Summary of Study ST002069
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001311. The data can be accessed directly via it's Project DOI: 10.21228/M88113 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002069 |
| Study Title | Systemic impact of the expression of the mitochondrial alternative oxidase on Drosophila development |
| Study Summary | Despite the beneficial effects shown when the mitochondrial alternative oxidase AOX from Ciona intestinalis (Tunicata: Ascidiacea) is xenotopically expressed in mammalian and insect models, important detrimental outcomes have also been reported, raising concerns regarding its envisioned deployment as a therapy enzyme for human mitochondrial and related diseases. We have shown previously that AOX-expressing flies present a dramatic drop in pupal viability when the larvae are cultured on a low nutrient (LN) diet, indicating that AOX interferes with normal developmental metabolism. Here, we applied the metabolomics approach to gain insights into the molecular basis of the fatal developmental interaction between AOX expression and LN diet. We investigated the whole-body metabolome of AOX-expressing and control larvae cultured on SD and LN diets. |
| Institute | Tampere University |
| Department | Faculty of Medicine and Health Technology |
| Last Name | Dufour |
| First Name | Eric |
| Address | Arvo Ylpön katu 34, 33520 Tampere, Finlândia |
| eric.dufour@tuni.fi | |
| Phone | +358 (0)50 413 0493 |
| Submit Date | 2022-01-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-01-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001311 |
| Project DOI: | doi: 10.21228/M88113 |
| Project Title: | Molecular alterations caused by mitochondrial alternative oxidase (AOX) expression in Drosophila melanogaster development |
| Project Summary: | Whole-body metabolome of AOX-expressing and control larvae of Drosophila melanogaster cultured on standard (SD) and low-nutrient (LN) diets |
| Institute: | Tampere University |
| Department: | Faculty of Medicine and Health Technology |
| Last Name: | Dufour |
| First Name: | Eric |
| Address: | Arvo Ylpön katu 34, 33520 Tampere, Finlândia |
| Email: | eric.dufour@tuni.fi |
| Phone: | +358 (0)50 413 0493 |
| Funding Source: | European Union (Marie Curie International Incoming Fellowship GA328988 |
Subject:
| Subject ID: | SU002155 |
| Subject Type: | Insect |
| Subject Species: | Drosophila melanogaster |
| Taxonomy ID: | 7227 |
| Age Or Age Range: | 3rd instar larvae |
Factors:
Subject type: Insect; Subject species: Drosophila melanogaster (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype of fly lines | Genotype Shorthand | Diet | Condition |
|---|---|---|---|---|---|
| SA194788 | SS-017 | 2/2;daGAL4/daGAL4 | C | Low Nutrient (LN) | LN |
| SA194789 | SS-015 | 2/2;daGAL4/daGAL4 | C | Low Nutrient (LN) | LN |
| SA194790 | SS-018 | 2/2;daGAL4/daGAL4 | C | Low Nutrient (LN) | LN |
| SA194791 | SS-019 | 2/2;daGAL4/daGAL4 | C | Low Nutrient (LN) | LN |
| SA194792 | SS-014 | 2/2;daGAL4/daGAL4 | C | Low Nutrient (LN) | LN |
| SA194793 | SS-020 | 2/2;daGAL4/daGAL4 | C | Low Nutrient (LN) | LN |
| SA194794 | SS-016 | 2/2;daGAL4/daGAL4 | C | Low Nutrient (LN) | LN |
| SA194795 | SS-005 | 2/2;daGAL4/daGAL4 | C | Standard (SD) | C |
| SA194796 | SS-004 | 2/2;daGAL4/daGAL4 | C | Standard (SD) | C |
| SA194797 | SS-003 | 2/2;daGAL4/daGAL4 | C | Standard (SD) | C |
| SA194798 | SS-001 | 2/2;daGAL4/daGAL4 | C | Standard (SD) | C |
| SA194799 | SS-002 | 2/2;daGAL4/daGAL4 | C | Standard (SD) | C |
| SA194785 | blank2 | - | - | - | - |
| SA194786 | blank1 | - | - | - | - |
| SA194787 | blank3 | - | - | - | - |
| SA194800 | SS-025 | UAS-AOXwtF6/2; daGAL4/3 | AOX | Low Nutrient (LN) | LN-AOX |
| SA194801 | SS-024 | UAS-AOXwtF6/2; daGAL4/3 | AOX | Low Nutrient (LN) | LN-AOX |
| SA194802 | SS-021 | UAS-AOXwtF6/2; daGAL4/3 | AOX | Low Nutrient (LN) | LN-AOX |
| SA194803 | SS-023 | UAS-AOXwtF6/2; daGAL4/3 | AOX | Low Nutrient (LN) | LN-AOX |
| SA194804 | SS-010 | UAS-AOXwtF6/2; daGAL4/3 | AOX | Standard (SD) | AOX |
| SA194805 | SS-009 | UAS-AOXwtF6/2; daGAL4/3 | AOX | Standard (SD) | AOX |
| SA194806 | SS-007 | UAS-AOXwtF6/2; daGAL4/3 | AOX | Standard (SD) | AOX |
| SA194807 | SS-011 | UAS-AOXwtF6/2; daGAL4/3 | AOX | Standard (SD) | AOX |
| SA194808 | SS-008 | UAS-AOXwtF6/2; daGAL4/3 | AOX | Standard (SD) | AOX |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO002148 |
| Collection Summary: | Ten randomly selected, wandering L3 larvae (100-115 hrs post-egg laying in SD diet; 125-140 hrs in LN diet) per biological replica (5 in total) were collected, briefly rinsed in ultrapure water, and flash-frozen in liquid N2. |
| Sample Type: | Larvae |
Treatment:
| Treatment ID: | TR002167 |
| Treatment Summary: | The fly lines were maintained on a standard (SD) or a low-nutrient (LN) diet, with a 12/12h of light/dark photoperiod cycle at 25 °C. The eggs were allowed to develop until reaching the wandering L3 larval stage for collection. The LN diet consisted of 3.5% yeast extract, 1% agar, and antimicrobials (0.1% nipagin and 0.5% propionic acid). |
Sample Preparation:
| Sampleprep ID: | SP002161 |
| Sampleprep Summary: | : Frozen larvae were homogenized in 1 ml cold (-80 °C) 80% methanol on dry ice using a probe homogenizer. Samples were clarified by centrifugation for 5 min at 16,000 x gmax at 4 °C and the supernatants were transferred to new Eppendorf tubes. The remaining pellets were resuspended in RIPA lysis buffer and total protein content was determined by the BCA method. A volume of the supernatant equivalent to 5 µg of protein was transferred to a glass vial, dried using an EZ-2 Elite evaporator (SP Scientific), and stored at -80 °C until analysis by LC-MS. |
Combined analysis:
| Analysis ID | AN003378 | AN003379 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | UltiMate 3000RSLC HPLC (Thermo Scientific) | UltiMate 3000RSLC HPLC (Thermo Scientific) |
| Column | Phenomenex Luna NH2 (150 x 2mm) | Phenomenex Luna NH2 (150 x 2mm) |
| MS Type | ESI | ESI |
| MS instrument type | Ion trap | Ion trap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | intensity (area under the curve) | intensity (area under the curve) |
Chromatography:
| Chromatography ID: | CH002497 |
| Chromatography Summary: | Separation was achieved using a linear gradient from 15% to 90% A over 18 min. This was followed by an isocratic step at 90% A for 9 min and re-equilibration to the initial 15% A for 7 min. |
| Instrument Name: | UltiMate 3000RSLC HPLC (Thermo Scientific) |
| Column Name: | Phenomenex Luna NH2 (150 x 2mm) |
| Column Temperature: | 27 C |
| Flow Rate: | 200 ul/min |
| Solvent A: | 100% water; 5 mM ammonium acetate, pH 9.9 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003145 |
| Analysis ID: | AN003378 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Ion trap |
| MS Type: | ESI |
| MS Comments: | MS1 scan range 65-975 m/z. MS/MS with inclusion list; target others when idle. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003146 |
| Analysis ID: | AN003379 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Ion trap |
| MS Type: | ESI |
| MS Comments: | MS1 scan range 65-975 m/z. MS/MS with inclusion list; target others when idle. |
| Ion Mode: | NEGATIVE |
