Difference between revisions of "Template talk:Next oroboros ecosystem agenda"

Revision as of 09:34, 15 January 2024

Antunes Diana (talk) 08:58, 5 May 2020 (CEST) Format for new Agenda/Alerts entries:

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e.g.,

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:

MitoPedia alert

Example:

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«

The sum of the O₂ fluxes measured in the presence of NADH-linked substrates alone and succinate as the single substrate is typically higher than the O₂ flux obtained using a combination of all these substrates. This effect is described as incomplete additivity:
- »Additive effect of convergent electron flow«
- communicated by »Cardoso Luiza« and »Grings Mateus«

January 2nd

New year, new state? What is REN state?

REN state is now distinguished from ROX state: REN is measured in mitochondrial preparations without addition of substrates, whereas ROX is due to oxidative side reactions remaining after inhibition of the electron transfer pathway.
- »REN«, »ROX«
- communicated by »Timon-Gomez Alba« and »Leo Elettra«

January 15th

Electron transport chain or electron transfer pathway?

The term „chain‟ suggests a linear sequence, however, the convergence of electron flow at the Q-junction indicates a higher degree of complexity. Although electron transfer and transport are used as synonyms, the transfer of a reactant involves a chemical reaction whereas the transport of an entity is a process. - »Electron transfer pathway«, »Gnaiger 2020 BEC MitoPathways«
- communicated by »Leo Elettra« and »Timon-Gomez Alba«

Under construction

on hold until the page is updated

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:

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«

O2k-Publications alert

Example:

"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

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:

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.

In the links should be “ Surname First N”

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.

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

4. Now it should look like that:

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.

Sundaram VK, Schütza V, Schröter NH, Backhaus A, Bilsing A, Joneck L, Seelbach A, Mutschler C, Gomez-Sanchez JA, Schäffner E, Sánchez EE, Akkermann D, Paul C, Schwagarus N, Müller S, Odle A, Childs G, Ewers D, Kungl T, Sitte M, Salinas G, Sereda MW, Nave KA, Schwab MH, Ost M, Arthur-Farraj P, Stassart RM, Fledrich R (2023) Adipo-glial signaling mediates metabolic adaptation in peripheral nerve regeneration. »Bioblast link«

from the O2k-Network »DE_Leipzip_Ost_M«

January 4

"Oxygen Consumption Rate (OCR) measurements of fresh and cryopreserved placental specimens are comparable whereas snap frozen procedure impairs mitochondrial activity"

Giovarelli M, Serati A, Zecchini S, Guelfi F, Clementi E, Mandò C (2023) Cryopreserved placental biopsies maintain mitochondrial activity for high-resolution respirometry. »Bioblast link«

from the O2k-Network »IT Milan Clementi E«

MiPNet

Example:

"No bubbles should be trapped in the electrolyte reservoir after membrane application and mounting"

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

O2k-Open Support alert

Examples:

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«

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«

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«

O2k-Feedback alert

Example (if the person has a profile, link the name to the profile with Cristiane Cecatto:

“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«

“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«

MitoFit Preprints

Example:

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«

Under discussion

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

Did you enter the correct oxygen solubility factor in DatLab?

The oxygen solubility factor of the incubation medium, F_M, 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:

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

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.

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«

@@ Line 160: / Line 160: @@
 * Giovarelli M, Serati A, Zecchini S, Guelfi F, Clementi E, Mandò C (2023) Cryopreserved placental biopsies maintain mitochondrial activity for high-resolution respirometry.  [[Giovarelli 2023 Mol Med|»Bioblast link«]]
 :from the O2k-Network »[[IT Milan Clementi E]]«
-|}
-January 16
-:{|
-| width="100" align="center" |[[Image:O2k-Publications.jpg|70px|link=http://wiki.oroboros.at/index.php/O2k-Publications:_Topics |O2k-Publications in the MiPMap]]
-|'''The study on rats by Jedlička et al indicates that "...the concept of general pattern of age-dependent decline in mitochondrial oxygen consumption across different organs and tissues could be misleading"."''' <br>
-*Jedlička J, Tůma Z, Razak K, Kunc R, Kala A, Proskauer Pena S, Lerchner T, Ježek K, Kuncová J (2022) Impact of aging on mitochondrial respiration in various organs. [[Jedlicka_2022a_Physiol_Res|»Bioblast link«]]
-:from the O2k-Network »[[CZ_Pilsen_Kuncova_J]]«
 |}