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

From Bioblast
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Prep for circular:
Prep for circular:


Platform comparison in fibroblast respirometry
Platelets
Ā 


:{|
| width="100" align="center" |[[File:MitoFit Preprints pdf.png|100px|link=https://www.mitofit.org/index.php/Zdrazilova_2021_MitoFit_ace-sce |MitoFit pdf]]
|'''Respirometry in attached and suspended cells'''<br>
* Zdrazilova L, Hansikova H, Gnaiger E (2021) Comparable respiratory activity in attached and suspended human fibroblasts. MitoFit Preprints 2021.7. [[Zdrazilova 2021 MitoFit ace-sce|doi:10.26124/mitofit:2021-0007]]
:from the O2k-Network Ā»[[CZ Prague Zeman J]]Ā« and Ā»[[AT Innsbruck Oroboros]]Ā«
|}
:{|
| width="100" align="center" |[[File:MitoFit Preprints pdf.png|100px|link=https://www.mitofit.org/index.php/Gnaiger_2021_MitoFit_BCA|MitoFit pdf]]
|'''Bioenergetic concept-driven normalization'''<br>
* Gnaiger E (2021) Bioenergetic cluster analysis ā€“ mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8 [[Gnaiger_2021_MitoFit_BCA|doi:10.26124/mitofit:2021-0008]]
:from the O2k-Network Ā»[[AT Innsbruck Oroboros]]Ā«
|}
:{|
| width="100" align="center" |[[Image:MitoFit Preprints.png|left|100px|link=http://www.mitofit.org/index.php/MitoFit |MitoFit Preprints]]
|'''Promoting transparency in scientific contributions'''<br>
MitoFit Preprints encourages Open Access to relevant scientific contributions of acknowledged persons<br>
Ā»'''[[MitoFit_Preprints#Open_Access_Acknowledgements|Open Access Acknowledgements]]'''Ā«
|}
Platelets
add Hoppel et al
:{|
:{|
| width="100" align="center" |[[File:MitoFit Preprints pdf.png|100px|link=https://www.mitofit.org/index.php/Vernerova_2021_MitoFit_PLT|MitoFit pdf]]
| width="100" align="center" |[[File:MitoFit Preprints pdf.png|100px|link=https://www.mitofit.org/index.php/Vernerova_2021_MitoFit_PLT|MitoFit pdf]]
|'''Comparison of isolation methods on mitochondrial respiration of platelets: apheresis versus density gradient centrifugation'''<br>
|'''Comparison of isolation methods on mitochondrial respiration of platelets: apheresis versus density gradient centrifugation'''<br>
* Vernerova A, Garcia-Souza LF, Soucek O, Kostal M, Rehacek V, Krcmova LK, Gnaiger E, Sobotka O (2021) Mitochondrial respiration of platelets: comparison of isolation methods. MitoFit Preprints 2021.6. [[Vernerova_2021_MitoFit_PLT|doi:10.26124/mitofit:2021-0006]]
* Vernerova A, Garcia-Souza LF, Soucek O, Kostal M, Rehacek V, Krcmova LK, Gnaiger E, Sobotka O (2021) Mitochondrial respiration of platelets: comparison of isolation methods. MitoFit Preprints 2021.6. [[Vernerova_2021_MitoFit_PLT|doi:10.26124/mitofit:2021-0006]]<br>
Ā 
:from the O2k-Network Ā»[[CZ Hradec Kralove Cervinkova Z]]Ā« and Ā»[[AT Innsbruck Oroboros]]Ā«
:from the O2k-Network Ā»[[CZ Hradec Kralove Cervinkova Z]]Ā« and Ā»[[AT Innsbruck Oroboros]]Ā«
|}
:{|
| width="100" align="center" |[[Image:O2k-Publications.jpg|70px|link=http://wiki.oroboros.at/index.php/O2k-Publications:_Topics |O2k-Publications in the MiPMap]]
|'''Protocol for field studies of human platelet mitochondrial function''' <br>
* Hoppel F, Garcia-Souza LF, Kantner-Rumplmair W, Burtscher M, Gnaiger E, Pesta D, Calabria E (2021) Human platelet mitochondrial function reflects systemic mitochondrial alterations: a protocol for application in field studies. Cells 10:2088. [[Hoppel 2021 Cells|Ā»Bioblast linkĀ«]]<br>
:from the O2k-Network Ā»[[AT Innsbruck Oroboros]]Ā« Ā»[[DE Duesseldorf Roden M]]Ā«, Ā»[[IT Verona Calabria E]]Ā«
|}
|}



Revision as of 08:45, 6 October 2021

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?

- Ā»Instrumental backgroundĀ« and Ā»TIP2k Filter PapersĀ«

See the scheme:


Agenda/Alerts body text format

Bioblast alert 2021

Prep for circular:

Platelets

MitoFit pdf Comparison of isolation methods on mitochondrial respiration of platelets: apheresis versus density gradient centrifugation
  • Vernerova A, Garcia-Souza LF, Soucek O, Kostal M, Rehacek V, Krcmova LK, Gnaiger E, Sobotka O (2021) Mitochondrial respiration of platelets: comparison of isolation methods. MitoFit Preprints 2021.6. doi:10.26124/mitofit:2021-0006
from the O2k-Network Ā»CZ Hradec Kralove Cervinkova ZĀ« and Ā»AT Innsbruck OroborosĀ«
O2k-Publications in the MiPMap Protocol for field studies of human platelet mitochondrial function
  • Hoppel F, Garcia-Souza LF, Kantner-Rumplmair W, Burtscher M, Gnaiger E, Pesta D, Calabria E (2021) Human platelet mitochondrial function reflects systemic mitochondrial alterations: a protocol for application in field studies. Cells 10:2088. Ā»Bioblast linkĀ«
from the O2k-Network Ā»AT Innsbruck OroborosĀ« Ā»DE Duesseldorf Roden MĀ«, Ā»IT Verona Calabria EĀ«

MitoPedia alert

Next

O2k-Brief alert

Next

O2k-Publications alert

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] ā€“ 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.
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 ā€œFirst Name Surnameā€:
In the gray box should be ā€œSurname FNā€ - From where references to be used as O2k-Publication/Brief alerts are copied from.

Gray box reference.png

In the links should be ā€œ Surname First Nā€

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 ā€œHow to move a profileā€ below.
B) Click in ā€œEdit with formā€.
C) The gray box is edited in ā€œReferenceā€ and the links are changed in ā€œAuthor(s)ā€. Change it accordingly and click in ā€œsave pageā€ at the end of the page.

Editing reference.png

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

So letā€™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. ā€œBeno Mā€ on edit
2. Click on ā€œMoveā€
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 ā€œMoveā€ 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.

Next

  • Oct-20 We
O2k-Publications in the MiPMap Impact of cell culture media lipids on mitochondrial function: exploring serum-free culture media

from the O2k-Network Ā»AT Innsbruck OroborosĀ« 

  • Oemer G, Edenhofer ML, Wohlfarter Y, Lackner K, Leman G, Koch J, Cardoso LHD, Lindner HH, Gnaiger E, Dubrac S, Zschocke J, Keller MA (2021) Fatty acyl availability modulates cardiolipin composition and alters mitochondrial function in HeLa cells. J Lipid Res 100111. Ā»Bioblast linkĀ«

or

O2k-Publications in the MiPMap Impact of lipids on mitochondrial function of cultured cells: exploring serum-free culture media

from the O2k-Network Ā»AT Innsbruck OroborosĀ« 

  • Oemer G, Edenhofer ML, Wohlfarter Y, Lackner K, Leman G, Koch J, Cardoso LHD, Lindner HH, Gnaiger E, Dubrac S, Zschocke J, Keller MA (2021) Fatty acyl availability modulates cardiolipin composition and alters mitochondrial function in HeLa cells. J Lipid Res 100111. Ā»Bioblast linkĀ«
  • Oct-##
O2k-Publications in the MiPMap Protocol for studying human platelet mitochondrial function in field studies

from the O2k-Network Ā»AT Innsbruck OroborosĀ« Ā»DE Duesseldorf Roden MĀ«, Ā»IT Verona Calabria EĀ«

  • Hoppel F, Garcia-Souza LF, Kantner-Rumplmair W, Burtscher M, Gnaiger E, Pesta D, Calabria E (2021) Human platelet mitochondrial function reflects systemic mitochondrial alterations: a protocol for application in field studies. Cells 10:2088. Ā»Bioblast linkĀ«


  • Oct-## To be published with the other H2O2 alert
O2k-Publications in the MiPMap Atorvastatin impairs mitochondrial respiration but does not increase H2O2 production

from the O2k-Network Ā»DK Copenhagen Larsen SĀ« 

  • Christiansen LB, Dohlmann TL, Ludvigsen TP, Parfieniuk E, Ciborowski M, Szczerbinski L, Kretowski A, Desler C, Tiano L, Orlando P, Martinussen T, Olsen LH, Larsen S (2021) Atorvastatin impairs liver mitochondrial function in obese Gƶttingen Minipigs but heart and skeletal muscle are not affected. Sci Rep 11:2167. Ā»Bioblast linkĀ«

O2k-Open Support alert

  • While in Home Office: Gnaigere (talk) 14:03, 19 March 2020 (CET) https://wiki.oroboros.at/index.php/Talk:O2k-Open_Support_alert - Many labs will move to home office mode. In line with our special DL7.4 home office offer (see Agenda today), therefore, I suggest to post in our Agenda analysis-linked O2k-Open Support cases during this time, and collect real-time operation cases for future releases.

Next

  • Oct-06
O2k-Open SupportInfo: improve New excel templates for H2O2 flux analysis with the Amplex UltraRed assay

- Ā» H2O2 flux Excel templatesĀ« and Ā»MiPNet24.10 H2O2 flux analysisĀ«
- communicated by Ā»Komlodi TimeaĀ« and Ā»Cardoso LuizaĀ«


This one needs a BioBlast link:
  • Month-##
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.
- Ā»LINK and O2 flux analysis with DatLab 7.4Ā«
- communicated by Ā»Cardoso LuizaĀ« and Ā»[[ ]]Ā«

Under discussion

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.
- Ā»Cleaning the electrical connectionsĀ« 
- communicated by Ā»Schmitt SabineĀ« and Ā»Komlodi TimeaĀ«

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.
- Ā»Leaky chamber testĀ« and Ā» https://intern.oroboros.at/index.php/Overnight_test_after_O2k-chamber_assemblyĀ«

O2k-Open Support alert circulars

In preparation

MitoFit Preprints

MitoFit Preprints
Promoting transparency in scientific contributions

MitoFit Preprints encourages Open Access to relevant scientific contributions of acknowledged persons
Ā»Open Access AcknowledgementsĀ« 



  • Oct-13 We
MitoFit pdf Cultured cells respirometry: Does respiration differ in attached and suspended cells?
from the O2k-Network Ā»CZ Prague Zeman JĀ« and Ā»AT Innsbruck OroborosĀ«
  • Zdrazilova L, Hansikova H, Gnaiger E (2021) Comparable respiratory activity in attached and suspended human fibroblasts. MitoFit Preprints 2021.7. doi:10.26124/mitofit:2021-0007


  • Oct-14 Th
MitoFit pdf A meta-analysis of human skin fibroblasts respirometry leading to the proposal of a concept-driven normalization and regression analysis
from the O2k-Network Ā»AT Innsbruck OroborosĀ«
  • Gnaiger E (2021) Bioenergetic cluster analysis ā€“ mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8 doi:10.26124/mitofit:2021-0008

OR

MitoFit pdf Bioenergetic cluster analysis

A meta-analysis of human skin fibroblasts respirometry leading to the proposal of a concept-driven normalization and regression analysis:

  • Gnaiger E (2021) Bioenergetic cluster analysis ā€“ mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8 doi:10.26124/mitofit:2021-0008

Data analysis templates and MipNets

For discussion

Here we discuss suggestions for the Oroboros Ecosystem Agenda 2020 (if the specific alert section is yet to be attributed)
MitoPedia: SUIT Controlled stability of the MitoKit-CII based on HPLC and LCMS analysis: No degradation of MitoKit-CII compounds MitoKit-CII/Succinate-nv (NV118) and MitoKit-CII/Malonate-nv (NV161) for following storage conditions:
  • Proven -80 Ā°C solid stability for more than 3 years (3 years 7 months)
  • Proven -20 Ā°C solid stability for 1 year
  • Proven DMSO stability at room temperature for 1 week
  • Proven DMSO stability at -20 Ā°C for 6 months (ongoing)

2021

Postponed events

link=https://wiki.oroboros.at/index.php/Asia_Society_for_Mitochondrial_Research_and_Medicine ASMRMASMRM 2020 Singapore SG
COST Action MitoEAGLE MitoEAGLE Summit Obergurgl 2020
COST Action MitoEAGLE MiPschool Obergurgl 2020


O2k-Workshops San Diego CA US
Bioenergetics Vienna 2020.jpg Bioenergetics Vienna 2020
O2k-Workshops IOC Schroecken AT


Ā»36th Congress Czech Nutrition Society 2020 Hradec Kralove CZĀ« (Sep 10-12)