Summary of Study ST001809

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 PR001143. The data can be accessed directly via it's Project DOI: 10.21228/M8ZH7D 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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001809
Study TitleThe Metabolic Benefits of Short Cycles of Very Low Caloric Intake are Dependent on Diet Composition in Middle-Aged Mice
Study SummaryDiet composition, calories, and fasting times contribute to maintenance of health. Here, middle-aged mice were maintained for 5 months on 4:10 feeding cycles, consisting of 4 days of very low-calorie intake (VLCI) achieved with either standard laboratory chow (SD) or a fasting mimicking diet (FMD), followed by 10 days of ad libitum access to SD. Fat and lean mass loss was accompanied with improved performance, glucoregulation, and metabolic flexibility independent of diet composition. However, only the 4:10/SD cycles elicited a long-lasting metabolomic reprograming in serum and liver that was preserved six days after refeeding. Challenged with an obesogenic diet, cycles of VLCI achieved with either high-fat diet (HFD) or FMD during the low-calorie period did not prevent diet-induced obesity nor did they elicited a long-lasting metabolic memory, despite achieving modest metabolic flexibility. Our results highlight the importance of diet composition in mediating the metabolic benefits of short cycles of VLCI.
Institute
National Institutes of Health
DepartmentExperimental Gerontology Section and Translational Gerontology Branch, NIA
Last Namede Cabo
First NameRafael
Address251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
EmaildeCaboRa@grc.nia.nih.gov
Phone+1-410-558-8510
Submit Date2021-05-27
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2021-09-15
Release Version1
Rafael de Cabo Rafael de Cabo
https://dx.doi.org/10.21228/M8ZH7D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001143
Project DOI:doi: 10.21228/M8ZH7D
Project Title:The Metabolic Benefits of Short Cycles of Very Low Caloric Intake are Dependent on Diet Composition in Middle-Aged Mice
Project Summary:Diet composition, calories, and fasting times contribute to maintenance of health. Here, middle-aged mice were maintained for 5 months on 4:10 feeding cycles, consisting of 4 days of very low-calorie intake (VLCI) achieved with either standard laboratory chow (SD) or a fasting mimicking diet (FMD), followed by 10 days of ad libitum access to SD. Fat and lean mass loss was accompanied with improved performance, glucoregulation, and metabolic flexibility independent of diet composition. However, only the 4:10/SD cycles elicited a long-lasting metabolomic reprograming in serum and liver that was preserved six days after refeeding. Challenged with an obesogenic diet, cycles of VLCI achieved with either high-fat diet (HFD) or FMD during the low-calorie period did not prevent diet-induced obesity nor did they elicited a long-lasting metabolic memory, despite achieving modest metabolic flexibility. Our results highlight the importance of diet composition in mediating the metabolic benefits of short cycles of VLCI.
Institute:National Institutes of Health
Department:Experimental Gerontology Section and Translational Gerontology Branch, NIA
Last Name:de Cabo
First Name:Rafael
Address:251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
Email:deCaboRa@grc.nia.nih.gov
Phone:+1-410-558-8510

Subject:

Subject ID:SU001886
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id treatment
SA167967L-FMD075_164ALHF-Liver
SA167968L-FMD063_155ALHF-Liver
SA167969L-FMD064_156ALHF-Liver
SA167970L-FMD061_153ALHF-Liver
SA167971L-FMD060_152ALHF-Liver
SA167972L-FMD058_150ALHF-Liver
SA167973L-FMD059_151ALHF-Liver
SA167974L-FMD065_157ALHF-Liver
SA167975L-FMD062_154ALHF-Liver
SA167976L-FMD067_158ALHF-Liver
SA167977L-FMD073_163ALHF-Liver
SA167978L-FMD072_162ALHF-Liver
SA167979L-FMD070_161ALHF-Liver
SA167980L-FMD068_159ALHF-Liver
SA167981L-FMD069_160ALHF-Liver
SA167982S-FMD064_111ALHF-Serum
SA167983S-FMD065_112ALHF-Serum
SA167984S-FMD063_110ALHF-Serum
SA167985S-FMD060_107ALHF-Serum
SA167986S-FMD067_113ALHF-Serum
SA167987S-FMD061_108ALHF-Serum
SA167988S-FMD062_109ALHF-Serum
SA167989S-FMD058_105ALHF-Serum
SA167990S-FMD075_119ALHF-Serum
SA167991S-FMD059_106ALHF-Serum
SA167992S-FMD073_118ALHF-Serum
SA167993S-FMD072_117ALHF-Serum
SA167994S-FMD069_115ALHF-Serum
SA167995S-FMD070_116ALHF-Serum
SA167996S-FMD068_114ALHF-Serum
SA167936L-FMD013_063AL-Liver
SA167937L-FMD012_062AL-Liver
SA167938L-FMD014_064AL-Liver
SA167939L-FMD016_066AL-Liver
SA167940L-FMD001_052AL-Liver
SA167941L-FMD011_061AL-Liver
SA167942L-FMD015_065AL-Liver
SA167943L-FMD018_067AL-Liver
SA167944L-FMD005_055AL-Liver
SA167945L-FMD002_053AL-Liver
SA167946L-FMD010_060AL-Liver
SA167947L-FMD006_056AL-Liver
SA167948L-FMD004_054AL-Liver
SA167949L-FMD009_059AL-Liver
SA167950L-FMD007_057AL-Liver
SA167951L-FMD008_058AL-Liver
SA167952S-FMD007_005AL-Serum
SA167953S-FMD008_006AL-Serum
SA167954S-FMD009_007AL-Serum
SA167955S-FMD005_003AL-Serum
SA167956S-FMD002_001AL-Serum
SA167957S-FMD010_008AL-Serum
SA167958S-FMD006_004AL-Serum
SA167959S-FMD015_013AL-Serum
SA167960S-FMD018_015AL-Serum
SA167961S-FMD004_002AL-Serum
SA167962S-FMD016_014AL-Serum
SA167963S-FMD014_012AL-Serum
SA167964S-FMD012_010AL-Serum
SA167965S-FMD013_011AL-Serum
SA167966S-FMD011_009AL-Serum
SA167997L-FMD036_085FMD-Liver
SA167998L-FMD024_073FMD-Liver
SA167999L-FMD025_074FMD-Liver
SA168000L-FMD026_075FMD-Liver
SA168001L-FMD023_072FMD-Liver
SA168002L-FMD022_071FMD-Liver
SA168003L-FMD035_084FMD-Liver
SA168004L-FMD020_069FMD-Liver
SA168005L-FMD021_070FMD-Liver
SA168006L-FMD027_076FMD-Liver
SA168007L-FMD019_068FMD-Liver
SA168008L-FMD034_083FMD-Liver
SA168009L-FMD028_077FMD-Liver
SA168010L-FMD032_081FMD-Liver
SA168011L-FMD033_082FMD-Liver
SA168012L-FMD031_080FMD-Liver
SA168013L-FMD030_079FMD-Liver
SA168014L-FMD029_078FMD-Liver
SA168015S-FMD026_023FMD-Serum
SA168016S-FMD028_025FMD-Serum
SA168017S-FMD025_022FMD-Serum
SA168018S-FMD027_024FMD-Serum
SA168019S-FMD021_018FMD-Serum
SA168020S-FMD029_026FMD-Serum
SA168021S-FMD022_019FMD-Serum
SA168022S-FMD023_020FMD-Serum
SA168023S-FMD024_021FMD-Serum
SA168024S-FMD033_030FMD-Serum
SA168025S-FMD036_033FMD-Serum
SA168026S-FMD020_017FMD-Serum
SA168027S-FMD019_016FMD-Serum
SA168028S-FMD035_032FMD-Serum
SA168029S-FMD034_031FMD-Serum
SA168030S-FMD031_028FMD-Serum
SA168031S-FMD032_029FMD-Serum
SA168032S-FMD030_027FMD-Serum
SA168033L-FMD111_196HCR-Liver
SA168034L-FMD105_190HCR-Liver
SA168035L-FMD104_189HCR-Liver
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 196

Collection:

Collection ID:CO001879
Collection Summary:Mice were euthanized and serum was collected thereafter. Liver was perfused in PBS, frozen in LN2 and pulverized thereafter.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR001899
Treatment Summary:6, 5-8 All mice were identified with FMD followed by a 3 digit number SD - day SD - night FMD - fed iFMD - fed FMD - fast iFMD - fast FMD - refed iFMD - refed

Sample Preparation:

Sampleprep ID:SP001892
Sampleprep Summary:Extraction of Mammalian Tissue Samples: Liver 1. References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ (in press) 2.Starting material: Liver sample: weigh 4mg per sample into 2mL Eppendorf tubes. 3. Equipment: Centrifuge (Eppendorf 5415 D) Calibrated pipettes 1-200μl and 100-1000μl Eppendorf tubes 2mL, clear (Cat. No. 022363204) Centrifuge tubes 50mL, polypropylene Eppendorff Tabletop Centrifuge (Proteomics core Lab.) ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer (VWR) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Turex mini homogenizer 4. Chemicals Acetonitrile, LCMS grade (JT Baker; Cat. No.9829-02) Isopropanol, HPLC grade (JT Baker; Cat. No. 9095-02) Methanol Acetone Crushed ice 18 MΩ pure water (Millipore) Nitrogen line with pipette tip pH paper 5-10 (EMD Chem. Inc.) 5. Procedure Preparation of extraction mix and material before experiment: Switch on bath to pre-cool at –20°C (±2°C validity temperature range) Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper Make the extraction solution by mixing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 De-gas the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization. The residue should contain membrane lipids because these are supposedly not soluble enough to be found in the 50% acetonitrile solution. Therefore, this ‘membrane residue’ is now taken for membrane lipidomic fingerprinting using the nanomate LTQ ion trap mass spectrometer. Likely, a good solvent to redissolve the membrane lipids is e.g. 75% isopropanol (degassed as given above). If the ‘analysis’ aliquot is to be used for semi lipophilic compounds such as tyrosine pathway intermediates (incl. dopamine, serotonine etc, i.e. polar aromatic compounds), then these are supposedly to be found together with the ‘GCTOF’ aliquot. We can assume that this mixture is still too complex for Agilent chipLCMS. Therefore, in order to develop and validate target analysis for such aromatic compounds, we should use some sort of Solid Phase purification. We re-suspend the dried ‘GCTOF’ aliquot in 300 l water (degassed as before) to take out sugars, aliphatic amino acids, hydroxyl acids and similar logP compounds. The residue should contain our target aromatics .We could also try to adjust pH by using low concentration acetate or phosphate buffer. The residue could then be taken up in 50% acetonitrile and used for GCTOF and Agilent chipMS experiments. The other aliquot should be checked how much of our target compounds would actually be found in the ‘sugar’ fraction. 6. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 7. Quality assurance For each sequence of sample extractions, perform one blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. 8. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules. Sample preparation of blood plasma or serum samples for GCTOF analysis Purpose: This SOP describes sample extraction and sample preparation for primary metabolism profiling by gas chromatography/time-of-flight mass spectrometry (GCTOF). References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ. Fiehn, O. Metabolomics by gas chromatography - mass spectrometry: combined targeted and untargeted profiling. 2016. Curr. Protoc. Mol. Biol. 114:30.4.1-30.4.32. doi: 10.1002/0471142727.mb3004s114. Starting material: Plasma/serum: 30 µL sample volume or aliquot Equipment: Centrifuge Eppendorf 5415 D Calibrated pipettes 1-200µL and 100-1000µL Multi-Tube Vortexer (VWR VX-2500) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Nitrogen line with Pasteur pipette Chemicals and consumables: Product Manufacturer & Part Number Eppendorf tubes 1.5 mL, uncolored Eppendorf 022363204 Crushed ice UC Davis Water, LC/MS Grade Fisher Optima W6-4 Acetonitrile, LC/MS Grade Fisher Optima A955-4 Isopropanol, LC/MS Grade Fisher A461-4 pH paper 5-10 Millipore Sigma 1095330001 Bioreclamation human plasma (disodium EDTA) Bioreclamation HMPLEDTA Sample Preparation: Preparation of extraction solvent For 1 L of extraction solvent, combine 375 mL of acetonitrile, 375 mL of isopropanol, and 250 mL water in a 1 L bottle conditioned with the aforementioned chemicals. If a different total volume of extraction solvent is needed, simply mix acetonitrile, isopropanol, and water in volumes in proportion 3:3:2. Purge the extraction solution mix for 5 min with nitrogen with small bubbles. Make sure that the nitrogen line is flushed out of air before using it for degassing the extraction solvent solution. Store at -20°C until use. Note: if solvent freezes, sonicate until thawed and mix before use. Extraction Thaw raw samples at room temperature (or in the refrigerator at 4˚C) and vortex 10 sec at low speed to homogenize. Aliquot 30 μL of plasma sample into a 1.5 mL Eppendorf tube. Keep all samples on ice. Add 1 mL 3:3:2 (v/v/v) ACN:IPA:H2O extraction solvent (prechilled in a -20°C freezer). Vortex the sample for 10 sec. Shake for 5 min at 4°C using the Orbital Mixing Chilling/Heating Plate. Continue to keep all extracted samples on ice. Centrifuge samples for 2 min at 14000 rcf. Aliquot two 450 μL portions of the supernatant into 1.5 mL Eppendorf tubes (one for analysis and one as a backup sample). Transfer 100 μL of the remaining supernatant from each sample to a 2, 15, or 50 mL tube for pools, depending on number of samples in the study. Evaporate one 450 μL aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. Proceed with cleanup or store tubes at -20°C until cleanup. Pooling Transfer multiple 475 µL aliquots of pooled samples to 1.5 mL Eppendorf tubes, one aliquot for every 10 samples in the study. If there is still pool remaining, prepare additional aliquots for backup. Centrifuge pool samples for 2 min at 14000 rcf. Remove 450 µL supernatant to new 1.5 mL Eppendorf tube. Evaporate to complete dryness in the Labconco Centrivap cold trap concentrator. Proceed with cleanup or store tubes at -20°C until cleanup. Cleanup Resuspend the dried aliquot with 500 μL 50:50 (v/v) ACN:H2O (degassed as given above) and vortex for about 10 sec. Centrifuge for 2 min at 14000 rcf. Remove 475 μL supernatant to a new 1.5 mL Eppendorf tube. Evaporate the transferred supernatant to complete dryness in the Labconco Centrivap cold trap concentrator. Submit to derivatization (see SOP “Derivatization of GC Samples & Standards”) or store at -20°C until ready for analysis. Quality assurance For every 50 samples, perform one method blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. If no combined pool was made from the extracted samples, use one commercial plasma/serum pool sample per 10 authentic subject samples as control instead. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules. Collect residual plasma/serum samples in specifically designed red ‘biohazard’ waste bags.

Combined analysis:

Analysis ID AN002932
Analysis type MS
Chromatography type GC
Chromatography system LECO Pegasus IV GC-time of flight mass spectrometers
Column Rtx-5Sil MS column
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode UNSPECIFIED
Units normalized peak height

Chromatography:

Chromatography ID:CH002173
Chromatography Summary:Primary metabolism by GCTOF
Instrument Name:LECO Pegasus IV GC-time of flight mass spectrometers
Column Name:Rtx-5Sil MS column
Chromatography Type:GC

MS:

MS ID:MS002723
Analysis ID:AN002932
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:GC-TOF Method: Instruments: Gerstel CIS4 –with dual MPS Injector/ Agilent 6890 GC- Pegasus III TOF MS Injector conditions: Agilent 6890 GC is equipped with a Gerstel automatic liner exchange system (ALEX) that includes a multipurpose sample (MPS2) dual rail, and a Gerstel CIS cold injection system (Gerstel, Muehlheim, Germany) with temperature program as follows: 50°C to 275°C final temperature at a rate of 12 °C/s and hold for 3 minutes. Injection volume is 0.5 μl with 10 μl/s injection speed on a splitless injector with purge time of 25 seconds. Liner (Gerstel #011711-010-00) is changed after every 10 samples, (using the Maestro1 Gerstel software vs. 1.1.4.18). Before and after each injection, the 10 μl injection syringe is washed three times with 10 μl ethyl acetate. Gas Chromatography conditions: A 30 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film) with additional 10 m integrated guard column is used (Restek, Bellefonte PA). 99.9999% pure Helium with built-in purifier (Airgas, Radnor PA) is set at constant flow of 1 ml/min. The oven temperature is held constant at 50°C for 1 min and then ramped at 20°C/min to 330°C at which it is held constant for 5 min. Mass spectrometer settings: A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da.
Ion Mode:UNSPECIFIED
  logo