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Template talk:Next oroboros ecosystem agenda

From Bioblast
Antunes Diana (talk) 08:58, 5 May 2020 (CEST) Format for new Agenda/Alerts entries:
 {|
 | logos
 | title in bold <br>
 - link
 |}
 

e.g.,

O2k-Open SupportWarning: loss of data Did you know that the proper use of TIP2k-Filter Papers may avoid an unstable O2 slope neg. signal during Instrumental background correction?

- »Instrumental background« and »TIP2k Filter Papers«

See the scheme:


Agenda/Alerts body text format


MitoPedia alert

Example:
MitoPedia
Measuring fatty acid oxidation (FAO)-linked respiration requires a low concentration of malate

In the absence of malate, accumulation of Acetyl-CoA inhibits FAO.
- »Fatty acid oxidation pathway control state«, »Mitochondrial Pathways: Chapter 5« 
- communicated by »Cecatto Cristiane« and »Cardoso Luiza« 


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March 11th

MitoPedia
Why is it important to perform respirometry with permeabilized muscle fibers (pfi) under a high [O2] regime?

Long diffusion distances in the pfi result in an O2 diffusion limitation, which is overcome by increasing the O2 partial pressure inside the chamber. Proper instrumental background correction is a must and O2 dependence of ROS production should be considered.
- »Permeabilized muscle fibers«, »Oxygen flux - instrumental background« 
- communicated by »Grings Mateus« and »Cardoso Luiza« 

March 25th

MitoPedia
Living cells or intact cells?

Living cells are frequently labelled as intact cells in the sense of the total cell count, but intact may suggest dual meanings of viable or unaffected by a disease or mitochondrial injury.
- »Living cells«, »BEC 2020.1«, »Gnaiger 2020 BEC MitoPathways« 
- communicated by »Leo Elettra« and »Timon-Gomez Alba« 

April 8th

MitoPedia
Is fatty acid oxidation (FAO) considered as CI- or CII-driven respiration?

Neither. FAO generates acetyl-coA, which will enter the TCA cycle, and FADH2, resulting in simultaneous electron transfer into the Q-junction through the electron transferring flavoprotein complex (CETF) and Complex I.
- »Fatty acid oxidation«, »Gnaiger 2020 BEC MitoPathways«, »Gnaiger 2023 MitoFit CII« 
- communicated by »Timon-Gomez Alba« and »Willis Jaime R« 

Under construction

on hold until the page is updated
FAT4BRAIN
A FAO-mito-CNS platform to help fatty acid-related respiration measurements was developed in the FAT4BRAIN project

- » FAT4BRAIN FAO-mito-CNS platform «

O2k-Brief alert

  • Example:
O2k-brief repository Antitumoral properties of triterpenic acid functionalized gold nanoparticles arise from decreasing mitochondrial respiration
  • Mioc M, Mioc A, Racoviceanu R, Ghiulai R, Prodea A, Milan A, Barbu Tudoran L, Oprean C, Ivan V, Șoica C (2023) The antimelanoma biological assessment of triterpenic acid functionalized gold nanoparticles. »Bioblast link«

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O2k-Publications alert

  • Example:
O2k-Publications in the MiPMap "Mitochondria–nucleus communication and its integration within the maintenance of cellular homeostasis constitute key determinants of cellular fate and organism health in the context of cellular stress, homeostasis perturbation, and disease"
  • Temelie M, Talpur R, Dominguez-Prieto M, Dantas Silva A, Cenusa C, Craciun L, Savu DI, Moisoi N (2023) Impaired integrated stress response and mitochondrial integrity modulate genotoxic stress impact and lower the threshold for immune signalling. »Bioblast link«
from the O2k-Network »UK Leicester Moisoi N«

Author names of O2k-Publications/ Brief for the Agenda vs Bioblast

Click to expand or collaps

Guidelines to update a reference

When creating an O2k-Publication/Brief alert, it is the responsibility of the author to check if the reference is accordingly to the correct guidelines:

Reference example.png

Correct format for a person called “First Name Surname”:
In the gray box should be “Surname FN” - From where references to be used as O2k-Publication/Brief alerts are copied from.

Gray box reference.png

In the links should be “ Surname First N”

Authors names links reference.png

How to edit:
A) Check if all authors with profiles in Bioblast (blue links) have their profiles with full name. If they have, proceed to next step (B). If not, you need to move it following the steps “How to move a profile” below.
B) Click in “Edit with form”.
C) The gray box is edited in “Reference” and the links are changed in “Author(s)”. Change it accordingly and click in “save page” at the end of the page.

Editing reference.png

How to move a profile (instructions sent by Marija):

So let’s take for example my page: Beno M [1]

As you can see there is a redirect from Beno Marija to Beno M. What has to be done is to switch the content of those pages. Here are the steps:
1. Go to e.g. “Beno M” on edit
2. Click on “Move”
3. Change the new title to the full name of the person. In my case it will be Beno M to Beno Marija

BenoMreference.jpg

4. Now it should look like that:

BenoMarijaReference.png

5. Click on “Move” and leave all the ticked boxes
6.Done
After that you can continue in step B.
If you have any doubt you can contact Cristiane, Marija or Mario.

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Oliveira 2023 BEC
A BEC Spotlight on Rodríguez et al's Drosophila mitochondrial research methodology
from the O2k-Network »BR Rio de Janeiro Oliveira MF«

March 14th

O2k-Publications in the MiPMap Mitochondrial ultrastructure and respiration are affected during EDL [Extensor digitorum longus muscle] aging.
  • Fernando R, Shindyapina AV, Ost M, Santesmasses D, Hu Y, Tyshkovskiy A, Yim SH, Weiss J, Gladyshev VN, Grune T, Castro JP (2023) Downregulation of mitochondrial metabolism is a driver for fast skeletal muscle loss during mouse aging. »Bioblast link«
from the O2k-Network »DE Leipzip Ost M«


April 11th - World Parkinson's Disease Day

O2k-Publications in the MiPMap "The analysis revealed that PD [Parkinson’s disease] fibroblasts tended to have lower basal and maximal respiration rates than the controls"
  • Kamienieva I, Charzyńska A, Duszyński J, Malińska D, Szczepanowska J (2023) In search for mitochondrial biomarkers of Parkinson's disease: Findings in parkin-mutant human fibroblasts. »Bioblast link«
from the O2k-Network »PL Warsaw Szewczyk A«

MiPNet

  • Example:
O2k-Open SupportInfo: improve "No bubbles should be trapped in the electrolyte reservoir after membrane application and mounting"

- »MiPNet28.10 SmartPOS-service«
- communicated by »Timon-Gomez Alba« and »[[]]«

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O2k-Open Support alert

  • Examples:
O2k-Open SupportInfo: take care Does your polarographic oxygen sensor (POS) need a deep clean?

A POS with a very dark anode might need several rounds of ammonia cleaning, possibly including prolonged exposure overnight to restore performance specifications.
- »POS service«
- communicated by »Cecatto Cristiane« and »Leo Elettra«

O2k-Open SupportWarning: loss of data Did you know that a humid environment and/or liquid spillage may lead to a high raw POS signal [V]?

See how to clean and dry the electrical connections of the OroboPOS-Connector.
- »Cleaning the electrical connections«
- communicated by »Cecatto Cristiane« and »Baglivo Eleonora«

O2k-Open SupportInfo: improve Unusual stirrer bar rotation?

A “jumping” stirrer or a slow rotation of the stirrer bar may indicate a problem either with the stirrer itself or with the cleaning of the glass chamber.
- »Stirrer bar - technical support«
- communicated by »Baglivo Eleonora« and »Grings Mateus«

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O2k-Open SupportInfo: improve How to store the POS overnight and up to several months?

Fill the chamber and the receptacle of the loosely inserted stopper with 70 % EtOH, add the Cover-slip and switch off the O2K.
- »O2k-cleaning and ISS«
- communicated by »Leo Elettra« and »Grings Mateus«

O2k-Open SupportInfo: improve Do you observe an unstable O2 slope negative following TIP2k titrations during an instrumental O2 background test?

Incorrect placement of TIP2k Filter Papers can lead to liquid accumulation and convective oxygen backdiffusion. Check for proper placement by confirming they are fully in contact with the stopper receptacle.
- »Instrumental O2 background«, »Unstable O2 slope negative«
- communicated by »Grings Mateus« and »Baglivo Eleonora«

March 18

O2k-Open SupportInfo: improve What if Alert: Error in titrations! appears in your O2 analysis template file?

The O2 analysis template recognizes discrepancies between the protocol selected in the first tab and the imported marks. Check the titration sequence and mark names against the protocol copied from the DLD file.
- »O2 flux analysis«
- communicated by »Timon-Gomez Alba« and »Leo Elettra«

O2k-Feedback alert

  • Example (if the person has a profile, link the name to the profile with Cristiane Cecatto:
O2k-Feedback “Thank you very much for your thorough help. I appreciate the time you took to provide me with all the answers and supportive literature to realize the potential of the O2k-respirometer in bioenergetics research”

Badr Ibrahim, PhD from Betterhumans Inc., US
- »O2k-Feedback«

O2k-Feedback “Thank you very much for your thorough help. I appreciate the time you took to provide me with all the answers and supportive literature to realize the potential of the O2k-respirometer in bioenergetics research”

Badr Ibrahim, PhD from the O2k-Network »UK Leicester Moisoi N«
- »O2k-Feedback«

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MitoFit Preprints

  • Example:
Bioenergetics Communications From preprint to BEC manuscript with published Open Peer Reviews:
  • Komlódi T, Sobotka O, Gnaiger E (2021) Facts and artefacts on the oxygen dependence of hydrogen peroxide production using Amplex UltraRed. Bioenerg Commun 2021.4. doi:10.26124/BEC:2021-0004
from the O2k-Network »AT Innsbruck Oroboros«

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Under discussion

This one needs an update of the Bioblast page and clarification of MiPNet06.03

O2k-Open SupportInfo: improve Did you enter the correct oxygen solubility factor in DatLab?

The oxygen solubility factor of the incubation medium, FM, expresses the effect of the salt concentration on oxygen solubility relative to pure water. The correct oxygen solubility factor of your experimental medium or buffer needs to be entered in DatLab for proper calculation of the oxygen concentration.
- »Oxygen solubility factor«
- communicated by »Schmitt Sabine« and »[[ ]]«

This one needs a BioBlast link:

O2k-Open SupportInfo: improve When filling in the volume of uncoupler in the DatLab mark or the excel template, should one enter the total volume added or the volume to get to the highest flux?

The volume added until the mark, equal to the highest flux, should be entered. Anything titrated after this mark should be summed to the other volumes before the next mark because this will be considered to calculate the sample dilution.
- »LINK and O2 flux analysis with DatLab 7.4«
- communicated by »Cardoso Luiza« and »[[ ]]«


Removed for correction

  • Nov-30 Mo
O2k-Open SupportInfo: improve Noisy oxygen signal? Check the OroboPOS and OroboPOS-Connector to clean electrical connections.

Contaminating grease, salt crystals and moisture can be removed with a dry paper cloth or a paper cloth moistened with water and then absolute ethanol.
- »Cleaning the electrical connections« 
- communicated by »Schmitt Sabine« and »Komlodi Timea«

WGT recommended not to use water for cleaning. Erich introduced water for cleaning to remove salt crystals.


O2k-Open SupportWarning: loss of data Do you perform the leaky chamber test after chamber assembly?

An unnoticed leak from the chamber may affect your data, therefore we recommend performing the Leaky chamber test - especially after chamber reassembly.
- »Leaky chamber test« and » https://intern.oroboros.at/index.php/Overnight_test_after_O2k-chamber_assembly«