
  • noPDF: no PDF was available for the implementation of this publication; labelling is merely based on the abstract.
  • [Epub ahead of print] helps in finding and complementing references with no available issue and page numbers at the time of implementation.
  • MitoFitPublication: To label publications affiliated with the MitoFit project.
  • Date in the format yyyy-mm, e.g. 2015-12: indicates the year and month the publication was implemented and helps in creating the table of recently added Publications.


Bioblast-publications.jpg

Publications in the MiPMap

Mitochondrial properties in organisms (species), cell types and tissues

Journals


Initiation