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

Revision as of 12:47, 8 August 2023

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

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 | logos
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 - link
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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«

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

1.Oroboros Ecosystem Agenda: SOP: Surname with long version and First name with short version. Please, see: Template alerts.

Example: Oroboros Ecosystem Agenda example

This means that we have to edit manually the author names within the O2k-Publications/ Brief alerts (i.e., Antunes Diana (from Bioblast) to Antunes D (to Agenda entries)) if they are long or copy from the gray box.

2.Bioblast: SOP: [1] – examples are available using both Surname and First name with long version (e.g., Antunes Diana). If in Bioblast the authors are with short surname in the links please update it to complete surname, guidelines are below.

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 [2]

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.

Nadeu F, Royo R, Massoni-Badosa R, Playa-Albinyana H, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N, Melero JL, Chapaprieta V, Dueso-Barroso A, Delgado J, Moia R, Ruiz-Gil S, Marchese D, Giró A, Verdaguer-Dot N, Romo M, Clot G, Rozman M, Frigola G, Rivas-Delgado A, Baumann T, Alcoceba M, González M, Climent F, Abrisqueta P, Castellví J, Bosch F, Aymerich M, Enjuanes A, Ruiz-Gaspà S, López-Guillermo A, Jares P, Beà S, Capella-Gutierrez S, Gelpí JL, López-Bigas N, Torrents D, Campbell PJ, Gut I, Rossi D, Gaidano G, Puente XS, Garcia-Roves PM, Colomer D, Heyn H, Maura F, Martín-Subero JI, Campo E (2022) Detection of early seeding of Richter transformation in chronic lymphocytic leukemia. »Bioblast link«

from the O2k-Network »ES Barcelona Garcia-Roves PM/ES Barcelona IDIBAPS Hospital Clinic«

"We recognized an oxidative phosphorylation (OXPHOS)^high–B cell receptor (BCR)^low-signaling transcriptional axis in Richter transformation (RT) and showed that OXPHOS inhibition reduces the proliferation of RT cells"

Nadeu F, Royo R, Massoni-Badosa R, Playa-Albinyana H, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N, Melero JL, Chapaprieta V, Dueso-Barroso A, Delgado J, Moia R, Ruiz-Gil S, Marchese D, Giró A, Verdaguer-Dot N, Romo M, Clot G, Rozman M, Frigola G, Rivas-Delgado A, Baumann T, Alcoceba M, González M, Climent F, Abrisqueta P, Castellví J, Bosch F, Aymerich M, Enjuanes A, Ruiz-Gaspà S, López-Guillermo A, Jares P, Beà S, Capella-Gutierrez S, Gelpí JL, López-Bigas N, Torrents D, Campbell PJ, Gut I, Rossi D, Gaidano G, Puente XS, Garcia-Roves PM, Colomer D, Heyn H, Maura F, Martín-Subero JI, Campo E (2022) Detection of early seeding of Richter transformation in chronic lymphocytic leukemia. »Bioblast link«

from the O2k-Network »ES Barcelona Garcia-Roves PM/ES Barcelona IDIBAPS Hospital Clinic«

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«

Oxygen signals obtained after proper calibration are independent of the gain settings, therefore oxygen concentrations (and fluxes) can be compared, as long as the corresponding air and zero calibrations are applied.
- »https://wiki.oroboros.at/index.php/Gain#Gain:_O2_channel_of_the_O2k«
- communicated by »Baglivo Eleonora« and »Leo Elettra«

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 153: / Line 153: @@
 Oxygen signals obtained after proper calibration are independent of the gain settings, therefore oxygen concentrations (and fluxes) can be compared, as long as the corresponding air and zero calibrations are applied.
 <br>
-- »'''[[Gain: O2 channel of the O2k]]'''«<br>
+- »'''[[Gain of the O2 channel|https://wiki.oroboros.at/index.php/Gain#Gain:_O2_channel_of_the_O2k]]'''«<br>
 - communicated by »[[Baglivo Eleonora]]« and »[[Leo Elettra]]«
 |}