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O2k-OpenSupportAlert2021 Archive

From Bioblast
Answered Questions from the »Oroboros Ecosystem Agenda 2021 Archive«

Dec 2021

  • Dec-09 Th
O2k-Open SupportInfo: improve How do you measure ROUTINE respiration?

ROUTINE respiration (R) of living cells is measured before permeabilization of the cell membrane either in cell culture medium or any other respiration media (e.g. MiR05) in the presence or absence of exogenous substrates. Allow R to stabilize for 15-20 min.
- »ROUTINE respiration« and »Doerrier 2018 Methods Mol Biol« 
- communicated by »Komlodi Timea« and »Schmitt Sabine«

Nov 2021

  • Nov-25 Th
O2k-Open SupportInfo: improve What is the difference between the O2k-Fluo Smart-Module and the O2k-Fluo LED2-Module?

The O2k-Fluo Smart-Module, compatible with O2k-series H-I, improves upon the O2k-Fluo LED2-Module for O2k-series D-G, with pre-calibrated Smart Fluo-Sensors that provide direct input into DatLab and have sensor-specific memory to obtain reproducible light intensities with different sensors.
- »O2k-Fluo Smart-Module and O2k-Fluo LED2-Module«
- communicated by »Komlodi Timea« and »Cecatto Cristiane «

Oct 2021

  • Oct-28 Th
O2k-Open SupportInfo: improve New excel templates for H2O2 flux analysis with the Amplex UltraRed assay

- » H2O2 flux Excel templates« and »MiPNet24.10 H2O2 flux analysis«
- communicated by »Komlodi Timea« and »Cardoso Luiza«

Sep 2021

  • Sep-29 We
O2k-Open SupportInfo: improve New excel templates and MiPNet for ATP production analysis with the Magnesium Green assay

- »MgG Excel templates« and »MiPNet26.10 MgG data analysis«
- communicated by »Cardoso Luiza« and »Komlodi Timea«

  • Sep-22 We
O2k-Open SupportInfo: improve New excel templates for mitochondrial membrane potential analysis using fluorescence dyes

- »mt-membrane potential Excel templates« and »MiPNet24.09 General Template for Mt-membrane Potential Analysis«
- communicated by »Komlodi Timea« and »Cardoso Luiza«

  • Sep-09 Th
O2k-Open SupportInfo: improve Can I compare Amplex UltraRed (AmR) experiments in which the H2O2 sensitivity is different?

The H2O2 sensitivity is calculated to calibrate the raw fluorescence signal to H2O2 equivalent concentration. Using the same gain and fluorescence intensity it is possible to compare experiments with different sensitivities.
- »AmR assay H2O2 sensitivity«
- communicated by »Cardoso Luiza« and »Komlodi Timea«

Aug 2021

  • Aug-26 Th
O2k-Open SupportInfo: improve Is it normal to see a pink coloring in the medium at the end of an experiment with Amplex UltraRed (AmR)?

The pink coloring is due to the accumulation of UltroxRed, generated from Amplex UltraRed reacting with H2O2.
- »AmR assay and color of the medium«
- communicated by »Cardoso Luiza« and »Komlodi Timea«

  • Aug-19 Th
O2k-Open SupportWarning: loss of data Which chemicals can I use in an experiment with Amplex UltraRed (AmR)?

Certain substances are incompatible due to their effect on the AmR assay sensitivity. Testing this effect before use is recommended.
- »Chemical compatibility with AmR«
- communicated by »Cardoso Luiza« and »Cecatto Cristiane«

  • Aug-12 Th
O2k-Open Support Take care Do you know how to minimize the dilution of the AmR assay components upon sample addition?

Learn more about our recommendations:
- » AmR assay dilution «
- communicated by »Komlodi Timea« and »Cecatto Cristiane«

  • Aug-05 Th
O2k-Open SupportInfo: improve What is the advantage of using flux control ratios (FCRs)?

FCRs provide information on coupling and pathway control of mitochondrial respiration independent of (i) mt-content in cells or tissues, (ii) purification of isolated mitochondrial preparations, and (iii) determination of tissue mass or mt-markers.
- »Flux control ratio«
- communicated by »Cardoso Luiza« and »Cecatto Cristiane«

Jul 2021

  • Jul-29 Th
O2k-Open SupportInfo: improve Do you know how to export a user-specific DL-protocol (*.DLPU)?

- »Export_DL-Protocol_User_(*.DLPU)« and »O2k-Videosupport:Export DL-Protocol User«
- communicated by »Schmitt Sabine«, »Cecatto Cristiane«, and »Komlodi Timea«

  • Jul-28 We
O2k-Open SupportInfo: improve Need to tailor a SUIT protocol to answer your research question?

See how to modify existing DL-protocols.
- »Enable_DL-Protocol_editing«
- communicated by »Schmitt Sabine«, »Cecatto Cristiane«, and »Komlodi Timea«

  • Jul-21 We
MitoPedia: SUIT Not sure which SUIT protocol to apply?

The SUITbrowser is the perfect tool to find the best SUIT protocol for your research question.
- » SUITbrowser« and »O2k-Videosupport: How to find a DL-Protocol«

- communicated by »Schmitt Sabine« and »Komlodi Timea«

Jun 2021

  • Jun-28 Mo
O2k-Open SupportInfo: improve Do I need to calibrate the fluorescence signal with safranin?

It is possible to run the experiment without calibration, presenting only the fluorescence intensity plot. However, a simple two-point or multiple-point calibration for safranin concentration is possible.
- »Safranin calibration«

  • Jun-16 We
O2k-Open SupportInfo: improve Simultaneous fluctuations in O2 slope neg. and the signal of the Peltier power?

This can indicate an electrical disturbance and changing the electrical supply may resolve this problem.
- »Troubleshooting«
- communicated by »Cecatto Cristiane« and »Schmitt Sabine«

  • Jun-07 Mo
O2k-Open SupportWarning: loss of data Do you observe high fluorescence signal even before adding the dye or sample?

Filters that have shifted from the correct position in the Fluo-Sensors might give rise to higher fluorescence signal than usual.
- »Troubleshooting: fluorescence module« 
- communicated by »Komlodi Timea« and »Schmitt Sabine«

  • Jun-03 Th
O2k-Open SupportWarning: loss of data How to ensure quality control when exchanging the 2-mL and the 0.5-mL chambers

Every time you exchange the chambers, a volume calibration and instrumental O2 background test should be performed.
- »MiPNet22.11 Section 5.4. O2k-chamber volume calibration« and »Oxygen flux - instrumental background«
- communicated by »Komlodi Timea« and »Cecatto Cristiane«

May 2021

  • May-25 Tu
O2k-Open SupportTake care Do you enter the correct instrumental background correction in DatLab for the experimental O2 concentrations?

After performing the instrumental background test at the appropriate O2 range, load the parameters in DatLab to ensure accurate correction for external fluxes.
- »O2 background correction in DatLab

- communicated by »Komlodi Timea« and »Cecatto Cristiane«

  • May-17 Mo
O2k-Open SupportInfo: improve Planning to measure proton flux or mitochondrial membrane potential with ion-selective electrodes in the O2k?

Learn how to assemble the reference electrodes:
- »O2k-Videosupport: Assembly of the reference electrode«
- communicated by »Cardoso Luiza« and »Schmitt Sabine«

  • May-04 Tu
O2k-Open SupportInfo: improve Do you know how to apply the air and zero calibration values in DatLab?

This important quality control step ensures accurate measurement of respiration.
For details on how to apply air and zero calibration in DatLab, see:
»Oxygen calibration - DatLab« and »Troubleshooting« 
- communicated by »Komlodi Timea« and »Cecatto Cristiane«

Apr 2021

  • Apr-27 Tu
O2k-Open SupportTake care Why is the fluorescence signal constantly at 10 V or at 0 V?

Follow these steps to localize and solve the problem:
- »Fluorescence signal is constantly at 10 V« and »0 V fluorescence signal«

  • Apr-20 Tu
O2k-Open SupportWarning: loss of data Noisy fluorescence signal?

Follow these steps to localize and solve the problem:
- »Noisy fluorescence signal«

  • Apr-13 Tu
O2k-Open SupportWarning: loss of data Do you know what to do when the fluorescence signal starts at a negative value?

A negative signal may be caused by wet Fluo-Sensors. For further information:
- »Negative fluorescence signal«

  • Apr-06 Tu
O2k-Open Support Warning: loss of data A damaged OroboPOS-Holder may cause medium to leak from the O2k-Chamber.

See how you can check that the OroboPOS-Holders are intact.
- »O2k-OroboPOS-Holder«

Mar 2021

  • Mar-25 Th
O2k-Open SupportInfo: improve O2k-checklist: Get started with an O2k-experiment

The O2k-checklist provides an overview of all essential steps for starting an O2k-experiment.
- » MiPNet20.04_O2k-checklist« 
- » communicated by »Cecatto Cristiane« and »Schmitt Sabine«

Feb 2021

  • Feb-17 We
O2k-Open SupportInfo: improve Do you know how to prepare permeabilized muscle fibers?

The application of high-resolution respirometry in permeabilized muscle fibers provides a sensitive diagnostic tool for the analysis of mitochondrial (dys)function in small biopsy samples.
- »O2k-Videosupport: Fiber permeabilization« 
- »Doerrier 2018 Methods Mol Biol« 
- communicated by »Doerrier Carolina« and »Tindle-Solomon Lisa«

  • Feb-08 Mo
O2k-Open SupportInfo: improve Do you know how to properly insert the ISS-tip into the O2k-chamber?

With the stirrer bar still rotating, insert the ISS-tip to the bottom of the O2k-Chamber, so that it points away from you.
- »MiPNet19.03 O2k-cleaning and ISS: Section 2« 
- communicated by »Doerrier Carolina«, »Cecatto Cristiane« and »Komlodi Timea«

  • Feb-02 Tu
O2k-Open SupportInfo: improve DatLab error messages: What do they mean and how to solve them?

- » DatLab error messages« 
- communicated by »Garcia-Souza Luiz F« and »Tindle-Solomon Lisa«

Jan 2021

  • Jan-11 Mo
O2k-Open SupportInfo: improve Are you a beginner or need a refresher on using SUIT protocols with DatLab7.4?

- » O2k-Videosupport: How to perform an experiment with a SUIT DL-Protocol« and » Run DL-Protocol/Set O2 limit in DatLab « 
- communicated by »Komlodi Timea« and Schmitt Sabine«