Project description:BackgroundMetabolic fluxes represent the functional phenotypes of biochemical pathways and are essential to reveal the distribution of precursors among metabolic networks. Although analysis of metabolic fluxes, facilitated by stable isotope labeling and mass spectrometry detection, has been applied in the studies of plant metabolism, we lack experimental measurements for carbon flux towards lignin, one of the most abundant polymers in nature.ResultsWe developed a feeding strategy of excised Arabidopsis stems with 13C labeled phenylalanine (Phe) for the analysis of lignin biosynthetic flux. We optimized the feeding methods and found the stems continued to grow and lignify. Consistent with lignification profiles along the stems, higher levels of phenylpropanoids and activities of lignin biosynthetic enzymes were detected in the base of the stem. In the feeding experiments, 13C labeled Phe was quickly accumulated and used for the synthesis of phenylpropanoid intermediates and lignin. The intermediates displayed two different patterns of labeling kinetics during the feeding period. Analysis of lignin showed rapid incorporation of label into all three subunits in the polymers.ConclusionsOur feeding results demonstrate the effectiveness of the stem feeding system and suggest a potential application for the investigations of other aspects in plant metabolism. The supply of exogenous Phe leading to a higher lignin deposition rate indicates the availability of Phe is a determining factor for lignification rates.
Project description:There is debate in the literature as to whether scales of fishes require acidification to remove inorganic carbonates prior to stable isotope analysis. Acid-treated and untreated scales from 208 Atlantic salmon from nine locations on both sides of the Atlantic were analysed for δ13C and δ15N. Linear mixed-effect models determined the effect of acid treatment to be statistically significant. However, the mean difference was small (δ13C 0.1 ± 0.2‰, δ15N -0.1 ± 0.2‰) and not of biological relevance. This study concludes that Atlantic salmon scales do not need to be acidified prior to stable isotope analysis.
Project description:We discovered that CO2 electroreduction strongly favors the conversion of the dominant isotope of carbon (12C) and discriminates against the less abundant, stable carbon 13C isotope. Both absorption of CO2 in the alkaline electrolyte and CO2 electrochemical reduction favor the lighter isotopologue. As a result, the stream of unreacted CO2 leaving the electrolyzer has an increased 13C content, and the depletion of 13C in the product is several times greater than that of photosynthesis. Using a natural abundance feed, we demonstrate enriching of the 13C fraction to ∼1.3% (i.e., +18%) in a single-pass reactor and propose a scalable and economically attractive process to yield isotopes of a commercial purity. Our finding opens pathways to both cheaper and less energy-intensive production of stable isotopes (13C, 15N) essential to the healthcare and chemistry research, and to an economically viable, disruptive application of electrolysis technologies developed in the context of sustainability transition.
Project description:Metabolic flux is the final output of cellular regulation and has been extensively studied for carbon but much less is known about nitrogen, which is another important building block for living organisms. For the tuberculosis pathogen, this is particularly important in informing the development of effective drugs targeting the pathogen's metabolism. Here we performed 13 C15 N dual isotopic labeling of Mycobacterium bovis BCG steady state cultures, quantified intracellular carbon and nitrogen fluxes and inferred reaction bidirectionalities. This was achieved by model scope extension and refinement, implemented in a multi-atom transition model, within the statistical framework of Bayesian model averaging (BMA). Using BMA-based 13 C15 N-metabolic flux analysis, we jointly resolve carbon and nitrogen fluxes quantitatively. We provide the first nitrogen flux distributions for amino acid and nucleotide biosynthesis in mycobacteria and establish glutamate as the central node for nitrogen metabolism. We improved resolution of the notoriously elusive anaplerotic node in central carbon metabolism and revealed possible operation modes. Our study provides a powerful and statistically rigorous platform to simultaneously infer carbon and nitrogen metabolism in any biological system.
Project description:We applied isotopically nonstationary 13C metabolic flux analysis (INST-MFA) to compare the pathway fluxes of wild-type (WT) Synechococcus elongatus PCC 7942 to an engineered strain (SA590) that produces isobutyraldehyde (IBA). The flux maps revealed a potential bottleneck at the pyruvate kinase (PK) reaction step that was associated with diversion of flux into a three-step PK bypass pathway involving the enzymes PEP carboxylase (PEPC), malate dehydrogenase (MDH), and malic enzyme (ME). Overexpression of pk in SA590 led to a significant improvement in IBA specific productivity. Single-gene overexpression of the three enzymes in the proposed PK bypass pathway also led to improvements in IBA production, although to a lesser extent than pk overexpression. Combinatorial overexpression of two of the three genes in the proposed PK bypass pathway (mdh and me) led to improvements in specific productivity that were similar to those achieved by single-gene pk overexpression. Our work demonstrates how 13C flux analysis can be used to identify potential metabolic bottlenecks and novel metabolic routes, and how these findings can guide rational metabolic engineering of cyanobacteria for increased production of desired molecules.
Project description:13C metabolic flux analysis (MFA) has become an indispensable tool to measure metabolic reaction rates (fluxes) in living organisms, having an increasingly diverse range of applications. Here, the choice of the13C labeled tracer composition makes the difference between an information-rich experiment and an experiment with only limited insights. To improve the chances for an informative labeling experiment, optimal experimental design approaches have been devised for13C-MFA, all relying on some a priori knowledge about the actual fluxes. If such prior knowledge is unavailable, e.g., for research organisms and producer strains, existing methods are left with a chicken-and-egg problem. In this work, we present a general computational method, termed robustified experimental design (R-ED), to guide the decision making about suitable tracer choices when prior knowledge about the fluxes is lacking. Instead of focusing on one mixture, optimal for specific flux values, we pursue a sampling based approach and introduce a new design criterion, which characterizes the extent to which mixtures are informative in view of all possible flux values. The R-ED workflow enables the exploration of suitable tracer mixtures and provides full flexibility to trade off information and cost metrics. The potential of the R-ED workflow is showcased by applying the approach to the industrially relevant antibiotic producer Streptomyces clavuligerus, where we suggest informative, yet economic labeling strategies.
Project description:Breast cancer is the most common cancer in women worldwide. Despite the information provided by anatomopathological assessment and molecular markers (such as receptor expression ER, PR, HER2), breast cancer therapies and prognostics depend on the metabolic properties of tumor cells. However, metabolomics have not provided a robust and congruent biomarker yet, likely because individual metabolite contents are insufficient to encapsulate all of the alterations in metabolic fluxes. Here, we took advantage of natural 13C and 15N isotope abundance to show there are isotopic differences between healthy and cancer biopsy tissues or between healthy and malignant cultured cell lines. Isotope mass balance further suggests that these differences are mostly related to lipid metabolism, anaplerosis and urea cycle, three pathways known to be impacted in malignant cells. Our results demonstrate that the isotope signature is a good descriptor of metabolism since it integrates modifications in C partitioning and N excretion altogether. Our present study is thus a starting point to possible clinical applications such as patient screening and biopsy characterization in every cancer that is associated with metabolic changes.
Project description:Stable isotope ratio analysis of carbon (δ13C) and hydrogen (δ2H) in vanillin has become a valuable tool for differentiating natural vanilla from synthetic or biosynthetic alternatives and for tracing its geographical origins. However, increasingly sophisticated fraud techniques necessitate ongoing refinement of analytical methods to ensure accurate detection. This study advanced the field by investigating minor volatile organic compounds as potential biomarkers for identifying botanical and geographical origins of vanilla products. Vanilla pods from the two main vanilla species, V. planifolia and V. tahitensis, were investigated using GC-MS/MS to analyze their aromatic profile and GC-C/Py-IRMS to determine compound-specific isotope ratios, providing, for the first time, detailed and authentic isotopic and aromatic profiles. Additionally, the potential natural presence of ethyl vanillin and its corresponding glucoside precursors-molecules commonly used as synthetic vanilla-scented fragrance agents in various foods and industrial products-was explored using UHPLC-HRMS. These findings contribute to robust methods for verifying vanilla authenticity, addressing flavor complexity and isotopic composition, and enhancing the detection of adulteration in vanilla-flavored products.
Project description:The measurement of naturally occurring glucocorticoids and stable isotopes of several elements has gained importance in wildlife studies in recent decades and opened a myriad of ecological applications. Cortisol and stable isotopes equilibrate in animal tissues over periods of integration related to the growth rate of the tissue, providing information reflecting systemic cortisol secretion and dietary intake. Sample preparation shares the common step of first cleaning the sample of external contamination. However, it is not well understood how different solvents used in sample preparation affect isotopic and cortisol values, and whether it is safe to follow the same procedures for both measures to optimize analyses of the same sample. We conducted an experiment to compare different preparation protocols for the analysis of cortisol concentrations and stable carbon (δ13C) and nitrogen (δ15N) isotope ratios in hair. Hair samples from 12 brown bears (Ursus arctos) were each divided into five aliquots; two aliquots were rinsed with a 2:1 chloroform:methanol (v/v) mixture with one aliquot ground prior to cortisol analysis and the other left intact for stable isotope analyses; two aliquots were washed with methanol with one aliquot ground prior to cortisol analysis and the other left intact for stable isotope analyses; and one aliquot washed with methanol and ground prior to stable isotope analyses. The cortisol, δ13C and δ15N values remained consistent following all treatments. Our results indicate that hair samples rinsed with a 2:1 chloroform:methanol mixture or washed with methanol can be used for both types of analyses. Further, hair that has been ground in a standard hair cortisol procedure can also be used for stable isotope analysis. This information is important for improving laboratory efficiency and compatibility of procedures used for wildlife physiological ecology studies where concurrent measurements of cortisol and stable isotopes in hair are required.
Project description:Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.