Metabolic Isotope Labeling via Intermediary Organisms
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Solution Overview
Problem
Current methods face challenges in achieving high isotope enrichment and efficient metabolic labeling of higher organisms like fish for quantitative proteomics, due to complexities in developing suitable synthetic media and maintaining isotopic labeling completeness.
Innovation Solution
The method involves creating a stable isotope food chain where the isotope is transferred through a series of ancestor organisms to the target fish, using a diet composition that includes labeled cells and tissues, allowing for high reproducibility and enrichment of stable isotopes, such as 13C, 15N, and 2H, facilitating quantitative proteomic analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Manufacturing precision
If synthetic media are developed for metabolic labeling of higher organisms, then isotopic labeling completeness can be improved, but the complexity of developing suitable synthetic media increases
Solution Approach 1:
The patent introduces an intermediary organism (bacteria or yeast) that is fed with stable isotope-labeled compounds and then used to produce labeled food organisms (algae, plants, insects, or small animals). This intermediary system mediates the transfer of isotopic labels from simple synthetic media to complex higher organisms, achieving high isotopic labeling completeness while avoiding the complexity of developing synthetic media for the target organism directly
Solution Approach 2:
The metabolic labeling process is segmented into multiple stages: (1) labeling the intermediary organism with stable isotopes, (2) using the labeled intermediary to produce labeled food organisms, and (3) feeding the labeled food organisms to the target higher organism. This segmentation allows each stage to be optimized independently, achieving high overall labeling efficiency
2Measurement precision
If stable isotope enrichment is increased to improve quantitation accuracy, then measurement precision improves, but the complexity of maintaining isotopic labeling completeness increases
Solution Approach 1:
The labeled food organisms serve as self-sustaining sources of stable isotopes for the target organism. The food organisms are produced with high isotopic enrichment through controlled feeding of the intermediary organism, and then automatically maintain the labeling when consumed by the target organism, reducing the need for continuous external intervention to maintain isotopic labeling completeness
Solution Approach 2:
The stable isotope labeling is performed in advance on the intermediary organism and food organisms before they are used to feed the target higher organism. This preliminary action ensures that the isotopic labels are already incorporated into the food organisms' tissues, guaranteeing high measurement precision when the target organism is analyzed without requiring complex real-time maintenance of labeling
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach achieves high isotope enrichment (up to 98%) in fish, enabling reproducible and accurate quantitation of proteins, suitable for investigating tissue regeneration and turnover under complex in vivo conditions, and provides a balanced diet that mimics the organism's natural habitat.
Implementation Method 1
metabolic labeling of a fish with a stable isotope
Implementation Method 2
the stable isotope is transferred from a label source to the target organism via one or more food chains
Data Source
Figure 1A
Figure 1B
Figure 2A~2B
AI summary
The invention generally relates to metabolic labeling of a target organism with a stable isotope. In a first aspect, the present invention relates to a method for metabolic labeling of a target organism with a stable isotope. The present invention also relates to a method of producing a diet for metabolic labeling of a target organism and to a diet composition for metabolic labeling of a target organism. In a further aspect the invention describes the use of the diet composition according to the present invention for producing a metabolically labeled target organism as a reference for a quantitative proteomic approach. The present invention also relates, in a further aspect, to the use of a diet composition for pulse SILAC labeling. The present invention also relates to the use of a target organism labeled by the method according to the first aspect of the present invention as a spike-in standard in quantitative proteomics approaches.