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4 protocols using putrescine d4

1

Metabolomic Analysis of Plant Pathogen Infection

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Samples were prepared from control and infected 5-week-old plants47 (link). 20 mg of grinded samples were mixed with 1 mL extraction buffer (20/20/60 v/v/v chloroform:water:methanol) including internal standards for GC–MS and LC–MS. LC–MS internal standards were: 13C9-phenylalanine, 13C3-caffeine, D4-cholic acid, D8-arachidonic acid and 13C9-caffeic acid (Sigma, St. Louis, MO, USA). GC–MS internal standards were: L-proline-13C5, alpha-ketoglutarate-13C4, myristic acid-13C3, cholesterol-D7 (Cambridge Isotope Laboratories, Inc., Andover, MA, USA) and succinic acid-D4, salicylic acid-D6, L-glutamic acid-13C5,15N, putrescine-D4, hexadecenoic acid-13C4, D-glucose-13C6, D-sucrose-13C12 from Sigma. The samples were bead-beated and centrifuged as described27 (link). Most of the supernatants, 200 µL for LC–MS analysis and 50 µL for GC–MS analysis, were transferred to micro vials, evaporated to dryness and stored at − 80 °C until analysis. Small aliquots of the remaining supernatants were pooled and used as quality control (QC) samples. MSMS analysis (LC–MS) was run on the QC samples for identification purposes. The samples were analyzed in batches according to a randomized run order on both GC–MS and LC–MS.
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Diverse Metabolite Profiling Techniques

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Rotenone (Sigma: R8875); PKM2 inhibitor compound 3 k (Sigma: AMBH303C6BA3); DASA-58 (Sigma: SML2853); Serine (Sigma: S4500), Cell Proliferation Kit II (XTT) (Sigma: 11465015001); DNA extraction with DNeasy Blood and Tissue Kit (Qiagen: 69506); RNA extraction with RNeasy Mini Kit (Qiagen: 74106); cDNA synthesis with High-Capacity cDNA Reverse Transcript Kit (Thermo Fisher Scientific: 4368814); Relative quantitative PCR with KAPA SYBR Fast Universal Kit (Sigma: KK4602). Absolute quantification PCR with KAPA PROBE Fast Universal Kit (Sigma: KK4702). Solvents: Methanol, HPLC-grade was obtained from Fischer Scientific (Waltham, MA, USA) Chloroform, Suprasolv for GC was obtained from Merck (Darmstadt, Germany) H2O, Milli-Q. Stable isotopes internal standards: L-proline-13C5, alpha-ketoglutarate-13C4, myristic acid-13C3, cholesterol-D7 were obtained from Cil (Andover, MA, USA). Succinic acid-D4, salicylic acid-D6, L-glutamic acid-13C5,15 N, putrescine-D4, hexadecanoic acid-13C4, D-glucose-13C6, D-sucrose-13C12 were obtained from Sigma (St. Louis, MO, USA).
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Quantitative Analysis of Polyamines

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Total polyamine detection was conducted with a total polyamine assay kit (Fluorometric) (Cat# K475, BioVision) according to the manufacturer’s instructions. Individual polyamines were measured using LC-MS after dansylation in the CRI’s Metabolomics Facility at UT Southwestern. Briefly, tissues and cultured cells were extracted with 80% acetonitrile (20–30 mg tissue per 300 μL, 1 million cells per 100 μL), and 100 μL of the supernatant was dried in SpeedVac. The samples were reconstituted in 45 μL of water, then 10 μL of 10 × PBS (pH 11, adjusted by ammonium hydroxide), 5 μL of 10 μM polyamine internal standards including d8-spermine (Cat# 705330, Sigma), d4-putrescine (Cat# 491136, Sigma) and d6-spermidine (Cat# 709891, Sigma) prepared in water, and 45 μL of 1 mg/mL dansyl chloride (Cat# 03641, Sigma) prepared in acetonitrile were added into the same tube. The mixture was incubated at 55 °C for 10 min and then 400 μL of water was added. The samples were then extracted with Oasis HLB 96-well plate (Cat# 186000679, Waters). Samples were eluted with 98% acetonitrile and dried under SpeedVac. Finally, samples were reconstituted with 50 μL of 0.1% formic acid in water, and 20 μL was subjected to LC-MS analysis. Final concentration of polyamines was normalized to internal standards and total soluble protein content.
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4

Quantitative Analysis of Polyamines

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Total polyamine detection was conducted with a total polyamine assay kit (Fluorometric) (Cat# K475, BioVision) according to the manufacturer’s instructions. Individual polyamines were measured using LC-MS after dansylation in the CRI’s Metabolomics Facility at UT Southwestern. Briefly, tissues and cultured cells were extracted with 80% acetonitrile (20–30 mg tissue per 300 μL, 1 million cells per 100 μL), and 100 μL of the supernatant was dried in SpeedVac. The samples were reconstituted in 45 μL of water, then 10 μL of 10 × PBS (pH 11, adjusted by ammonium hydroxide), 5 μL of 10 μM polyamine internal standards including d8-spermine (Cat# 705330, Sigma), d4-putrescine (Cat# 491136, Sigma) and d6-spermidine (Cat# 709891, Sigma) prepared in water, and 45 μL of 1 mg/mL dansyl chloride (Cat# 03641, Sigma) prepared in acetonitrile were added into the same tube. The mixture was incubated at 55 °C for 10 min and then 400 μL of water was added. The samples were then extracted with Oasis HLB 96-well plate (Cat# 186000679, Waters). Samples were eluted with 98% acetonitrile and dried under SpeedVac. Finally, samples were reconstituted with 50 μL of 0.1% formic acid in water, and 20 μL was subjected to LC-MS analysis. Final concentration of polyamines was normalized to internal standards and total soluble protein content.
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