Stable Isotope Tracer Research Articles

Arginine dependency is a therapeutically exploitable vulnerability in chronic myeloid leukaemic stem cells.

To fuel accelerated proliferation, leukaemic cells undergo metabolic deregulation, which can result in specific nutrient dependencies. Here, we perform an amino acid drop-out screen and apply pre-clinical models of chronic phase chronic myeloid leukaemia (CML) to identify arginine as a nutrient essential for primary human CML cells. Analysis of the Microarray Innovations in Leukaemia (MILE) dataset uncovers reduced ASS1 levels in CML compared to most other leukaemia types. Stable isotope tracing reveals repressed activity of all urea cycle enzymes in patient-derived CML CD34+ cells, rendering them arginine auxotrophic. Thus, arginine deprivation completely blocks proliferation of CML CD34+ cells and induces significantly higher levels of apoptosis when compared to arginine-deprived cell lines. Similarly, primary CML cells, but not normal CD34+ samples, are particularly sensitive to treatment with the arginine-depleting enzyme, BCT-100, which induces apoptosis and reduces clonogenicity. Moreover, BCT-100 is highly efficacious in a patient-derived xenograft model, causing > 90% reduction in the number of human leukaemic stem cells (LSCs). These findings indicate arginine depletion to be a promising and novel strategy to eradicate therapy resistant LSCs.

Determination of Indispensable Amino Acid Digestibility of the Red Kidney Bean in Humans Using a Dual Stable Isotope Tracer Method

BackgroundProtein quality of the red kidney bean (RKB), a common source of dietary protein, has been assessed using the protein digestibility-corrected amino acid score (PDCAAS) determined in animal models using mainly oro-fecal digestibility. More recently, the FAO recommended to use digestible indispensable amino acid score (DIAAS) instead of PDCAAS but highlighted insufficient data on true ileal indispensable amino acid (IAA) digestibility of proteins because amino acids are absorbed in the ileum. ObjectivesUsing a recently developed dual stable isotope tracer method, we aimed to measure each IAA digestibility as representation of true ileal digestibility of the RKB, Phaseolus vulgaris, in humans consuming a typical Jamaican meal. MethodsRKB-IAAs were intrinsically labeled by adding 2H2O to the plants. Uniformly labeled-[13C]-spirulina (standard protein) was added to a meal prepared with the labeled RKB and fed to 10 healthy adults (5 males, 5 females) in a nonrandomized trial as primed/intermittent doses to achieve a steady state IAA enrichment in plasma. Enrichment of 2H- and 13C-labeled IAA in plasma and the bean was measured by mass spectrometry. Each IAA digestibility (except tryptophan and histidine) was calculated as the ratio of plasma 2H-IAA to meal 2H-IAA divided by the ratio of plasma 13C-IAA to meal 13C-IAA adjusted for loss of 2H-atom during transamination and digestibility of spirulina. ResultsAdequate IAA labeling (>1000 ppm 2H excess) and plasma plateau isotopic enrichment were achieved. Mean RKB-IAA digestibility (%) was 79.4 ± 0.5, ranging from 69.0 ± 1.2 (threonine) to 85.7 ± 1.7 (lysine). ConclusionThe dual stable isotope tracer digestibility data are similar to published oro-fecal digestibility supporting substantial nitrogen exchange in the colon. The individual IAA digestibility is useful to derive DIAAS to replace PDCAAS. Using published RKB-IAA composition, extrapolated DIAAS was 0.63 based on the lowest score for methionine. Clinical trial registrationhttps://register.clinicaltrials.gov; ID: NCT-04118517.

Late Pleistocene Neanderthal exploitation of stable and mosaic ecosystems in northern Iberia shown by multi-isotope evidence

AbstractDuring the last glacial period, rapidly changing environments posed substantial challenges to Neanderthal populations in Europe. Southern continental regions, such as Iberia, have been proposed as important climatic “buffer” zones during glacial phases. Contextualising the climatic and ecological conditions Neanderthals faced is relevant to interpreting their resilience. However, records of the environments and ecosystems they exploited across Iberia exhibit temporal and spatial gaps in coverage. Here we provide new evidence for palaeotemperatures, vegetation structure, and prey herbivore ecology during the late Pleistocene (MIS 5–3) in northern Spain, by applying multiple stable isotope tracers (δ18O, δ13C, δ15N, δ34S) to herbivore skeletal remains associated with Neanderthal occupations at Axlor Cave, Bizkaia. The results show little change over time and indicate stable climatic conditions and ecosystems across different occupations. Large within-layer isotopic variability in nitrogen and sulphur suggests the presence of a mosaic environment and a variety of isotopic ecotones that were exploited by Neanderthals and their prey. We implement a combination of carbonate and phosphate δ18O measurements to estimate palaeotemperatures using a cost-effective workflow. We show that the targeted use of phosphate δ18O measurements to anchor summer peak and winter trough areas enables high-precision seasonal palaeoclimatic reconstructions.

Rainfall intensity affects the recharge mechanisms of groundwater in a headwater basin of the North China plain

Understanding the origins of groundwater and its movement from mountain to plain during different high intensity rainfall events is critical for conserving water supplies, determining water-use policies and controlling pollution. These factors are also the keys for understanding the dominant processes in hydrological models. In this study, groundwater resources and recharge processes during heavy precipitation were explored by using stable isotope tracers in the hilly area of Taihang Mountain. It was found that the δ2H and δ18O values of precipitation exhibited obvious precipitation amount effect during different precipitation intensity events. The stable isotopic values in groundwater and river water showed significantly varied during the single extreme heavy precipitation and the continuous heavy precipitation events. In the rainy season, precipitation amounts greater than 40 mm/d could effectively recharge the shallow groundwater in the study area. By comparing the spatial isotopic distribution of groundwater, soil water, and river water with precipitation, we showed distinct groundwater recharge patterns in terms of their water resources, timing, and the degree of river water and groundwater interaction during the single extreme heavy precipitation and the continuous heavy precipitation. After the single extreme heavy precipitation, the δ2H and δ18O values of groundwater, soil water, and river water showed stable over time and had the same similar variations, suggested that the groundwater recharge was mainly dominated by precipitation with preferential flow or bypass flow. While after the continuous heavy precipitation, the variation of δ2H and δ18O in all water is consistent with the previous precipitation, which shown a mixing effect of previous enrich precipitation and depleted heavy precipitation, suggested that groundwater source was dominated by a continuous recharge of previous heavier precipitation with translatory flow. The groundwater main recharge mechanism is not constant, but changes with rainfall intensity. The rainfall intensity play an important role in groundwater recharge change affecting runoff process. Overall, this paper presents a new insight to understand the effect of rainfall intensity on hydrological process, which could be used to provide vital information in the semi-humid and semi-arid regions where water resources are critical in climate change adaptation strategies.

Polyethylene degradation and assimilation by the marine yeast Rhodotorula mucilaginosa

Ocean plastic pollution is a severe environmental problem but most of the plastic that has been released to the ocean since the 1950s is unaccounted for. Although fungal degradation of marine plastics has been suggested as a potential sink mechanism, unambiguous proof of plastic degradation by marine fungi, or other microbes, is scarce. Here we applied stable isotope tracing assays with 13C-labeled polyethylene to measure biodegradation rates and to trace the incorporation of plastic-derived carbon into individual cells of the yeast Rhodotorula mucilaginosa, which we isolated from the marine environment. 13C accumulation in the CO2 pool during 5-day incubation experiments with R. mucilaginosa and UV-irradiated 13C-labeled polyethylene as a sole energy and carbon source translated to degradation rates of 3.8% yr–1 of the initially added substrate. Furthermore, nanoSIMS measurements revealed substantial incorporation of polyethylene-derived carbon into fungal biomass. Our results demonstrate the potential of R. mucilaginosa to mineralize and assimilate carbon from plastics and suggest that fungal plastic degradation may be an important sink for polyethylene litter in the marine environment.

Sewer subsidies from overflows and pipe leaks dominate urban stream solute loads in all storm events

Stream channel burial drastically alters watershed flowpaths by routing surface waters underground and increasing the potential for interactions between stream water and urban infrastructure such as storm and sanitary sewers. While numerous studies have investigated storm event solute loads from urban watersheds, the influences of stream channel burial and sewer overflows are often overlooked. This study uses grab samples and natural abundance stable isotope tracers to quantify the event dynamics of solute concentration-discharge relationships as well as cumulative loads in a buried urban stream. Our results demonstrate that different solutes, as well as different sources of the same solute (atmospheric NO3− and sewer-derived NO3− differentiated by the Δ17O tracer), are delivered via separate watershed flowpaths and thus have different timings within the event and contrasting relationships to flow. This inter-event variability reveals dynamics that result from temporal and spatial heterogeneity in infiltration, exfiltration, and pipe overflows. These results can help guide system-wide infrastructure maintenance as cities seek to meet challenges in sustaining and improving water quality as infrastructural systems age.

Critical role of antioxidant programs in enzalutamide-resistant prostate cancer.

Therapy resistance to second-generation androgen receptor (AR) antagonists, such as enzalutamide, is common in patients with advanced prostate cancer (PCa). To understand the metabolic alterations involved in enzalutamide resistance, we performed metabolomic, transcriptomic, and cistromic analyses of enzalutamide-sensitive and -resistant PCa cells, xenografts, patient-derived organoids, patient-derived explants, and tumors. We noted dramatically higher basal and inducible levels of reactive oxygen species (ROS) in enzalutamide-resistant PCa and castration-resistant PCa (CRPC), in comparison to enzalutamide-sensitive PCa cells or primary therapy-naive tumors respectively. Unbiased metabolomic evaluation identified that glutamine metabolism was consistently upregulated in enzalutamide-resistant PCa cells and CRPC tumors. Stable isotope tracing studies suggest that this enhanced glutamine metabolism drives an antioxidant program that allows these cells to tolerate higher basal levels of ROS. Inhibition of glutamine metabolism with either a small-molecule glutaminase inhibitor or genetic knockout of glutaminase enhanced ROS levels, and blocked the growth of enzalutamide-resistant PCa. The critical role of compensatory antioxidant pathways in maintaining enzalutamide-resistant PCa cells was validated by targeting another antioxidant program driver, ferredoxin 1. Taken together, our data identify a metabolic need to maintain antioxidant programs and a potentially targetable metabolic vulnerability in enzalutamide-resistant PCa.

Skeletal muscle protein turnover responses to parenteral nutrition in patients with alcoholic liver cirrhosis and sarcopenia.

Alcoholic liver cirrhosis (ALC) is accompanied by sarcopenia. The aim of this study was to investigate the acute effects of balanced parenteral nutrition (PN) on skeletal muscle protein turnover in ALC. Eight male patients with ALC and seven age- and sex-matched healthy controls were studied for 3 h of fasting followed by 3 h of intravenous PN (SmofKabiven 1,206 mL: amino acid = 38 g, carbohydrates = 85 g, and fat = 34 g) 4 mL/kg/h. We measured leg blood flow and sampled paired femoral arteriovenous concentrations and quadriceps muscle biopsies while providing a primed continuous infusion of [ring-2d5]-phenylalanine to quantify muscle protein synthesis and breakdown. Patients with ALC exhibited shorter 6-min walking distance (ALC: 487 ± 38 vs. controls: 722 ± 14 m, P < 0.05), lower hand-grip strength (ALC: 34 ± 2 vs. controls: 52 ± 2 kg, P < 0.05), and computed tomography (CT)-verified leg muscle loss (ALC: 5,922 ± 246 vs. controls: 8,110 ± 345 mm2, P < 0.05). Net leg muscle phenylalanine uptake changed from negative (muscle loss) during fasting to positive (muscle gain) in response to PN (ALC: -0.18 ± +0.01 vs. 0.24 ± 0.03 µmol/kg muscle·min-1; P < 0.001 and controls: -0.15 ± 0.01 vs. 0.09 ± 0.01 µmol/kg muscle·min-1; P < 0.001) but with higher net muscle phenylalanine uptake in ALC than controls (P < 0.001). Insulin concentrations were substantially higher in patients with ALC during PN. Our results suggest a higher net muscle phenylalanine uptake during a single infusion of PN in stable patients with ALC with sarcopenia compared with healthy controls.NEW & NOTEWORTHY Muscle protein turnover responses to parenteral nutritional (PN) supplementation have not previously been studied in stable alcoholic liver cirrhosis (ALC). We applied stable isotope tracers of amino acids to directly quantify net muscle protein turnover responses to PN in sarcopenic males with ALC and healthy controls. We found a higher net muscle protein gain in ALC during PN, thereby providing the physiological rationale for future clinical trials of PN as a potential countermeasure to sarcopenia.

406-P: Spatial Metabolomics of Human Kidney Tissues Reveal Impaired Tricarboxylic Acid (TCA) Cycle Turnover in Type 1 Diabetes (T1D)

In abstract 2023-A-3497-Diabetes, we show impaired TCA cycle turnover using 11C acetate PET and lower proximal tubular transcripts of TCA cycle enzymes by single-cell RNA sequencing of kidney biopsies in young adults with T1D vs. healthy controls (HC). Spatial metabolomics analyses of the kidney tissue were conducted to further explore perturbations in kidney oxidative metabolism in T1D. Matrix-assisted laser desorption/ionization-mass spectrometry imaging-based spatial metabolomics was used to analyze metabolites in situ (spatial resolution: 20 μm) in kidney tissues from 8 participants with T1D and preserved kidney function and 5 HC. Univariate analysis (t-test or Wilcoxon Mann Whitney test) demonstrated that 36 of 456 METASPACE annotated metabolites were altered (P&amp;lt;0.05) in T1D vs. HC. Partial least squares-discriminant analysis (PLS-DA) and heatmaps showed clearly separated clusters of metabolites. To identify the most significant discriminators for T1D, a variable importance in projection (VIP) plot from PLS-DA model was applied. Of the top 15 metabolites, two TCA cycle intermediates, succinic acid (m/z 117.0193, -H; P = 0.016) and malic acid (m/z 133.0142, -H; P = 0.026), were reduced in kidney tissues of participants with T1D. Pathway analysis revealed that the TCA cycle, mitochondrial electron transport chain, glutamate metabolism, malate-aspartate shuttle, and purine pathway were the dominant metabolic pathways perturbed in T1D kidney tissue. Spatial metabolomics comparing T1D kidney biopsies vs. HC reveal alterations of TCA cycle intermediates indicating mitochondrial dysfunction in the subclinical stages of diabetic kidney disease. The spatial metabolomics data are consistent with the data from transcriptomics and stable isotope tracing analysis in a subset of same participants. Further analysis with pathologic features will identify potential pathways linked to disease development. Disclosure G.Zhang: None. C.Birznieks: None. I.De boer: Advisory Panel; AstraZeneca, Boehringer Ingelheim and Eli Lilly Alliance, Boehringer Ingelheim International GmbH, Otsuka America Pharmaceutical, Inc., Bayer Inc., Consultant; George Clinical, Gilead Sciences, Inc., Medscape, Research Support; Dexcom, Inc. J.A.Schaub: None. K.J.Nadeau: None. V.Nair: None. F.Alakwaa: None. P.J.Mccown: None. A.Naik: Advisory Panel; CareDx. L.Pyle: None. D.Blondin: None. L.Liu: None. G.Richard: None. M.Kretzler: Research Support; Lilly, Boehringer Ingelheim Inc., Traveere Pharmaceuticals, Novo Nordisk, certa, Chinook Therapeutics Inc., Janssen Research &amp; Development, LLC, AstraZeneca, Moderna, Inc., Gilead Sciences, Inc., Regeneron, Ionis Pharmaceuticals, Angioin, Renalytix. P.Bjornstad: Advisory Panel; AstraZeneca, Novo Nordisk, Lilly, Horizon Therapeutics plc, Boehringer Ingelheim (Canada) Ltd., LG Chem, Consultant; Bayer Inc., Bristol-Myers Squibb Company. K.Sharma: Advisory Panel; Reata Pharmaceuticals, Inc., Otsuka America Pharmaceutical, Inc. I.M.Tamayo: None. N.Garcia ponce de leon: None. T.B.Vigers: None. K.L.Tommerdahl: None. R.G.Nelson: None. P.E.Ladd: None. T.Alexandrov: None. Funding National Institutes of Health (UH3DK114920); JDRF (2-SRA-2019-845-S-B); Diabetes Research Center (P30DK116073)

Intracellular distribution of bis-allylic deuterated linoleic acid into the lipidome of human keratinocytes

Polyunsaturated fatty acids (PUFA) are particularly susceptible to free radical-induced lipid peroxidation (LPO). Specific deuteration at bis-allylic positions of PUFA (D-PUFA) has been recently proposed as a way to inhibit the LPO. Here, a high mass resolution untargeted lipidomic analysis protocol was applied to examine the changes in the lipidome of keratinocytes supplemented with bis-allylic deuterated linoleic acid (D2-LA). Incorporation of D2-LA occurs preferentially in membrane phospholipids such as phosphatidylcholine and phosphatidylethanolamine, followed by triglycerides. However, the relative contribution of D2-LA among membrane lipids is highest in cardiolipin (60%) followed by its precursor phosphatidylglycerol (50%). Cardiolipins are enriched in PUFA and exclusively located in mitochondrial membranes, thus representing major targets for lipid peroxidation. These findings indicate that D2-LA supplementation is linked to the preservation of mitochondrial function under oxidative stress. Finally, our study highlights the suitability of high mass resolution lipidomic analysis to investigate lipid metabolism at the level of individual molecular species in stable isotope tracing experiments.

Effects of connectivity on carbon and nitrogen stocks in mangrove and seagrass ecosystems

Seascape connectivity increases carbon and nitrogen exchange across coastal ecosystems through flow of particulate organic matter (POM). However, there are still critical gaps in knowledge about the drivers that mediate these processes, especially at regional seascape scales. The aim of this study was to associate three seascape-level drivers which could influence carbon and nitrogen stocks in intertidal coastal seascape: connectivity between ecosystems, ecosystem surface area, and standing vegetation biomass of ecosystems. Firstly, we compared whether connected mangrove and seagrass ecosystems contain larger carbon and nitrogen storage than isolated mangrove and seagrass ecosystems. Secondly, we compared autochthonous and allochthonous POM in mangrove patches and seagrass beds, simultaneously estimating the area and biomass relative contribution to POM of the different coastal vegetated ecosystem. Connected vs isolated mangrove and seagrass ecosystems were studied at six locations in a temperate seascape, and their carbon and nitrogen content in the standing vegetation biomass and sediments were measured. POM contributions of these and surrounding ecosystems were determined using stable isotopic tracers. In connected mangrove-seagrass seascapes, mangroves occupied 3 % of total coastal ecosystem surface area, however, their standing biomass carbon content and nitrogen per unit area was 9–12 times higher than seagrasses and twice as high as macroalgal beds (both in connected and isolated seascapes). Additionally in connected mangrove-seagrass seascapes, the largest contributors to POM were mangroves (10–50 %) and macroalgal beds (20–50 %). In isolated seagrasses, seagrass (37–77 %) and macroalgal thalli (9–43 %) contributed the most, whilst in the isolated mangrove, salt marshes were the main contributor (17–47 %). Seagrass connectivity enhances mangrove carbon sequestration per unit area, whilst internal attributes enhance seagrass carbon sequestration. Mangroves and macroalgal beds are potential critical contributors of nitrogen and carbon to other ecosystems. Considering all ecosystems as a continuing system with seascape-level connectivity will support management and improve knowledge of critical ecosystem services.

Pathways and biological mechanisms of N2O emission reduction by adding biochar in the constructed wetland based on 15N stable isotope tracing

Constructed wetlands (CWs) added with biochar were built to study pollutant removal efficiencies, nitrous oxide (N2O) emission characteristics, and biological mechanisms in nitrogen transformation. The results showed that biochar addition enhanced the average removal rates of ammonium (NH4+–N), total nitrogen, and chemical oxygen demand by 4.03–18.5%, 2.90–4.99%, and 2.87–5.20% respectively while reducing N2O emissions by 25.85–83.41%. Based on 15N stable isotope tracing, it was found that nitrification, denitrification, and simultaneous nitrification and denitrification were the main processes contributing to N2O emission. The addition of biochar resulted in maximum reduction rates of 71.50%, 80.66%, and 73.09% for these three processes, respectively. The relative abundance of nitrogen-transforming microbes, such as Nitrospira, Dechloromonas, and Denitratisoma, increased after the addition of biochar, promoting nitrogen removal and reducing N2O emissions. Adding biochar could increase the functional gene copy number and enzyme activity responsible for nitrogen conversion, which helped achieve efficient NH4+–N oxidation and eliminate nitrite accumulation, thereby reducing N2O emissions.

Geochemical Stratigraphy of the Prima Porta Travertine Deposit (Roma, Italy)

A stratigraphy of a buried travertine deposit was developed using stable isotope geochemistry, trace elements, and radiometric dating. The travertine was identified in a well at Prima Porta (north of Rome, Italy), located at the western boundary of the Tiber Valley, a morpho-tectonic depression of extensional origin. It deposited close to a spring that discharged groundwaters from the nearby volcanic aquifer and was associated with the rise of a deep-seated CO2-rich fluid. The deposition occurred between 53.5 ± 10 ka to 24.2 ± 4.7 ka; its activation was probably coeval with the wettest climatic conditions occurring during Marine Isotope Stage 3, and the end coincided with the cold and arid phase of the last glacial maximum. The chronostratigraphy showed a strong variation in the accumulation rate along the depositional sequence, greater in the lower half and much slower in the upper part, with a sharp decrease in the accumulation rate occurring between 47 and 43 ka. Isotope and chemical stratigraphy described a temporal evolution of events that are correlated to the global climatic variability; palaeoclimatic changes, in fact, influenced the hydrological regime and indirectly the tectonic activity by modulating the emission of deep CO2, the chemistry of the groundwater, and ultimately the precipitation of the travertine.

Preclinical Bioavailability Assessment of a Poorly Water-Soluble Drug, HGR4113, Using a Stable Isotope Tracer.

Drug solubility limits intravenous dosing for poorly water-soluble medicines, which misrepresents their bioavailability estimation. The current study explored a method using a stable isotope tracer to assess the bioavailability of drugs that are poorly water-soluble. HGR4113 and its deuterated analog, HGR4113-d7, were tested as model drugs. To determine the level of HGR4113 and HGR4113-d7 in rat plasma, a bioanalytical method using LC-MS/MS was developed. The HGR4113-d7 was intravenously administered to rats that were orally pre-administered HGR4113 at different doses; subsequently, the plasma samples were collected. HGR4113 and HGR4113-d7 were simultaneously determined in the plasma samples, and bioavailability was calculated using plasma drug concentration values. The bioavailability of HGR4113 was 53.3% ± 19.5%, 56.9% ± 14.0%, and 67.8% ± 16.7% after oral dosages of 40, 80, and 160 mg/kg, respectively. By eliminating the differences in clearance between intravenous and oral dosages at different levels, acquired data showed that the current method reduced measurement errors in bioavailability when compared to the conventional approach. The present study suggests a prominent method for evaluating the bioavailability of drugs with poor aqueous solubility in preclinical studies.

Mitochondrial pyruvate metabolism and glutaminolysis toggle steady-state and emergency myelopoiesis.

To define the metabolic requirements of hematopoiesis, we examined blood lineages in mice conditionally deficient in genes required for long-chain fatty acid oxidation (Cpt2), glutaminolysis (Gls), or mitochondrial pyruvate import (Mpc2). Genetic ablation of Cpt2 or Gls minimally impacted most blood lineages. In contrast, deletion of Mpc2 led to a sharp decline in mature myeloid cells and a slower reduction in T cells, whereas other hematopoietic lineages were unaffected. Yet MPC2-deficient monocytes and neutrophils rapidly recovered due to a transient and specific increase in myeloid progenitor proliferation. Competitive bone marrow chimera and stable isotope tracing experiments demonstrated that this proliferative burst was progenitor intrinsic and accompanied by a metabolic switch to glutaminolysis. Myeloid recovery after loss of MPC2 or cyclophosphamide treatment was delayed in the absence of GLS. Reciprocally, MPC2 was not required for myeloid recovery after cyclophosphamide treatment. Thus, mitochondrial pyruvate metabolism maintains myelopoiesis under steady-state conditions, while glutaminolysis in progenitors promotes emergency myelopoiesis.

Daylight-driven carbon exchange through a vertically structured microbial community.

Interactions between autotrophs and heterotrophs are central to carbon (C) exchange across trophic levels in essentially all ecosystems and metabolite exchange is a frequent mechanism for distributing C within spatially structured ecosystems. Yet, despite the importance of C exchange, the timescales at which fixed C is transferred in microbial communities is poorly understood. We employed a stable isotope tracer combined with spatially resolved isotope analysis to quantify photoautotrophic uptake of bicarbonate and track subsequent exchanges across a vertical depth gradient in a stratified microbial mat over a light-driven diel cycle. We observed that C mobility, both across the vertical strata and between taxa, was highest during periods of active photoautotrophy. Parallel experiments with 13C-labeled organic substrates (acetate and glucose) showed comparably less exchange of C within the mat. Metabolite analysis showed rapid incorporation of 13C into molecules that can both comprise a portion of the extracellular polymeric substances in the system and serve to transport C between photoautotrophs and heterotrophs. Stable isotope proteomic analysis revealed rapid C exchange between cyanobacterial and associated heterotrophic community members during the day with decreased exchange at night. We observed strong diel control on the spatial exchange of freshly fixed C within tightly interacting mat communities suggesting a rapid redistribution, both spatially and taxonomically, primarily during daylight periods.

Gene and protein expression and metabolic flux analysis reveals metabolic scaling in liver ex vivo and in vivo.

Metabolic scaling, the inverse correlation of metabolic rates to body mass, has been appreciated for more than 80 years. Studies of metabolic scaling have largely been restricted to mathematical modeling of caloric intake and oxygen consumption, and mostly rely on computational modeling. The possibility that other metabolic processes scale with body size has not been comprehensively studied. To address this gap in knowledge, we employed a systems approach including transcriptomics, proteomics, and measurement of in vitro and in vivo metabolic fluxes. Gene expression in livers of five species spanning a 30,000-fold range in mass revealed differential expression according to body mass of genes related to cytosolic and mitochondrial metabolic processes, and to detoxication of oxidative damage. To determine whether flux through key metabolic pathways is ordered inversely to body size, we applied stable isotope tracer methodology to study multiple cellular compartments, tissues, and species. Comparing C57BL/6 J mice with Sprague-Dawley rats, we demonstrate that while ordering of metabolic fluxes is not observed in in vitro cell-autonomous settings, it is present in liver slices and in vivo. Together, these data reveal that metabolic scaling extends beyond oxygen consumption to other aspects of metabolism, and is regulated at the level of gene and protein expression, enzyme activity, and substrate supply.

Automated analysis for multiplet identification from ultra-high resolution 2D- 1H, 13C-HSQC NMR spectra.

Background: Metabolism is essential for cell survival and proliferation. A deep understanding of the metabolic network and its regulatory processes is often vital to understand and overcome disease. Stable isotope tracing of metabolism using nuclear magnetic resonance (NMR) and mass spectrometry (MS) is a powerful tool to derive mechanistic information of metabolic network activity. However, to retrieve meaningful information, automated tools are urgently needed to analyse these complex spectra and eliminate the bias introduced by manual analysis. Here, we present a data-driven algorithm to automatically annotate and analyse NMR signal multiplets in 2D- 1H, 13C-HSQC NMR spectra arising from 13C - 13C scalar couplings. The algorithm minimises the need for user input to guide the analysis of 2D- 1H, 13C-HSQC NMR spectra by performing automated peak picking and multiplet analysis. This enables non-NMR specialists to use this technology. The algorithm has been integrated into the existing MetaboLab software package. Methods: To evaluate the algorithm performance two criteria are tested: is the peak correctly annotated and secondly how confident is the algorithm with its analysis. For the latter a coefficient of determination is introduced. Three datasets were used for testing. The first was to test reproducibility with three biological replicates, the second tested the robustness of the algorithm for different amounts of scaling of the apparent J-coupling constants and the third focused on different sampling amounts. Results: The algorithm annotated overall >90% of NMR signals correctly with average coefficient of determination ρ of 94.06 ± 5.08%, 95.47 ± 7.20% and 80.47 ± 20.98% respectively. Conclusions: Our results indicate that the proposed algorithm accurately identifies and analyses NMR signal multiplets in ultra-high resolution 2D- 1H, 13C-HSQC NMR spectra. It is robust to signal splitting enhancement and up to 25% of non-uniform sampling.

PFKFB3 Inhibits Fructose Metabolism in Pulmonary Microvascular Endothelial Cells.

Pulmonary microvascular endothelial cells contribute to the integrity of the lung gas exchange interface, and they are highly glycolytic. Although glucose and fructose represent discrete substrates available for glycolysis, pulmonary microvascular endothelial cells prefer glucose over fructose, and the mechanisms involved in this selection are unknown. 6-Phosphofructo-2-kinase/fructose-2, 6-bisphosphatase 3 (PFKFB3) is an important glycolytic enzyme that drives glycolytic flux against negative feedback and links glycolytic and fructolytic pathways. We hypothesized that PFKFB3 inhibits fructose metabolism in pulmonary microvascular endothelial cells. We found that PFKFB3 knockout cells survive better than wild-type cells in fructose-rich medium under hypoxia. Seahorse assays, lactate and glucose measurements, and stable isotope tracing showed that PFKFB3 inhibits fructose-hexokinase-mediated glycolysis and oxidative phosphorylation. Microarray analysis revealed that fructose upregulates PFKFB3, and PFKFB3 knockout cells increase fructose-specific GLUT5 (glucose transporter 5) expression. Using conditional endothelial-specific PFKFB3 knockout mice, we demonstrated that endothelial PFKFB3 knockout increases lung tissue lactate production after fructose gavage. Last, we showed that pneumonia increases fructose in BAL fluid in mechanically ventilated ICU patients. Thus, PFKFB3 knockout increases GLUT5 expression and the hexokinase-mediated fructose use in pulmonary microvascular endothelial cells that promotes their survival. Our findings indicate that PFKFB3 is a molecular switch that controls glucose versus fructose use in glycolysis and help better understand lung endothelial cell metabolism during respiratory failure.

Impact of acute stress on murine metabolomics and metabolic flux

Plasma metabolite concentrations and labeling enrichments are common measures of organismal metabolism. In mice, blood is often collected by tail snip sampling. Here, we systematically examined the effect of such sampling, relative to gold-standard sampling from an in-dwelling arterial catheter, on plasma metabolomics and stable isotope tracing. We find marked differences between the arterial and tail circulating metabolome, which arise from two major factors: handling stress and sampling site, whose effects were deconvoluted by taking a second arterial sample immediately after tail snip. Pyruvate and lactate were the most stress-sensitive plasma metabolites, rising ~14 and ~5-fold. Both acute handling stress and adrenergic agonists induce extensive, immediate production of lactate, and modest production of many other circulating metabolites, and we provide a reference set of mouse circulatory turnover fluxes with noninvasive arterial sampling to avoid such artifacts. Even in the absence of stress, lactate remains the highest flux circulating metabolite on a molar basis, and most glucose flux into the TCA cycle in fasted mice flows through circulating lactate. Thus, lactate is both a central player in unstressed mammalian metabolism and strongly produced in response to acute stress.