Difference between revisions of "Oroboros Ecosystem Agenda 2024 Archive"

Revision as of 17:14, 18 March 2024

Oroboros Ecosystem Agenda 2024 Archive

Mitochondria and Cell Research - the Oroboros Ecosystem

Last week

2024 Week 11

Mar-11 Mo

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«

Mar-12 Tu

Mar-13 We

Rewarded Open Access - compensating authors

Together with the MiPsociety, BEC is raising funds to reward the first 10 papers accepted for publication in BEC in 2024: 600 EUR to attend EBEC2024 and 2-year MiPmembership. -»Support open access in science«
- »Submit a manuscript«

Mar-14 Th

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«

Mar-15 Fr

Next Week

2024 Week 10

Mar-04 Mo

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«

Mar-05 Tu

Mar-06 We

The tale of two “best-friends,” proteins BID & MTCH2, pivotal regulators of the apoptosis and metabolism programs at the mitochondria.

Gross A, (2024) A BID-MTCH2 love story: Energizing mitochondria until apoptosis do them part? Bioenerg Commun 2024.1. https://doi.org/10.26124/bec:2024-0001

Mar-07 Th

Which medium can be used for the instrumental background test?

When using dithionite, the instrumental background test should be performed in mitochondrial respiration medium MiR05, MiR05-Kit or MiR06; or alternatively, in a strong alkaline phosphate buffer (>100 mM; >pH 8), to avoid side reactions that might interfere with the test.
- »MiPNet14.06_Instrumental_O2_background«
- communicated by »Schmitt Sabine« and »Timon-Gomez Alba«

Mar-08 Fr

Feb 2024

2024 Week 06

Feb-05 Mo

"We demonstrated deficient platelet mitochondrial respiratory chain functions, oxidative phosphorylation (OXPHOS), and electron transfer (ET) capacity with complex I (CI)-linked substrates, and reduced [...] endogenous platelet coenzyme Q10 (CoQ10) concentration in UC [urothelial carcinoma] patients."

Palacka P, Gvozdjáková A, Rausová Z, Kucharská J, Slopovský J, Obertová J, Furka D, Furka S, Singh KK, Sumbalová Z (2021) Platelet mitochondrial bioenergetics reprogramming in patients with urothelial carcinoma. »Bioblast link«

from the O2k-Network »SK Bratislava Sumbalova Z«

Feb-06 Tu

Feb-07 We

Feb-08 Th

Can I use the same stock solutions for all reagents for different O2k-chamber volumes?

For some reagents, the concentration of the stock solution differs between the 2.0-mL and the 0.5-mL chamber (O2k-sV-Module) to facilitate a precise volume titration.
-»MiPNet09.12 O2k-Titrations«
- communicated by »Timon-Gomez Alba« and »Leo Elettra«

Feb-09 Fr

Feb-10 Sa

2024 Week 07

Feb-12 Mo

What is the O₂ solubility factor of the medium (F_M) and why is it important?

F_M expresses the effect of the salt concentration on oxygen solubility relative to pure water, and varies depending on the temperature and composition of the medium. The correct F_M needs to be entered in DatLab when performing an air calibration.
- »Oxygen solubility factor« , »Air calibration in DatLab«
- communicated by »Baglivo Eleonora« and »Timon-Gomez Alba«

Feb-13 Tu

Feb-14 We

Feb-15 Th - International Childhood Cancer Day

"Deleterious mtDNA mutations contribute significantly to the tumorigenesis of pediatric cancers"

Triska P, Kaneva K, Merkurjev D, Sohail N, Falk MJ, Triche TJ Jr, Biegel JA, Gai X (2019) Landscape of germline and somatic mitochondrial DNA mutations in pediatric malignancies. »Bioblast link«

from the O2k-Network »US_PA_Philadelphia_Falk_MJ«

Feb-16 Fr

2024 Week 08

Feb-19 Mo

“We just published this paper on SOMMA, possibly one of the largest aging studies involving permeabilized muscle energetics. Couldn't have done it without the training your teams provided.”

Kramer Philip A from the O2k-Network Lab »US NC Winston-Salem Kramer PA«
- »O2k-Feedback«

Feb-20 Tu

Feb-21 We

Feb-22 Th

What to do if the glass of the O2k-chamber starts to become opaque?

"Turbidity on the glass wall may be caused by precipitated protein. Remove the chambers from the O2k and with the O2k-stirrers removed, immerse in a beaker filled with HCl (10 M) overnight under a hood."
-»MiPNet19.03_O2k-cleaning_and_ISS«
- communicated by »Cardoso Luiza« and »Leo Elettra«

Feb-23 Fr

2024 Week 09

Feb-26 Mo

ATP synthase = phosphorylation system?

No, the phosphorylation system consists of adenine nucleotide translocase, phosphate carrier, and ATP synthase, which carry out the steps in the phosphorylation pathway.
- »Phosphorylation pathway«, »Mitochondrial Pathways: Chapter 2.2«
- communicated by »Schmitt Sabine« and »Timon-Gomez Alba«

Feb-27 Tu

Feb-28 We

Feb-29 Th

"Bed rest results in a decrease in skeletal muscle mitochondrial respiratory capacity, mainly as a result of an observed decrease in mitochondrial content"

Noone J, Damiot A, Kenny H, Chery I, Zahariev A, Normand S, Crampes F, de Glisezinski I, Rochfort KD, Laurens C, Bareille MP, Simon C, Bergouignan A, Blanc S, O'Gorman DJ (2023) The impact of 60 days of -6° head down tilt bed rest on mitochondrial content, respiration and regulators of mitochondrial dynamics. »Bioblast link«

from the O2k-Networks »US FL Orlando Goodpaster BH« , »FR Strasbourg Blanc S« , »IE Dublin O Gorman D«

Mar-01 Fr

Jan 2024

2024 Week 01

Jan-01 Mo

Jan-02 Tu

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«

Jan-03 We

Jan-04 Th

"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«

Jan-05 Fr

2024 Week 02

Jan-08 Mo

Do you need to export DatLab traces for your publication?

Save your graph as an editable picture using "Copy to clipboard" in DatLab 7.4 (.wmf) or "Save" in DatLab 8 (.svg).
- »Copy to clipboard in DatLab 7«, »Download DatLab 8«
- communicated by »Baglivo Eleonora« and »Grings Mateus«

Jan-09 Tu

Jan-10 We

»AICBC 2024 Navi Mumbai IN« Jan 10-12

Jan-11 Th

What are special features of the new SmartPOS (O2k-Series J and NextGen-O2k-Series XB)?

- "The electrical connections of the SmartPOS are protected thus there is no need to clean them."
- "The serial number of the SmartPOS is automatically recognized by the DatLab 8 software."

»MiPNet28.10 SmartPOS-service«
- communicated by »Grings Mateus« and »Baglivo Eleonora«

Jan-12 Fr

2024 Week 03

Jan-15 Mo

Why electron transfer pathway and not electron transfer chain?

The term “chain” suggests a linear sequence, however, the convergence of electron flow at the Q-junction indicates a higher degree of complexity, making “pathway” a more fitting descriptor.
- »Electron transfer pathway«, »Gnaiger 2020 BEC MitoPathways«
- communicated by »Leo Elettra« and »Timon-Gomez Alba«

Jan-16 Tu

Jan-17 We

Jan-18 Th

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."

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. »Bioblast link«

from the O2k-Network »CZ_Pilsen_Kuncova_J«

Jan-19 Fr

2024 Week 04

Jan-22 Mo

“We are truly glad to have your continued support and partnership.”

Lu Amelia from the O2k-Network Lab »TW Taoyuan Sunpoint«
- »O2k-Feedback«

Jan-23 Tu

Jan-24 We

Jan-25 Th

How do I view and change the settings of a measurement/file in DatLab 8?

"O2k control (active) will always show the settings of the active recording [and allow changes], while O2k info (view) will show the settings of the recorded selected file."

-»MiPNet28.07 NextGen-O2k Series XB manual«; »MiPNet28.08 Oroboros O2k Series J manual«
- communicated by »Baglivo Eleonora« and »Grings Mateus«

Jan-26 Fr

 2024 Week 05

Jan-29 Mo

»E-mit Winter School 2024 Brixen IT« Jan 28 - Feb 02

Jan-30 Tu

16:30 Erich Gnaiger presenting at E-mit Winter School 2024 Brixen IT - Coupling control and pathway control in mitochondrial high-resolution respirometry

Jan-31 We

Can the S-pathway O₂ flux be derived by subtracting N-pathway O₂ flux from NS-pathway O₂ flux?

No, 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 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«

Feb-01 Th

“Doing the entire hands-on module from start to finish was the best for really “cementing” theory and hands-on application together.”

Cosgrove Richard from Eli Lilly Research Labs, on what he liked best on IOC162
- »O2k-Feedback«

Feb-02 Fr

@@ Line 8: / Line 8: @@
 == Last week ==
+Week 11
+* '''Mar-11 Mo'''
+:{|
+| width="110" align="center" | [[File:MitoPedia.jpg|left|80px|MitoPedia|link=MitoPedia]]
+|''' Why is it important to perform respirometry with permeabilized muscle fibers (pfi) under a high [O<sub>2</sub>] regime? '''<br>
+Long diffusion distances in the pfi result in an O<sub>2</sub> diffusion limitation, which is overcome by increasing the O<sub>2</sub> partial pressure inside the chamber. Proper instrumental background correction is a must and O<sub>2</sub> dependence of ROS production should be considered.   <br>
+- »'''[[Permeabilized muscle fibers]]'''«, »'''[[Oxygen flux - instrumental background]]'''« <br>
+- communicated by »[[Grings Mateus]]« and »[[Cardoso Luiza]]«
+|}
+----
+* '''Mar-12 Tu'''
+----
+* '''Mar-13 We'''
+:{|
+| width="100" align="center" |[[Image:BEC-logo.png|100px|link=https://www.bioenergetics-communications.org/index.php/bec |Bioenergetics Communications]]
+|'''''Rewarded'' Open Access - compensating authors'''<br>
+Together with the MiP''society'', BEC is raising funds to reward the first 10 papers accepted for publication in BEC in 2024: 600 EUR to attend EBEC2024 and 2-year MiP''membership''.
+-»[https://whydonate.com/en/fundraising/BEC Support open access in science]«<br>
+- »[https://www.bioenergetics-communications.org/index.php/bec/about/submissions Submit a manuscript]«
+|}
+----
+* '''Mar-14 Th'''
+:{|
+| width="100" align="center" |[[Image:O2k-Publications.jpg|70px|link=http://wiki.oroboros.at/index.php/O2k-Publications:_Topics |O2k-Publications in the MiPMap]]
+|'''Mitochondrial ultrastructure and respiration are affected during EDL [''Extensor digitorum longus'' muscle] aging.''' <br>
+* 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.  [[Fernando 2023 Commun Biol|»Bioblast link«]]
+:from the O2k-Network »[[DE Leipzip Ost M]]«
+|}
+----
+* '''Mar-15 Fr'''
+----
+'''<big>Next Week</big>'''
 Week 10