Difference between revisions of "Talk:Bioblast alert 2020"

Latest revision as of 14:53, 2 November 2020

In prep

Open Support Might fit with gif

How can you reduce the amount of biological sample needed for high-resolution respirometry?

The O2k-sV-Module provides all the components necessary for a smaller operation volume (0.5 mL) whereby the sample amount used for measuring oxygen flux can be reduced.
- »O2k-sV-Module«
- communicated by »Komlodi Timea« and »Schmitt Sabine«

Are whitish deposits forming on the glass wall of the O2k-Chamber?

These deposits might be an accumulation of proteins and subsequent embedding of other biological material or small glass splinters, and a sign that the O2k-Chamber requires cleaning.
For further details on how to clean the O2k-Chamber properly, see:
- »Cleaning the O2k-chamber«
- communicated by »Komlodi Timea«, »Sabine Schmitt«, and »Lisa Tindle-Solomon«

Other topics:

Why are permeabilized muscle fibers (pfi) a poor sample type for studying reactive oxygen species (ROS) production?

In experiments with pfi, high oxygen concentrations are needed to avoid oxygen limitation. However, the high oxygen pressures used may artificially increase ROS, including H₂O₂ production, making pfi a less optimal model for ROS production studies.
- »Oxygen dependence of ROS production in pfi«
- communicated by »Komlodi Timea« and »Cardoso Luiza«

Why it is necessary to perform multiple H₂O₂ calibrations when using the Amplex UltraRed (AmR) assay?

The sensitivity to H₂O₂ of the Amplex UltraRed assay changes during the experiment, thus requires multiple calibrations. These sensitivity changes may be the function of: 1) experimental time, 2) changes in the optical properties of the respiration medium due to sample/chemical titration, 3) the radical scavenging capacity of the sample, and 4) the concentration of accumulating resorufin (UltroxRed in the case of Amplex UltraRed). Therefore, it is recommended to perform H₂O₂ calibration before sample addition, after sample addition and multiple times during the experiment.
- »Komlodi 2018 Methods Mol Biol«

The DLPs for AmR SUIT protocols already come with multiple steps of H₂O₂ calibrations implemented.
- » SUITbrowser«
- communicated by »Komlodi Timea« and »Cardoso Luiza«

How can you compare respirometric experiments using an internal normalization?

Flux control ratios (FCR) are independent of external measurements (e.g. protein determination, citrate synthase activity) and therefore can be used to analyze data when other normalization methods cannot be applied. Learn more about how to use this option to assess qualitative changes of mitochondrial respiratory control with DatLab and the “O2 analysis template DL7.4”.
- »Flux control ratio«

Read more: Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1 »Bioblast link«

Non-mitochondrial respiration or residual oxygen consumption (Rox)? — Concept-driven constructive terminology frames our perception.

After inhibition of electron-transfer (ET) pathways or in the absence of fuel substrates, both mitochondrial non-ET reactions and non-mitochondrial reactions contribute to residual oxygen consumption in mt-preparations and living cells.
- »BEC: Mitochondrial physiology« — Table 1: Rox induced by non-ET pathway oxidation reactions

SUIT special

Jun-04 Th

Mitochondria show variable preferences for glutamate & malate or pyruvate & malate to support NADH-linked respiration, depending on species, tissues, and pathophysiological state.

DatLab 7.4 provides a step-by-step guide through SUIT-008 and SUIT-014, which can be used in parallel to compare respiratory capacities supported by these NADH-linked fuel substrates.
-»SUIT-008« and »SUIT-014«

Sep-22 Tu

Did you know the reverse electron flow from Complex II to Complex I can be investigated in mitochondrial preparations by measuring hydrogen peroxide production using Amplex UltraRed assay?

The reverse electron flow, also called reverse electron transfer (RET), happens when electrons are transferred from Complex II to the Q-junction and then back to Complex I at high mt-membrane potential. This phenomenon results in high hydrogen peroxide production in some mitochondrial preparations. The SUIT-026 protocol was designed to investigate this effect.
- »SUIT-026«
- communicated by »Komlodi Timea« and »Cardoso Luiza«

Sep-17 Th

Did you know that you can measure the respiratory activity available for phosphorylation of ADP to ATP in living cells?

SUIT protocols from the SUIT-003 family will guide you through the titrations needed to analyze free ROUTINE activity.
- »SUIT-003 O2 ce D009« and »SUIT-003 O2 ce-pce D020«
- communicated by »Cardoso Luiza« and »Komlodi Timea«

On hold

Do you know how to select the proper fluorescence sensors and filter set?

Using different fluorescence sensors, LED and photodiode filters, the O2k-Fluo Smart-Module (or O2k-Fluo LED2-Module) allows for measurement of hydrogen peroxide, ATP, mitochondrial membrane potential, calcium, and numerous other applications open for O2k-user innovation.
- »Selecting the Smart Fluo-Sensor« and »Selecting a Filter Set«

@@ Line 1: / Line 1: @@
 == In prep ==
-::::[[Image:O2k-Publications.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Publications:_Topics |O2k-Publications in the MiPMap]]'''  The mitochondrial gas pedal: Cytosolic calcium controls extramitochondrial pyruvate generation and mitochondrial pyruvate uptake '''
+Open Support
-::::::: - from the O2k-Network » [[FI Helsinki Jacobs HT]] « » [[DE Magdeburg Gellerich FN]] « and»[[DE Magdeburg Debska-Vielhaber G]]«
+Might fit with gif
-::::::* Szibor Marten, Gizatullina Zemfira, Gainutdinov Timur, Endres Thomas, Debska-Vielhaber Grazyna, Kunz Matthias, Karavasili Niki, Hallmann Kerstin, Schreiber Frank, Bamberger Alexandra, Schwarzer Michael, Doenst Torsten, Heinze Hans-Jochen, Leßmann Volkmar, Vielhaber Stefan, Kunz Wolfram S, Gellerich Frank Norbert (2020) Cytosolic, but not matrix, calcium is essential for adjustment of mitochondrial pyruvate supply. J Biol Chem [Epub ahead of print]. [[Szibor 2020 J Biol Chem|»Bioblast link«]]
+:{|
-::::[[Image:O2k-Publications.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Publications:_Topics |O2k-Publications in the MiPMap]]''' Expression of alternative oxidase prevents reverse electron transfer formation in heart mitochondria isolated from mouse'''
-::::::: - from the O2k-Network »[[FI Helsinki Jacobs HT]]«  »[[DE Magdeburg Gellerich FN]]« »[[FI Tampere Dufour E]]« »[[DE Magdeburg Debska-Vielhaber G]]« »[[DE Frankfurt Wittig I]]« and »[[UK Brighton Moore AL]]«
+| width="110" align="center" | [[File:MitoPedia.jpg|left|80px|MitoPedia|link=MitoPedia]]
-::::::* Szibor Marten, Gainutdinov Timur, Fernandez-Vizarra Erika, Dufour Eric, Gizatullina Zemfira, Debska-Vielhaber Grazyna, Heidler Juliana, Wittig Ilka, Viscomi Carlo, Gellerich Frank Norbert, Moore Anthony L (2019) Bioenergetic consequences from xenotopic expression of a tunicate AOX in mouse mitochondria: switch from RET and ROS to FET. Biochim Biophys Acta Bioenerg 1861:148137. [[Szibor 2019 Biochim Biophys Acta Bioenerg|»Bioblast link«]]
+|''' How can you reduce the amount of biological sample needed for high-resolution respirometry?  '''<br>
+The O2k-sV-Module  provides all the components necessary for a smaller operation volume (0.5 mL) whereby the sample amount used for measuring oxygen flux can be reduced.   <br>
+- »'''[[O2k-sV-Module]]'''«  <br>
+- communicated by »[[Komlodi Timea]]« and »[[Schmitt Sabine]]«
+|}
+:{|
+| width="110" align="center" | [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]][[File:Blue-info.png|25px|Info: improve]]
+|'''Are whitish deposits forming on the glass wall of the O2k-Chamber? '''<br>
+These deposits might be an accumulation of proteins and subsequent embedding of other biological material or small glass splinters, and a sign that the O2k-Chamber requires cleaning. <br>
+For further details on how to clean the O2k-Chamber properly, see: <br>
+- »[[O2k-chamber#Cleaning_the_O2k-chamber|Cleaning the O2k-chamber]]«<br>
+- communicated by »[[Komlodi Timea]]«, »Sabine Schmitt«, and »Lisa Tindle-Solomon«
+|}
+Other topics:
-::::[[Image:O2k-Publications.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Publications:_Topics |O2k-Publications in the MiPMap]] Parkinson’s Disease Awareness Month:''' Dominant mutation in Parkinson’s Disease causes loss of protein function in mitochondria'''
+:{|
-::::::: - from the O2k-Network »[[FR Angers Gueguen N]]« and »[[BE Leuven Spinazzi M]]«
-::::::* Cornelissen T, Spinazzi M, Martin S, Imberechts D, Vangheluwe P, Bird M, De Strooper B, Vandenberghe W (2020) CHCHD2 harboring the Parkinson's disease-linked T61I mutation precipitates inside mitochondria and induces precipitation of wild-type CHCHD2. Hum Mol Genet [Epub ahead of print]. [[Cornelissen 2020 Hum Mol Genet|»Bioblast link«]]
+| width="110" align="center" | [[File:MitoPedia.jpg|left|80px|MitoPedia|link=MitoPedia]]
+|''' Why are permeabilized muscle fibers (pfi) a poor sample type for studying reactive oxygen species (ROS) production?  '''<br>
+In experiments with pfi, high oxygen concentrations are needed to avoid oxygen limitation. However, the high oxygen pressures used may artificially increase ROS, including H<sub>2</sub>O<sub>2</sub> production, making pfi a less optimal model for ROS production studies. <br>
+- »'''[[Permeabilized_muscle_fibers#Oxygen_dependence_of_ROS_production_-_are_permeabilized_fibers_a_valid_model.3F|Oxygen dependence of ROS production in pfi]]'''« <br>
+- communicated by »[[Komlodi Timea]]« and »[[Cardoso Luiza]]«
+|}
-:::: [[Image:SUIT icon.jpg|80px|link=https://wiki.oroboros.at/index.php/MitoPedia:_SUIT |MitoPedia: SUIT]]'''Do you want to search the best [[SUIT]] protocol for your research questions?'''  Use the SUITbrowser: »'''[[SUITbrowser]]'''«
+:{|
+| width="110" align="center" | [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Yellow-take care.png|25px|Take care]]
+| '''Why it is necessary to perform multiple H<sub>2</sub>O<sub>2</sub> calibrations when using the [[Amplex UltraRed]] (AmR) assay?'''<br>
+The sensitivity to H<sub>2</sub>O<sub>2</sub> of the Amplex UltraRed assay changes during the experiment, thus requires multiple calibrations. These sensitivity changes may be the function of: 1) experimental time, 2) changes in the optical properties of the respiration medium due to sample/chemical titration, 3) the radical scavenging capacity of the sample, and 4) the concentration of accumulating resorufin (UltroxRed in the case of Amplex UltraRed). Therefore, it is recommended to perform H<sub>2</sub>O<sub>2</sub> calibration before sample addition, after sample addition and multiple times during the experiment.  <br>
+- »[[Komlodi 2018 Methods Mol Biol]]« <br>
-:::: [[File:O2k-brief.png|45px|link=http://wiki.oroboros.at/index.php/O2k-brief|O2k-brief repository]]  '''Novel diurnal action of of mitochondrial stress-induced GDF15 in systemic metabolism regulation'''
+The DLPs for AmR [[SUIT]] protocols already come with multiple steps of H<sub>2</sub>O<sub>2</sub> calibrations implemented. <br>
+- » [https://www.bioblast.at/index.php/SUITbrowser SUITbrowser]« <br>
-::::::: - from the O2k-Network »[[DE Nuthetal Klaus S]]«
+- communicated by »[[Komlodi Timea]]« and »[[Cardoso Luiza]]«
-::::::* Ost M, Igual Gil C, Coleman V, Keipert S, Efstathiou S, Vidic V, Weyers M, Klaus S (2020) Muscle-derived GDF15 drives diurnal anorexia and systemic metabolic remodeling during mitochondrial stress. EMBO Rep [Epub ahead of print].  - [[Ost 2020 EMBO Rep |»Bioblast link«]]
+|}
-<br />
-:::: [[Image:O2k-Network.png|left|70px|link=http://wiki.oroboros.at/index.php/O2k-Network|O2k-Network]] An amazing number of new [[O2k-Publications: Topics |O2k-Publications]] from China » '''[[O2k-Network Labs China]]''' «
-<br />
-:::: [[Image:Gentle-Science_Ganesha.jpg|left|60px|link=http://www.bioblast.at/index.php/Gentle_Science|Gentle Science]] '''Let's talk COVID-19 - a new culture of communication in science.''' - [https://www.sciencemag.org/news/2020/02/completely-new-culture-doing-research-coronavirus-outbreak-changes-how-scientists Kay Kupferschmidt in Science]
-<br />
-:::: [[Image:MitoFit.jpg|left|50px|link=http://www.mitofit.org/index.php/MitoFit |MitoFit]] The MitoFit Preprint Archives was created as an Open Access preprint server for mitochondrial physiology and bioenergetics - »'''[[MitoFit Preprint Archives]]'''«
-<br />
-::::[[Image:O2k-Publications.jpg|60px|left|link=http://wiki.oroboros.at/index.php/O2k-Publications:_Topics |O2k-Publications in the MiPMap]] ''' Zika virus infection leads to mitochondrial dysfunction'''
-::::::: - from the O2k-Network »[[BR Rio de Janeiro Galina A]]«
-::::::* Ledur PF, Karmirian K, Pedrosa CDSG, Souza LRQ, Assis-de-Lemos G, Martins TM, Ferreira JCCG, de Azevedo Reis GF, Silva ES, Silva D, Salerno JA, Ornelas IM, Devalle S, Madeiro da Costa RF, Goto-Silva L, Higa LM, Melo A, Tanuri A, Chimelli L, Murata MM, Garcez PP, Filippi-Chiela EC, Galina A, Borges HL, Rehen SK (2020) Zika virus infection leads to mitochondrial failure, oxidative stress and DNA damage in human iPSC-derived astrocytes. Sci Rep 10:1218. - [[Ledur 2020 Sci Rep |»Bioblast link«]]
-:::: [[File:O2k-brief.png|45px|link=http://wiki.oroboros.at/index.php/O2k-brief|O2k-brief repository]]  '''Could exercise protect against the effects of aging on mitochondrial function?'''
-::::::: - from the O2k-Network »[[KR Busan Han J]]« »[[KR Incheon Kwak HB]]«
-::::::* No MH, Heo JW, Yoo SZ, Kim CJ, Park DH, Kang JH, Seo DY, Han J, Kwak HB (2020) Effects of aging and exercise training on mitochondrial function and apoptosis in the rat heart. Pflugers Arch 472:179-93.  - [[No 2020 Pflugers Arch |»Bioblast link«]]
-<br />
+:{|
+| width="110" align="center" | [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]][[File:Blue-info.png|25px|Info: improve]]
+|'''How can you compare respirometric experiments using an internal normalization?'''<br>
+Flux control ratios (''FCR'') are independent of external measurements (''e.g.'' protein determination, citrate synthase activity) and therefore can be used to analyze data when other normalization methods cannot be applied. Learn more about how to use this option to assess qualitative changes of mitochondrial respiratory control with DatLab and the “O2 analysis template DL7.4”.
+<br>
+- »[[Flux control ratio]]«
+Read more: Gnaiger Erich ''et al'' ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1 »[[BEC_2020.1_doi10.26124bec2020-0001.v1|Bioblast link]]«
+|}
+:{|
+| width="110" align="center" | [[File:MitoPedia.jpg|left|80px|MitoPedia|link=MitoPedia]]
+| '''Non-mitochondrial respiration or [[residual oxygen consumption]] (''Rox'')? — Concept-driven constructive terminology frames our perception.'''
+After inhibition of electron-transfer (ET) pathways or in the absence of fuel substrates, both ''mitochondrial'' non-ET reactions and ''non-mitochondrial'' reactions contribute to ''residual oxygen consumption'' in mt-preparations and living cells.  <br>
+- »'''[https://www.bioenergetics-communications.org/index.php/BEC_2020.1_doi10.26124bec2020-0001.v1 BEC: Mitochondrial physiology]'''« — Table 1: ''Rox'' induced by non-ET pathway oxidation reactions
+|}
+SUIT special
+* '''Jun-04 Th'''
+:{|
+| width="110" align="center" | [[Image:SUIT icon.jpg|80px|link=https://wiki.oroboros.at/index.php/MitoPedia:_SUIT |MitoPedia: SUIT]]
+| '''Mitochondria show variable preferences for [[GM|glutamate & malate]] or [[PM|pyruvate & malate]] to support NADH-linked respiration, depending on species, tissues, and pathophysiological state.''' <br>
+DatLab 7.4 provides a step-by-step guide through SUIT-008 and SUIT-014, which can be used in parallel to compare respiratory capacities supported by these NADH-linked fuel substrates. <br>
+-»'''[[SUIT-008]]'''« and »'''[[SUIT-014]]'''«
+|}
+* '''Sep-22 Tu'''
+:{|
+| width="110" align="center" | [[Image:SUIT icon.jpg|80px|link=https://wiki.oroboros.at/index.php/MitoPedia:_SUIT |MitoPedia: SUIT]]
+|''' Did you know the reverse electron flow from Complex II to Complex I can be investigated in mitochondrial preparations by measuring hydrogen peroxide production using [[Amplex UltraRed]] assay?'''<br>
+The reverse electron flow, also called reverse electron transfer (RET), happens when electrons are transferred from Complex II to the Q-junction and then back to Complex I at high mt-membrane potential. This phenomenon results in high hydrogen peroxide production in some mitochondrial preparations. The SUIT-026 protocol was designed to investigate this effect.  <br>
+- »'''[[SUIT-026]]'''« <br>
+- communicated by »[[Komlodi Timea]]« and »[[Cardoso Luiza]]«
+|}
+* '''Sep-17 Th'''
+:{|
+| width="110" align="center" | [[Image:SUIT icon.jpg|80px|link=https://wiki.oroboros.at/index.php/MitoPedia:_SUIT |MitoPedia: SUIT]]
+|''' Did you know that you can measure the respiratory activity available for phosphorylation of ADP to ATP in living cells?'''<br>
+SUIT protocols from the [[SUIT-003]] family will guide you through the titrations needed to analyze [[free ROUTINE activity]].<br>
+- »'''[[SUIT-003 O2 ce D009]]'''« and '''»[[SUIT-003 O2 ce-pce D020]]'''« <br>
+- communicated by »[[Cardoso Luiza]]« and »[[Komlodi Timea]]«
+|}
 == On hold ==
-::::[[File:MitoPedia.jpg|60px|MitoPedia]] Did you ever think that units for body mass could be an issue? » '''[[Body mass]]''' «
-:::: [[File:MitoPedia.jpg|60px|MitoPedia]] Why do we fight gas bubbles? - Dive deep into '''[[Oxygen solubility]]'''
+:{|
+| width="110" align="center" | [[File:MitoPedia.jpg|left|80px|MitoPedia]]
+| '''Do you know how to select the proper fluorescence sensors and filter set?''' <br>
+Using different fluorescence sensors, LED and photodiode filters, the [https://www.oroboros.at/index.php/product/o2k-fluo-smart-module/ O2k-Fluo Smart-Module] (or [https://www.oroboros.at/index.php/product/o2k-fluo-led2-module/ O2k-Fluo LED2-Module]) allows for measurement of [[hydrogen peroxide]], [[ATP]], [[mitochondrial membrane potential]], [[calcium]], and numerous other applications open for O2k-user innovation.<br>
+- »'''[[O2k-Fluo_Smart-Module#Select_the_Smart_Fluo-Sensors|Selecting the Smart Fluo-Sensor]]'''« and »'''[[O2k-Fluo_LED2-Module#Setup_of_the_O2k-Fluo_LED2-Module|Selecting a Filter Set]]'''«
+|}