scholarly journals NMR Methods for Quantitative Isotopomer Rates in Real-Time Metabolism of Cells

2019 ◽  
Author(s):  
Michelle AC Reed ◽  
Jennie Roberts ◽  
Peter Gierth ◽  
Ēriks Kupče ◽  
Ulrich L Günther
Keyword(s):  
Real Time ◽  
Metabolic Flux ◽  
Coupling Constants ◽  
Special Focus ◽  
Flux Analysis ◽  
Coupling Constant ◽  
Difference Spectra ◽  
Precise Knowledge ◽  
Label Incorporation ◽  
Nmr Methods

AbstractTracer-based metabolism is becoming increasingly important to study metabolic mechanisms in cells. NMR offers several approaches to measure label incorporation in metabolites, including 13C and 1H-detected spectra. The latter are generally more sensitive but quantification depends on the proton carbon 1JCH coupling constant which varies significantly between different metabolites. It is therefore not possible to have one experiment optimised for all metabolites and quantification of 1H-edited spectra such as HSQCs requires precise knowledge of coupling constants. Increasing interest in tracer-based and metabolic flux analysis requires robust analyses with reasonably small acquisition times. Here we compare 13C-filtered and 13C-edited methods for quantification with a special focus towards application in real-time NMR of cancer cells under near-physiological conditions. We find an approach using a double-filter most suitable and sufficiently robust to reliably obtain 13C-incorporations from difference spectra. This is demonstrated for JJN3 multiple myeloma cells processing glucose over 24h.

scholarly journals Metabolic Flux Analysis of Catechin Biosynthesis Pathways Using Nanosensor

Antioxidants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 288
Author(s):  
Habiba Kausar ◽  
Ghazala Ambrin ◽  
Mohammad K. Okla ◽  
Walid Soufan ◽  
Abdullah A. Al-Ghamdi ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Real Time ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Regulatory Element ◽  
Flux Analysis ◽  
Bacterial Cells ◽  
Biosynthesis Pathway ◽  
Real Time Monitoring ◽  
E Coli

(+)-Catechin is an important antioxidant of green tea (Camelia sinensis (L.) O. Kuntze). Catechin is known for its positive role in anticancerous activity, extracellular matrix degradation, cell death regulation, diabetes, and other related disorders. As a result of enormous interest in and great demand for catechin, its biosynthesis using metabolic engineering has become the subject of concentrated research with the aim of enhancing (+)-catechin production. Metabolic flux is an essential concept in the practice of metabolic engineering as it helps in the identification of the regulatory element of a biosynthetic pathway. In the present study, an attempt was made to analyze the metabolic flux of the (+)-catechin biosynthesis pathway in order to decipher the regulatory element of this pathway. Firstly, a genetically encoded fluorescence resonance energy transfer (FRET)-based nanosensor (FLIP-Cat, fluorescence indicator protein for (+)-catechin) was developed for real-time monitoring of (+)-catechin flux. In vitro characterization of the purified protein of the nanosensor showed that the nanosensor was pH stable and (+)-catechin specific. Its calculated Kd was 139 µM. The nanosensor also performed real-time monitoring of (+)-catechin in bacterial cells. In the second step of this study, an entire (+)-catechin biosynthesis pathway was constructed and expressed in E. coli in two sets of plasmid constructs: pET26b-PT7-rbs-PAL-PT7-rbs-4CL-PT7-rbs-CHS-PT7-rbs-CHI and pET26b-T7-rbs-F3H-PT7-rbs- DFR-PT7-rbs-LCR. The E. coli harboring the FLIP-Cat was transformed with these plasmid constructs. The metabolic flux analysis of (+)-catechin was carried out using the FLIP-Cat. The FLIP-Cat successfully monitored the flux of catechin after adding tyrosine, 4-coumaric acid, 4-coumaroyl CoA, naringenin chalcone, naringenin, dihydroquercetin, and leucocyanidin, individually, with the bacterial cells expressing the nanosensor as well as the genes of the (+)-catechin biosynthesis pathway. Dihydroflavonol reductase (DFR) was identified as the main regulatory element of the (+)-catechin biosynthesis pathway. Information about this regulatory element of the (+)-catechin biosynthesis pathway can be used for manipulating the (+)-catechin biosynthesis pathway using a metabolic engineering approach to enhance production of (+)-catechin.

Metabolic Flux Analysis of Mammalian Cells in High Cell Density Perfusion Cultures Targetting Real-Time Application

2001 ◽  
Vol 34 (5) ◽  
pp. 137-142
Author(s):  
Richard Biener ◽  
Chetan Goudar ◽  
Renato Meneses ◽  
Maria Ng ◽  
Chun Zhang ◽  
...  
Keyword(s):  
Real Time ◽  
Cell Density ◽  
Metabolic Flux Analysis ◽  
Mammalian Cells ◽  
Metabolic Flux ◽  
High Cell Density ◽  
Flux Analysis ◽  
High Cell ◽  
Perfusion Cultures ◽  
Real Time Application

scholarly journals Towards better understanding of an industrial cell factory: investigating the feasibility of real-time metabolic flux analysis in Pichia pastoris

2013 ◽  
Vol 12 (1) ◽  
pp. 51 ◽  
Author(s):  
Mariana L Fazenda ◽  
Joao ML Dias ◽  
Linda M Harvey ◽  
Alison Nordon ◽  
Ruan Edrada-Ebel ◽  
...  
Keyword(s):  
Pichia Pastoris ◽  
Real Time ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Cell Factory ◽  
Flux Analysis

Assessing the Calculation of Exchange Coupling Constants and Spin Crossover Gaps Using the Approximate Projection Model to Improve Density Function Calculations

2019 ◽  
Author(s):  
Xianghai Sheng ◽  
Lee Thompson ◽  
Hrant Hratchian
Keyword(s):  
Density Functional Theory ◽  
Exchange Coupling ◽  
Density Functional ◽  
Spin Crossover ◽  
Coupling Constants ◽  
Spin Projection ◽  
Coupling Constant ◽  
Projection Model ◽  
Functional Theory

This work evaluates the quality of exchange coupling constant and spin crossover gap calculations using density functional theory corrected by the Approximate Projection model. Results show that improvements using the Approximate Projection model range from modest to significant. This study demonstrates that, at least for the class of systems examined here, spin-projection generally improves the quality of density functional theory calculations of J-coupling constants and spin crossover gaps. Furthermore, it is shown that spin-projection can be important for both geometry optimization and energy evaluations. The Approximate Project model provides an affordable and practical approach for effectively correcting spin-contamination errors in molecular exchange coupling constant and spin crossover gap calculations.

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