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

Revision as of 11:26, 5 May 2020

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

 {|
 | logos
 | title in bold <br>
 - link
 |}

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:

Bioblast alert 2020

Prep for circular done here: Talk:Bioblast alert 2020

MitoPedia alert

Respiration measurements with living cells provides information on parameters such as free ROUTINE activity. MitoPedia may help to clarify why defining it as ATP production is inappropriate
-»SUIT protocols to measure ATP production« Learn more about how to measure ATP production in mitochondrial preparations with Magnesium Green -
-»Magnesium Green«

Already added to Agenda - Next and to be added to Mitopedia alert

O2k-Publications alert

Already added to Agenda - Next and to be added to O2k-Publications alert

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.

Jun-01 Mo

width="110" align="center"

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 «

Already added to Agenda - Next and to be added to O2k-Open support alert

May-18 Mo

width="110" align="center"

Do you know that a humid O2k-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«

May-25 Mo

width="110" align="center"

Do you know how the "switch components" approach can help you find what is causing your O2k to not reach the quality control specifications?

Do not despair if specifications given in the O2k-Manuals are not obtained. See how to troubleshoot on your own.
-»Switch components approach«

Removed for correction

width="110" align="center"

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«

O2k-Open Support alert circulars

O2k-Open Support alert circular 2020(01): in prep

width="110" align="center"New

A damaged OroboPOS-Holder may cause medium to leak from the O2k-Chamber.

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

width="110" align="center"New

Calibration parameters are transferred to experimental DatLab files

Save calibration information from selected Marks while DatLab is connected to the O2k during an instrumental calibration run. Air calibration and zero oxygen calibration can be performed and saved in a single DatLab file or in separate DatLab files.
- » Oxygen calibration - DatLab«

width="110" align="center"

Do you perform O2k-Chamber volume calibration?

The volume calibration is essential to ensure that the chamber volume is correctly calibrated to its standard volume of 2 mL (or 0.5 mL for the O2k-sV-Module).
- »O2k-Chamber MitoPedia«

width="110" align="center"

Do you use the correct O₂ solubility factor (F_M) in the ‘O2 calibration’ window in DatLab?

The O₂ solubility factor varies according to the medium used and influences the air calibration.

- »Oxygen solubility factor«

In preparation

For discussion

Here we discuss suggestions for the Oroboros Ecosystem Agenda 2020

width="110" align="center"

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 °C solid stability for more than 3 years (3 years 7 months)
Proven -20 °C solid stability for 1 year
Proven DMSO stability at room temperature for 1 week
Proven DMSO stability at -20 °C for 6 months (ongoing)

width="110" align="center"

As part of the H2020 SME NextGen-O2k project we are developing a PhotoBiology module that will allow to study the effect of different light intensities on O₂ consumption and production

-»PhotoBiology«

width="110" align="center"

Do you perform a stirrer test during oxygen calibration?

In DatLab 7.4, instrumental DL-Protocols guide you automatically towards performing the stirrer test in the process of air calibration. It shows immediately, if your OroboPOS has a satisfactory response time. Further details in
-» MitoPedia: »Oxygen calibration - DatLab

width="110" align="center"

Is the noise of the ‘O2 slope neg’ acceptable?

If you are not certain that the noise of the ‘O2 slope neg’ is within a suitable range or you want to confirm that your experimental data will not be affected, see:
-» MiPNet06.03 POS-calibration-SOP

2021

2021-01-06 https://www.jstor.org/stable/1706346?seq=1

Postponed events

» FAT4BRAIN School Riga LV IOC147«

»APS2020 Chicago US«

San Diego CA US

@@ Line 17: / Line 17: @@
 |}
-:::: ''See the scheme'': [[File:Agenda alerts body text format 2020-05-05.PNG|600px|Agenda/Alerts body text format]]
+:::: ''See the scheme'': [[File:Agenda alerts body text format 2020-05-05.PNG|left|600px|Agenda/Alerts body text format]]
@@ Line 29: / Line 29: @@
 * '''Jun-14 Th'''
-::::
-{|
+:{|
 | width="110" align="center"[[Image:SUIT icon.jpg|80px|link=https://wiki.oroboros.at/index.php/MitoPedia:_SUIT |MitoPedia: SUIT]]
-|How can I measure '''ATP production''' in '''cells'''?
+|How can I measure '''ATP production''' in '''cells'''? <br>
-| Respiration measurements with living cells provides information on parameters such as [[free ROUTINE activity]]. MitoPedia may help to clarify why defining it as ATP production is inappropriate <br>
+Respiration measurements with living cells provides information on parameters such as [[free ROUTINE activity]]. MitoPedia may help to clarify why defining it as ATP production is inappropriate <br>
-»'''[[Magnesium_Green#Is_it_possible_to_measure_ATP_production_in_the_protocol_SUIT-003_O2_ce_D009.3F|SUIT protocols to measure ATP production]]'''«
+-»'''[[Magnesium_Green#Is_it_possible_to_measure_ATP_production_in_the_protocol_SUIT-003_O2_ce_D009.3F|SUIT protocols to measure ATP production]]'''«
-|- Learn more about how to measure ATP production in mitochondrial preparations with Magnesium Green - <br> »'''[[Magnesium_Green#SUIT_protocol_for_mitochondrial_ATP_production_measurement_with_MgG|Magnesium Green]]'''«
+Learn more about how to measure ATP production in mitochondrial preparations with Magnesium Green - <br> -»'''[[Magnesium_Green#SUIT_protocol_for_mitochondrial_ATP_production_measurement_with_MgG|Magnesium Green]]'''«
-<br />
+|}
 === Already added to [https://wiki.oroboros.at/index.php?title=Template:Next_oroboros_ecosystem_agenda Agenda - Next] and to be added to [https://www.bioblast.at/index.php/MitoPedia_alert Mitopedia alert] ===
@@ Line 53: / Line 52: @@
 * '''Jun-01 Mo'''
-:::: [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: 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?'''»[https://wiki.oroboros.at/index.php/Oxygen_flux_-_instrumental_background#Unstable_O2_slope_neg._signal_in_O2_instrumental_BG  Instrumental background]« and  »[[TIP2k Filter Papers]] «
+:{|
+| width="110" align="center"[[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: 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?''' <br>
+-»[https://wiki.oroboros.at/index.php/Oxygen_flux_-_instrumental_background#Unstable_O2_slope_neg._signal_in_O2_instrumental_BG  Instrumental background]« and  »[[TIP2k Filter Papers]] «
+|}
 === Already added to [https://wiki.oroboros.at/index.php?title=Template:Next_oroboros_ecosystem_agenda Agenda - Next] and to be added to [https://wiki.oroboros.at/index.php/O2k-Open_Support_alert O2k-Open support alert] ===
 * '''May-18 Mo'''
-:::: [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: loss of data]] '''Do you know that a humid O2k-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.-»[[OroboPOS-Connector#Cleaning_the_electrical_connections|Cleaning the electrical connections]]«
+:{|
+| width="110" align="center"[[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: loss of data]]
+|'''Do you know that a humid O2k-environment and/or liquid spillage may lead to a high raw POS signal [V]?'''<br>
+ See how to clean and dry the electrical connections of the OroboPOS-Connector.<br>
+-»[[OroboPOS-Connector#Cleaning_the_electrical_connections|Cleaning the electrical connections]]«
+|}
 * '''May-25 Mo'''
-:::: [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Yellow-take care.png|40px|Take care]] '''Do you know how the "switch components" approach can help you find what is causing your O2k to not reach the quality control specifications?'''
+:{|
-::::::: Do not despair if specifications given in the O2k-Manuals are not obtained. See how to troubleshoot on your own.-»[[Oxygen_sensor_test#Switch_components_approach|Switch components approach]]«
+| width="110" align="center"[[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Yellow-take care.png|40px|Take care]]
+|'''Do you know how the "switch components" approach can help you find what is causing your O2k to not reach the quality control specifications?'''<br>
+Do not despair if specifications given in the O2k-Manuals are not obtained. See how to troubleshoot on your own.<br>
+-»[[Oxygen_sensor_test#Switch_components_approach|Switch components approach]]«
+|}
 === Removed for correction ===
-:::: [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: 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. - »[[Talk:O2k-Chamber_MitoPedia#Leaky_Chamber|Leaky chamber test]]«
+:{|
-<br />
+| width="110" align="center"[[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: loss of data]]
-:::::::» https://intern.oroboros.at/index.php/Overnight_test_after_O2k-chamber_assembly
+|'''Do you perform the ''leaky chamber test'' after chamber assembly? '''<br>
+An unnoticed leak from the chamber may affect your data, therefore we recommend performing the ''Leaky chamber test'' - especially after chamber reassembly. <br>
+-»[[Talk:O2k-Chamber_MitoPedia#Leaky_Chamber|Leaky chamber test]]« and » https://intern.oroboros.at/index.php/Overnight_test_after_O2k-chamber_assembly«
+|}
 == O2k-Open Support alert circulars ==
 === O2k-Open Support alert circular 2020(01): in prep ===
-::'''''New''''' [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: loss of data]] '''A damaged OroboPOS-Holder may cause medium to leak from the O2k-Chamber.'''
-::::::: See how you can check that the two blue OroboPOS-Holders are intact. - »[[O2k-OroboPOS-Holder_MitoPedia#O2k-OroboPOS-Holder:_Leaky_chamber_due_to_damaged_OroboPOS-Holder |O2k-OroboPOS-Holder]]«
-<br />
-::'''''New''''' [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]][[File:Yellow-take care.png|40px|Take care]] '''Calibration parameters are transferred to experimental DatLab files'''
-::::::: Save calibration information from selected [[Marks - DatLab |Marks]] while DatLab is connected to the O2k during an instrumental calibration run. Air calibration and zero oxygen calibration can be performed and saved in a single DatLab file or in separate DatLab files. - »[[Oxygen_calibration_-_DatLab#Oxygen_calibration_in_instrumental_and_experimental_DatLab_files | Oxygen calibration - DatLab]]«
-:::: [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: loss of data]] '''Do you perform O2k-Chamber volume calibration?'''
-::::::: The volume calibration is essential to ensure that the chamber volume is correctly calibrated to its standard volume of 2 mL (or 0.5 mL for the [[O2k-sV-Module]]). - »[[O2k-Chamber MitoPedia]]«
-:::: [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Yellow-take care.png|40px|Take care]] '''Do you use the correct O<sub>2</sub> solubility factor (F<sub>M</sub>) in the ‘O2 calibration’ window in DatLab?
-::::::: The O<sub>2</sub> solubility factor varies according to the medium used and influences the air calibration. - »[[Oxygen solubility factor]]«== In preparation ==
+:{|
+| width="110" align="center"'''''New''''' [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: loss of data]]
+|'''A damaged OroboPOS-Holder may cause medium to leak from the O2k-Chamber.'''<br>
+See how you can check that the two blue OroboPOS-Holders are intact. <br>
+- »[[O2k-OroboPOS-Holder_MitoPedia#O2k-OroboPOS-Holder:_Leaky_chamber_due_to_damaged_OroboPOS-Holder |O2k-OroboPOS-Holder]]«
+|}
+:{|
+| width="110" align="center"'''''New''''' [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]][[File:Yellow-take care.png|40px|Take care]]
+|'''Calibration parameters are transferred to experimental DatLab files'''<br>
+Save calibration information from selected [[Marks - DatLab |Marks]] while DatLab is connected to the O2k during an instrumental calibration run. Air calibration and zero oxygen calibration can be performed and saved in a single DatLab file or in separate DatLab files.<br>
+- »[[Oxygen_calibration_-_DatLab#Oxygen_calibration_in_instrumental_and_experimental_DatLab_files | Oxygen calibration - DatLab]]«
+|}
+:{|
+| width="110" align="center" [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: loss of data]]
+|'''Do you perform O2k-Chamber volume calibration?'''<br>
+The volume calibration is essential to ensure that the chamber volume is correctly calibrated to its standard volume of 2 mL (or 0.5 mL for the [[O2k-sV-Module]]). <br>
+- »[[O2k-Chamber MitoPedia]]«
+|}
+:{|
+| width="110" align="center" [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Yellow-take care.png|40px|Take care]]
+|'''Do you use the correct O<sub>2</sub> solubility factor (F<sub>M</sub>) in the ‘O2 calibration’ window in DatLab?<br>
+ The O<sub>2</sub> solubility factor varies according to the medium used and influences the air calibration. <br>
+- »[[Oxygen solubility factor]]«
+|}
+== In preparation ==
 == For discussion ==
   ''Here we discuss suggestions for the Oroboros Ecosystem Agenda 2020''
-::: Controlled stability of the [https://www.oroboros.at/index.php/product/mitokit-cii MitoKit-CII] based on HPLC and LCMS analysis: No degradation of [[MitoKit-CII_MitoPedia| MitoKit-CII]] compounds [[MitoKit-CII/Succinate-nv| MitoKit-CII/Succinate-nv (NV118)]] and [[MitoKit-CII/Malonate-nv| MitoKit-CII/Malonate-nv (NV161)]] for following storage conditions:
+:{|
+| width="110" align="center"
+|Controlled stability of the [https://www.oroboros.at/index.php/product/mitokit-cii MitoKit-CII] based on HPLC and LCMS analysis: No degradation of [[MitoKit-CII_MitoPedia| MitoKit-CII]] compounds [[MitoKit-CII/Succinate-nv| MitoKit-CII/Succinate-nv (NV118)]] and [[MitoKit-CII/Malonate-nv| MitoKit-CII/Malonate-nv (NV161)]] for following storage conditions:
 :::* Proven -80 °C solid stability for more than 3 years (3 years 7 months)
 :::* Proven -20 °C solid stability for 1 year
 :::* Proven DMSO stability at room temperature for 1 week
 :::* Proven DMSO stability at -20 °C for 6 months (ongoing)
+|}
+:{|
+| width="110" align="center" [[File:MitoPedia.jpg|left|60px|MitoPedia]]
+|As part of the [[NextGen-O2k|H2020 SME NextGen-O2k]] project we are developing a PhotoBiology module that will allow to study the effect of different light intensities on O<sub>2</sub> consumption and production<br>
+-»'''[[PhotoBiology]]'''«
+|}
-:::: [[File:MitoPedia.jpg|left|60px|MitoPedia]] As part of the [[NextGen-O2k|H2020 SME NextGen-O2k]] project we are developing a PhotoBiology module that will allow to study the effect of different light intensities on O<sub>2</sub> consumption and production: »'''[[PhotoBiology]]'''«
+:{|
+| width="110" align="center" [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Yellow-take care.png|40px|Take care]]
-:::: [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Yellow-take care.png|40px|Take care]] '''Do you perform a stirrer test during oxygen calibration?'''
+| '''Do you perform a stirrer test during oxygen calibration?'''<br>
-::::::: In DatLab 7.4, instrumental DL-Protocols guide you automatically towards performing the stirrer test in the process of air calibration. It shows immediately, if your OroboPOS has a satisfactory response time. ''Further details in'' [[MitoPedia: DatLab |MitoPedia]]: »[[Oxygen calibration - DatLab]]
+In DatLab 7.4, instrumental DL-Protocols guide you automatically towards performing the stirrer test in the process of air calibration. It shows immediately, if your OroboPOS has a satisfactory response time. ''Further details in'' <br>
+-» [[MitoPedia: DatLab |MitoPedia]]: »[[Oxygen calibration - DatLab]]
-:::: [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: loss of data]] '''Is the noise of the ‘O2 slope neg’ acceptable?'''
+|}
-::::::: If you are not certain that the noise of the ‘O2 slope neg’ is within a suitable range or you want to confirm that your experimental data will not be affected, see ''further details'': [[MiPNet06.03 POS-calibration-SOP]]
+:{|
+| width="110" align="center" [[Image:O2k-Support.jpg|60px|link=http://wiki.oroboros.at/index.php/O2k-Open_Support |O2k-Open Support]] [[File:Red-loss of data.png|40px|Warning: loss of data]]
+|'''Is the noise of the ‘O2 slope neg’ acceptable?'''<br>
+If you are not certain that the noise of the ‘O2 slope neg’ is within a suitable range or you want to confirm that your experimental data will not be affected, see:<br>
+-» [[MiPNet06.03 POS-calibration-SOP]]
+|}
 == 2021 ==