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Salvador AF, Shyu CR, Parks EJ. Measurement of lipid flux to advance translational research: evolution of classic methods to the future of precision health. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1348-1353. [PMID: 36075949 PMCID: PMC9534914 DOI: 10.1038/s12276-022-00838-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/22/2022] [Accepted: 07/12/2022] [Indexed: 02/08/2023]
Abstract
Over the past 70 years, the study of lipid metabolism has led to important discoveries in identifying the underlying mechanisms of chronic diseases. Advances in the use of stable isotopes and mass spectrometry in humans have expanded our knowledge of target molecules that contribute to pathologies and lipid metabolic pathways. These advances have been leveraged within two research paths, leading to the ability (1) to quantitate lipid flux to understand the fundamentals of human physiology and pathology and (2) to perform untargeted analyses of human blood and tissues derived from a single timepoint to identify lipidomic patterns that predict disease. This review describes the physiological and analytical parameters that influence these measurements and how these issues will propel the coming together of the two fields of metabolic tracing and lipidomics. The potential of data science to advance these fields is also discussed. Future developments are needed to increase the precision of lipid measurements in human samples, leading to discoveries in how individuals vary in their production, storage, and use of lipids. New techniques are critical to support clinical strategies to prevent disease and to identify mechanisms by which treatments confer health benefits with the overall goal of reducing the burden of human disease. Personalized tracking of how lipid (fat) metabolism changes over time could lead to improvements in the diagnosis and treatment of several diseases. Elizabeth Parks and colleagues from the University of Missouri, Columbia, USA, discuss the ways in which researchers use stable isotope labeling to monitor the kinetics of fatty acids and other lipids in the body. Usually, lipid quantities are measured only at a single timepoint, however the tracking of lipid turnover over time provides further diagnostic information. Aided by new techniques such as high-throughput mass spectrometry and machine learning, researchers are now able to continuously map total lipid contents in individual patients. The transition of measurements of lipid flux from the research laboratory to the doctor’s office will likely play a role in a new era of precision medicine.
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Affiliation(s)
- Amadeo F Salvador
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, MO, 65212, USA.,Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.,Department of Electrical Engineering and Computer Science, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Chi-Ren Shyu
- Department of Electrical Engineering and Computer Science, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Elizabeth J Parks
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, MO, 65212, USA. .,Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
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Coss-Bu JA, Hamilton-Reeves J, Patel JJ, Morris CR, Hurt RT. Protein Requirements of the Critically Ill Pediatric Patient. Nutr Clin Pract 2017; 32:128S-141S. [PMID: 28388381 DOI: 10.1177/0884533617693592] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This article includes a review of protein needs in children during health and illness, as well as a detailed discussion of protein metabolism, including nitrogen balance during critical illness, and assessment and prescription/delivery of protein to critically ill children. The determination of protein requirements in children has been difficult and challenging. The protein needs in healthy children should be based on the amount needed to ensure adequate growth during infancy and childhood. Compared with adults, children require a continuous supply of nutrients to maintain growth. The protein requirement is expressed in average requirements and dietary reference intake, which represents values that cover the needs of 97.5% of the population. Critically ill children have an increased protein turnover due to an increase in whole-body protein synthesis and breakdown with protein degradation leading to loss of lean body mass (LBM) and development of growth failure, malnutrition, and worse clinical outcomes. The results of protein balance studies in critically ill children indicate higher protein needs, with infants and younger children requiring higher intakes per body weight compared with older children. Monitoring the side effects of increased protein intake should be performed. Recent studies found a survival benefit in critically ill children who received a higher percentage of prescribed energy and protein goal by the enteral route. Future randomized studies should evaluate the effect of protein dosing in different age groups on patient outcomes, including LBM, muscle structure and function, duration of mechanical ventilation, intensive care unit and hospital length of stay, and mortality.
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Affiliation(s)
- Jorge A Coss-Bu
- 1 Section of Critical Care, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,2 Texas Children's Hospital, Houston, Texas, USA
| | - Jill Hamilton-Reeves
- 3 Department of Dietetics & Nutrition, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jayshil J Patel
- 4 Division of Pulmonary & Critical Care Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Claudia R Morris
- 5 Department of Pediatrics, Emory-Children's Center for Cystic Fibrosis and Airways Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ryan T Hurt
- 6 Division of General Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Haribal M, Jander G. Stable isotope studies reveal pathways for the incorporation of non-essential amino acids in Acyrthosiphon pisum (pea aphids). ACTA ACUST UNITED AC 2017; 218:3797-806. [PMID: 26632455 DOI: 10.1242/jeb.129189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Plant roots incorporate inorganic nitrogen into the amino acids glutamine, glutamic acid, asparagine and aspartic acid, which together serve as the primary metabolites of nitrogen transport to other tissues. Given the preponderance of these four amino acids, phloem sap is a nutritionally unbalanced diet for phloem-feeding insects. Therefore, aphids and other phloem feeders typically rely on microbial symbionts for the synthesis of essential amino acids. To investigate the metabolism of the four main transport amino acids by the pea aphid (Acyrthosiphon pisum), and its Buchnera aphidicola endosymbionts, aphids were fed defined diets with stable isotope-labeled glutamine, glutamic acid, asparagine or aspartic acid (U-(13)C, U-(15)N; U-(15)N; α-(15)N; or γ-(15)N). The metabolic fate of the dietary (15)N and (13)C was traced using gas chromatography-mass spectrometry (GC-MS). Nitrogen was the major contributor to the observed amino acid isotopomers with one additional unit mass (M+1). However, there was differential incorporation, with the amine nitrogen of asparagine being incorporated into other amino acids more efficiently than the amide nitrogen. Higher isotopomers (M+2, M+3 and M+4) indicated the incorporation of varying numbers of (13)C atoms into essential amino acids. GC-MS assays also showed that, even with an excess of dietary labeled glutamine, glutamic acid, asparagine or aspartic acid, the overall content of these amino acids in aphid bodies was mostly the product of catabolism of dietary amino acids and subsequent re-synthesis within the aphids. Thus, these predominant dietary amino acids are not passed directly to Buchnera endosymbionts for synthesis of essential amino acids, but are rather are produced de novo, most likely by endogenous aphid enzymes.
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Affiliation(s)
- Meena Haribal
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
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Newton S, Owusu-Agyei S, Asante KP, Amoaful E, Mahama E, Tchum SK, Ali M, Adjei K, Davis CR, Tanumihardjo SA. Vitamin A status and body pool size of infants before and after consuming fortified home-based complementary foods. ACTA ACUST UNITED AC 2016; 74:10. [PMID: 26955479 PMCID: PMC4780150 DOI: 10.1186/s13690-016-0121-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/13/2016] [Indexed: 11/26/2022]
Abstract
Background Home fortification using sachets of micronutrient powder (e.g. “Sprinkles”) is a food-based approach offering an alternative to high dose vitamin A (VA) supplements for infants. The primary objective was to investigate the impact of VA-home fortification on infant VA pool size. The secondary objective was to compare VA status of infants assessed by the modified relative dose response (MRDR) test before and the 13C-retinol isotope dilution (13C-RID) test in the same infants after vitamin A supplementation. Methods A randomized-controlled trial was conducted in 7–9 month old infants in Ghana. Eligible children were randomly allocated to receive a daily sachet of “Sprinkles” with or without VA for 5 months added to complementary foods. The MRDR test indirectly determined VA liver reserves at baseline and the 13C-RID determined VA body pool at follow-up in the same cohort of children. Results At baseline, the MRDR values (95 % CI) for infants were comparable in the intervention and control groups: normal at 0·032 (SD 0·018) (0·025–0·038) and 0·031 (SD 0·018) (0·024–0·038), respectively. After intervention, total body stores (TBS) and liver retinol concentrations did not differ between intervention and control groups; TBS were 436 (SD 303) and 434 (SD 186) μmol, respectively, and estimated liver concentrations were 0·82 (SD 0·53) and 0·79 (SD 0·36) μmol/g liver, indicating adequate reserves in all children. Conclusions Both the MRDR and 3C-RID tests confirmed that the infants had adequate VA status before and after home fortification of their complementary foods. These tests offered more information than serum retinol concentrations alone, which predicted VA deficiency using current suggested cutoffs not corrected for inflammation status.
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Affiliation(s)
- Sam Newton
- Kintampo Health Research Centre, P. O. Box 200, Kintampo, Brong Ahafo Region Ghana
| | - Seth Owusu-Agyei
- Kintampo Health Research Centre, P. O. Box 200, Kintampo, Brong Ahafo Region Ghana
| | - Kwaku Poku Asante
- Kintampo Health Research Centre, P. O. Box 200, Kintampo, Brong Ahafo Region Ghana
| | - Esi Amoaful
- Nutrition Department, Ghana Health Service, Accra, Ghana
| | - Emmanuel Mahama
- Kintampo Health Research Centre, P. O. Box 200, Kintampo, Brong Ahafo Region Ghana
| | - Samuel Kofi Tchum
- Kintampo Health Research Centre, P. O. Box 200, Kintampo, Brong Ahafo Region Ghana
| | - Martha Ali
- Kintampo Health Research Centre, P. O. Box 200, Kintampo, Brong Ahafo Region Ghana
| | - Kwame Adjei
- Kintampo Health Research Centre, P. O. Box 200, Kintampo, Brong Ahafo Region Ghana
| | - Christopher R Davis
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI USA
| | - Sherry A Tanumihardjo
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI USA
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McCue MD, Welch KC. (13)C-Breath testing in animals: theory, applications, and future directions. J Comp Physiol B 2015; 186:265-85. [PMID: 26660654 DOI: 10.1007/s00360-015-0950-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/11/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
Abstract
The carbon isotope values in the exhaled breath of an animal mirror the carbon isotope values of the metabolic fuels being oxidized. The measurement of stable carbon isotopes in carbon dioxide is called (13)C-breath testing and offers a minimally invasive method to study substrate oxidation in vivo. (13)C-breath testing has been broadly used to study human exercise, nutrition, and pathologies since the 1970s. Owing to reduced use of radioactive isotopes and the increased convenience and affordability of (13)C-analyzers, the past decade has witnessed a sharp increase in the use of breath testing throughout comparative physiology--especially to answer questions about how and when animals oxidize particular nutrients. Here, we review the practical aspects of (13)C-breath testing and identify the strengths and weaknesses of different methodological approaches including the use of natural abundance versus artificially-enriched (13)C tracers. We critically compare the information that can be obtained using different experimental protocols such as diet-switching versus fuel-switching. We also discuss several factors that should be considered when designing breath testing experiments including extrinsic versus intrinsic (13)C-labelling and different approaches to model nutrient oxidation. We use case studies to highlight the myriad applications of (13)C-breath testing in basic and clinical human studies as well as comparative studies of fuel use, energetics, and carbon turnover in multiple vertebrate and invertebrate groups. Lastly, we call for increased and rigorous use of (13)C-breath testing to explore a variety of new research areas and potentially answer long standing questions related to thermobiology, locomotion, and nutrition.
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Gannon BM, Tanumihardjo SA. Comparisons among Equations Used for Retinol Isotope Dilution in the Assessment of Total Body Stores and Total Liver Reserves. J Nutr 2015; 145:847-54. [PMID: 25809683 PMCID: PMC6619684 DOI: 10.3945/jn.114.208132] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/27/2015] [Accepted: 02/20/2015] [Indexed: 11/14/2022] Open
Abstract
Vitamin A plays an essential role in animal biology and has negative effects associated with both hypo- and hypervitaminosis A. Many notable interventions are being done globally to eliminate vitamin A deficiency, including supplementation, fortification, and biofortification. At the same time, it is important to monitor vitamin A status in nations where preformed vitamin A intake is high because of consumption of animal source foods (e.g., liver, dairy, eggs), fortified foods (e.g., milk, cereals, oil, sugar, margarine), or vitamin supplements (e.g., one-a-day multivitamins) to ensure the population does not reach hypervitaminosis A. To accurately assess population status and evaluate interventions aimed at improving vitamin A status, accurate assessment methods are needed. The primary storage site of vitamin A is the liver; however, routinely obtaining liver samples from humans is impractical and unethical. Isotope dilution using deuterium- or (13)C-labeled retinol is currently the most sensitive indirect biomarker of vitamin A status across a wide range of liver reserves. The major drawback to its application is the increased technicality in sample analysis and data calculations when compared to less sensitive methodology, such as serum retinol concentrations and dose response tests. Two main equations have emerged for calculating vitamin A body pool size or liver concentrations from isotope dilution data: the "Olson equation" and the "mass balance equation." Different applications of these equations can lead to confusion and lack of consistency if the underlying principles and assumptions used are not clarified. The purpose of this focused review is to describe the evolution of the equations used in retinol stable-isotope work and the assumptions appropriate to different applications of the test. Ultimately, the 2 main equations are shown to be fundamentally the same and differ only in assumptions made for each specific research application.
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Affiliation(s)
- Bryan M Gannon
- Interdepartmental Graduate Program in Nutritional Sciences, Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI
| | - Sherry A Tanumihardjo
- Interdepartmental Graduate Program in Nutritional Sciences, Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI
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Yates JR. The revolution and evolution of shotgun proteomics for large-scale proteome analysis. J Am Chem Soc 2013; 135:1629-40. [PMID: 23294060 PMCID: PMC3751590 DOI: 10.1021/ja3094313] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mass spectrometry has evolved at an exponential rate over the last 100 years. Innovations in the development of mass spectrometers have created powerful instruments capable of analyzing a wide range of targets, from rare atoms and molecules to very large molecules, such as a proteins, protein complexes, and DNA. These performance gains have been driven by sustaining innovations, punctuated by the occasional disruptive innovation. The use of mass spectrometry for proteome analysis was driven by disruptive innovations that created a capability for large-scale analysis of proteins and modifications.
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Affiliation(s)
- John R. Yates
- 10550 North Torrey Pines, SR11, Department of Chemical Physiology, The Scripps Research Institute, LaJolla, CA 92037, TEL: (858) 784-8862
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Arsova B, Kierszniowska S, Schulze WX. The use of heavy nitrogen in quantitative proteomics experiments in plants. TRENDS IN PLANT SCIENCE 2012; 17:102-12. [PMID: 22154826 DOI: 10.1016/j.tplants.2011.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/28/2011] [Accepted: 11/04/2011] [Indexed: 05/04/2023]
Abstract
In the growing field of plant systems biology, there is an undisputed need for methods allowing accurate quantitation of proteins and metabolites. As autotrophic organisms, plants can easily metabolize different nitrogen isotopes, resulting in proteins and metabolites with distinct molecular mass that can be separated on a mass spectrometer. In comparative quantitative experiments, treated and untreated samples are differentially labeled by nitrogen isotopes and jointly processed, thereby minimizing sample-to-sample variation. In recent years, heavy nitrogen labeling has become a widely used strategy in quantitative proteomics and novel approaches have been developed for metabolite identification. Here, we present an overview of currently used experimental strategies in heavy nitrogen labeling in plants and provide background on the history and function of this quantitation technique.
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Affiliation(s)
- Borjana Arsova
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
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9
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Tracking the Oxidative and Nonoxidative Fates of Isotopically Labeled Nutrients in Animals. Bioscience 2011. [DOI: 10.1525/bio.2011.61.3.7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Escaron AL, Green MH, Howe JA, Tanumihardjo SA. Mathematical modeling of serum 13C-retinol in captive rhesus monkeys provides new insights on hypervitaminosis A. J Nutr 2009; 139:2000-6. [PMID: 19710158 PMCID: PMC2744618 DOI: 10.3945/jn.109.111922] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hypervitaminosis A is increasingly a public health concern, and thus noninvasive quantitative methods merit exploration. In this study, we applied the (13)C-retinol isotope dilution test to a nonhuman primate model with excessive liver stores. After baseline serum chemistries, rhesus macaques (Macaca mulatta; n = 16) were administered 3.5 mumol (13)C(2)-retinyl acetate. Blood was drawn at baseline, 5 h, and 2, 4, 7, 14, 21, and 28 d following the dose. Liver biopsies were collected 7 d before and 2 d after dosing (n = 4) and at 7, 14, and 28 d (n = 4/time) after dosing. Serum and liver were analyzed by HPLC and GC-combustion-isotope ratio MS for retinol and its enrichment, respectively. Model-based compartmental analysis was applied to serum data. Lactate dehydrogenase was elevated in 50% of the monkeys. Total body reserves (TBR) of vitamin A (VA) were calculated at 28 d. Predicted TBR (3.52 +/- 2.01 mmol VA) represented measured liver stores (4.56 +/- 1.38 mmol VA; P = 0.124). Predicted liver VA concentrations (13.3 +/- 9.7 micromol/g) were similar to measured liver VA concentrations (16.4 +/- 5.3 micromol/g). The kinetic models predict that 27-52% of extravascular VA is exchanging with serum in hypervitaminotic A monkeys. The test correctly diagnosed hypervitaminosis A in all monkeys, i.e. 100% sensitivity. Stable isotope techniques have important public health potential for the classification of VA status, including hypervitaminosis, because no other technique besides invasive liver biopsies, correctly identifies excessive liver VA stores.
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Affiliation(s)
- Anne L. Escaron
- Interdepartmental Graduate Program in Nutritional Sciences, University of Wisconsin, Madison, WI 53706; Department of Nutritional Sciences, Pennsylvania State University, University Park, PA 16802; and Department of Agronomy and Soils, Auburn University, Auburn, AL 36849
| | - Michael H. Green
- Interdepartmental Graduate Program in Nutritional Sciences, University of Wisconsin, Madison, WI 53706; Department of Nutritional Sciences, Pennsylvania State University, University Park, PA 16802; and Department of Agronomy and Soils, Auburn University, Auburn, AL 36849
| | - Julie A. Howe
- Interdepartmental Graduate Program in Nutritional Sciences, University of Wisconsin, Madison, WI 53706; Department of Nutritional Sciences, Pennsylvania State University, University Park, PA 16802; and Department of Agronomy and Soils, Auburn University, Auburn, AL 36849
| | - Sherry A. Tanumihardjo
- Interdepartmental Graduate Program in Nutritional Sciences, University of Wisconsin, Madison, WI 53706; Department of Nutritional Sciences, Pennsylvania State University, University Park, PA 16802; and Department of Agronomy and Soils, Auburn University, Auburn, AL 36849
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Kumar V, Atherton P, Smith K, Rennie MJ. Human muscle protein synthesis and breakdown during and after exercise. J Appl Physiol (1985) 2009; 106:2026-39. [DOI: 10.1152/japplphysiol.91481.2008] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Skeletal muscle demonstrates extraordinary mutability in its responses to exercise of different modes, intensity, and duration, which must involve alterations of muscle protein turnover, both acutely and chronically. Here, we bring together information on the alterations in the rates of synthesis and degradation of human muscle protein by different types of exercise and the influences of nutrition, age, and sexual dimorphism. Where possible, we summarize the likely changes in activity of signaling proteins associated with control of protein turnover. Exercise of both the resistance and nonresistance types appears to depress muscle protein synthesis (MPS), whereas muscle protein breakdown (MPB) probably remains unchanged during exercise. However, both MPS and MPB are elevated after exercise in the fasted state, when net muscle protein balance remains negative. Positive net balance is achieved only when amino acid availability is increased, thereby raising MPS markedly. However, postexercise-increased amino acid availability is less important for inhibiting MPB than insulin, the secretion of which is stimulated most by glucose availability, without itself stimulating MPS. Exercise training appears to increase basal muscle protein turnover, with differential responses of the myofibrillar and mitochondrial protein fractions to acute exercise in the trained state. Aging reduces the responses of myofibrillar protein and anabolic signaling to resistance exercise. There appear to be few, if any, differences in the response of young women and young men to acute exercise, although there are indications that, in older women, the responses may be blunted more than in older men.
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Krüger M, Moser M, Ussar S, Thievessen I, Luber CA, Forner F, Schmidt S, Zanivan S, Fässler R, Mann M. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 2008; 134:353-64. [PMID: 18662549 DOI: 10.1016/j.cell.2008.05.033] [Citation(s) in RCA: 509] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 04/29/2008] [Accepted: 05/20/2008] [Indexed: 01/25/2023]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) has become a versatile tool for quantitative, mass spectrometry (MS)-based proteomics. Here, we completely label mice with a diet containing either the natural or the (13)C(6)-substituted version of lysine. Mice were labeled over four generations with the heavy diet, and development, growth, and behavior were not affected. MS analysis of incorporation levels allowed for the determination of incorporation rates of proteins from blood cells and organs. The F2 generation was completely labeled in all organs tested. SILAC analysis from various organs lacking expression of beta1 integrin, beta-Parvin, or the integrin tail-binding protein Kindlin-3 confirmed their absence and disclosed a structural defect of the red blood cell membrane skeleton in Kindlin-3-deficient erythrocytes. The SILAC-mouse approach is a versatile tool by which to quantitatively compare proteomes from knockout mice and thereby determine protein functions under complex in vivo conditions.
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Affiliation(s)
- Marcus Krüger
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, 82152 Martinsried, Germany
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Sidossis LS, Magkos F, Mittendorfer B, Wolfe RR. Stable isotope tracer dilution for quantifying very low-density lipoprotein-triacylglycerol kinetics in man. Clin Nutr 2004; 23:457-66. [PMID: 15297080 DOI: 10.1016/j.clnu.2003.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2003] [Accepted: 11/11/2003] [Indexed: 11/24/2022]
Abstract
BACKGROUND & AIM A number of approaches have been employed in the past to measure very low-density lipoprotein (VLDL) triacylglycerol (TG) kinetics in humans in vivo, varying in the selection of tracer and mode of administration. All, however, make use of labeled TG precursors and more or less complicated mathematical models to derive the kinetic parameters of interest. The aim of the present study was to develop a conceptually straightforward method, based on the traditional tracer infusion technique, for quantifying VLDL-TG production rates in man using stable isotopes. METHOD Our approach involves ingestion of [U-13C3]glycerol to endogenously label the glycerol in VLDL-TG, plasmapheresis, isolation of the newly 13C-labeled VLDL from plasma, and administration within the next 2-3 days via a primed constant autologous reinfusion. This procedure produces enough tracer for a priming dose plus 2-3 h of infusion. In the physiological conditions examined (basal and hyperglycemic states, fat- and carbohydrate-rich diets), with almost 3-fold ranging VLDL-TG pool sizes, a steady state in plasma VLDL-TG glycerol tracer-to-tracee ratio was readily achieved within 2 h. Consequently, calculations are made according to the isotope dilution principle, thus avoiding assumptions implicit in more complicated models. CONCLUSION The stable isotope VLDL-TG tracer dilution method offers an alternative and reliable tool for the determination of endogenous VLDL-TG kinetics in man under a variety of metabolic states.
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Affiliation(s)
- Labros S Sidossis
- Laboratory of Nutrition and Clinical Dietetics, Department of Nutrition and Dietetics, Harokopio University, 70 El. Venizelou Ave, 17671 Athens, Greece.
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Affiliation(s)
- Ronald E Kleinman
- Department of Pediatrics, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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15
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Hess S, van Beek J, Pannell LK. Acid hydrolysis of silk fibroins and determination of the enrichment of isotopically labeled amino acids using precolumn derivatization and high-performance liquid chromatography-electrospray ionization-mass spectrometry. Anal Biochem 2002; 311:19-26. [PMID: 12441148 DOI: 10.1016/s0003-2697(02)00402-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Silk fibroins from moth larvae and spiders are composed of highly repetitive Ala- and Gly-rich blocks that determine their structure, properties, and function. To investigate the metabolic integration of isotopically labeled amino acids in the excreted silk, the enrichment of ingested tracers was determined after acid hydrolysis of the fibroins. Thus, spiders and moth larvae were fed with stable isotope tracers such as [1-13C]Ala or [1-13C]Gly and silked. After hydrolysis of the silk proteins, the corresponding amino acids were derivatized with Nalpha-(2,4-dinitro-5-fluorophenyl)-L-alaninamide (Marfey's reagent) and separated by liquid chromatography. The isotopical enrichment of the amino acids was determined by online electrospray mass spectrometry and calculated by newly developed software. Depending on the feeding protocol, enrichments of up to 58% in Gly and 31% in Ala were found in the investigated silks. The highly enriched silk fibroins are suitable for further structural investigation such as solid-state nuclear magnetic resonance.
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Affiliation(s)
- Sonja Hess
- Structural Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8, Rm B2A27, Bethesda, MD 20892-0805, USA.
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Jeffrey FMH, Roach JS, Storey CJ, Sherry AD, Malloy CR. 13C isotopomer analysis of glutamate by tandem mass spectrometry. Anal Biochem 2002; 300:192-205. [PMID: 11779111 DOI: 10.1006/abio.2001.5457] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tandem mass spectrometry allows a compound to be isolated from the rest of the sample and dissociated into smaller fragments. We show here that fragmentation of glutamate mass isotopomers yields additional mass spectral data that significantly improve the analysis of metabolic fluxes compared to full-scan mass spectrometry. In order to validate the technique, tandem and full-scan mass spectrometry were used along with (13)C NMR to analyze glutamate from rat hearts perfused with three substrate mixtures (5 mM glucose plus 5 mM [2-(13)C]acetate, 5 mM [1-(13)C]glucose plus 5 U/L insulin, and 5 mM glucose plus 1 mM [3-(13)C]pyruvate). Analysis by tandem mass spectrometry showed that the enriched substrate contributed 98 +/- 2, 53 +/- 2, and 84 +/- 7%, respectively, of acetyl-coenzyme A while the rate of anaplerotic substrate entry was 7 +/- 3, 25 +/- 8, and 16 +/- 8%. Similar results were obtained with (13)C NMR data, while values from full-scan data had higher error. We believe that this is the first use of tandem mass spectrometry to determine pathway flux using (13)C-enriched substrates. Although analysis of the citric acid cycle by NMR is simpler (and more intuitive), tandem mass spectrometry has the potential to combine high sensitivity with the high information yield previously available only by NMR.
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Affiliation(s)
- F Mark H Jeffrey
- The Mary Nell and Ralph B. Rogers Magnetic Resonance Center, Department of Radiology, University of Texas Southwestern Medical Center, Dallas 75390-9085, USA
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Kleger GR, Turgay M, Imoberdorf R, McNurlan MA, Garlick PJ, Ballmer PE. Acute metabolic acidosis decreases muscle protein synthesis but not albumin synthesis in humans. Am J Kidney Dis 2001; 38:1199-207. [PMID: 11728951 DOI: 10.1053/ajkd.2001.29215] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Chronic metabolic acidosis induces negative nitrogen balance by either increased protein breakdown or decreased protein synthesis. Few data exist regarding effects of acute metabolic acidosis on protein synthesis. We investigated fractional synthesis rates (FSRs) of muscle protein and albumin, plasma concentrations of insulin-like growth factor-I (IGF-I), thyroid-stimulating hormone (TSH), and thyroid hormones (free thyroxin [fT(4)] and triiodothyronine [fT(3)]) in seven healthy human volunteers after a stable controlled metabolic period of 5 days and again 48 hours later after inducing metabolic acidosis by oral ammonium chloride intake (4.2 mmol/kg/d divided in six daily doses). Muscle and albumin FSRs were obtained by the [(2)H(5)ring]phenylalanine flooding technique. Ammonium chloride induced a significant decrease in pH (7.43 +/- 0.02 versus 7.32 +/- 0.04; P < 0.0001) and bicarbonate concentration (24.6 +/- 1.6 versus 16.0 +/- 2.7 mmol/L; P < 0.0001) within 48 hours. Nitrogen balance decreased significantly on the second day of acidosis. The FSR of muscle protein decreased (1.94 +/- 0.25 versus 1.30 +/- 0.39; P < 0.02), whereas the FSR of albumin remained constant. TSH levels increased significantly (1.1 +/- 0.5 versus 1.9 +/- 1.1 mU/L; P = 0.03), whereas IGF-I, fT(4), and fT(3) levels showed no significant change. We conclude that acute metabolic acidosis for 48 hours in humans induces a decrease in muscle protein synthesis, which contributes substantially to a negative nitrogen balance. In contrast to prolonged metabolic acidosis of 7 days, a short period of acidosis in the present study did not downregulate albumin synthesis.
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Affiliation(s)
- G R Kleger
- Department of Medicine, Inselspital Bern, Bern, Switzerland
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Bodamer OA, Halliday D. Uses of stable isotopes in clinical diagnosis and research in the paediatric population. Arch Dis Child 2001; 84:444-8. [PMID: 11316697 PMCID: PMC1718760 DOI: 10.1136/adc.84.5.444] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- O A Bodamer
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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Fouillet H, Gaudichon C, Mariotti F, Mahé S, Lescoat P, Huneau JF, Tomé D. Compartmental modeling of postprandial dietary nitrogen distribution in humans. Am J Physiol Endocrinol Metab 2000; 279:E161-75. [PMID: 10893336 DOI: 10.1152/ajpendo.2000.279.1.e161] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A linear 11-compartment model was developed to describe and simulate the postprandial distribution of dietary nitrogen. The values of its 15 constant diffusion coefficients were estimated from the experimental measurement of (15)N nitrogen kinetics in the intestine, blood, and urine after the oral administration of (15)N-labeled milk protein in humans. Model structure development, parameter estimation, and sensibility analysis were achieved using SAAM II and SIMUSOLV softwares. The model was validated at each stage of its development by testing successively its a priori and a posteriori identifiability. The model predicted that, 8 h after a meal, the dietary nitrogen retained in the body comprised 28% free amino acids and 72% protein, approximately 30% being recovered in the splanchnic bed vs. 70% in the peripheral area. Twelve hours after the meal, these values had decreased to 18 and 23% for the free amino acid fraction and splanchnic nitrogen, respectively. Such a model constitutes a useful, explanatory tool to describe the processes involved in the metabolic utilization of dietary proteins.
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Affiliation(s)
- H Fouillet
- Nutrition humaine et physiologie intestinale, Unité Institut National de la Recherche Agronomique, Institut National Agronomique Paris-Grignon, 75231 Paris Cédex 05, France
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Young VR, Ajami AM. 1999 Jonathan E. Rhoads lecture. Isotopic metaprobes, nutrition, and the roads ahead. JPEN J Parenter Enteral Nutr 1999; 23:175-94. [PMID: 10421386 DOI: 10.1177/0148607199023004175] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The 1999 Jonathan E. Rhoads lecture, delivered by Vernon R. Young at the annual meeting of American Society for Parenteral and Enteral Nutrition (A.S.P.E.N.), San Diego, February 2, 1999, with the printed version coauthored with Alfred M. Ajami, is concerned with the application of isotopic probes and how, in particular, they may be used as diagnostic tools to enhance the role of nutrition in the comprehensive medical management of the patient. Following a brief review of the early uses of stable isotopes in metabolic research we consider the present and possible future application of stable isotope probes. The concept of a "gateway" enzyme in a discrete biochemical pathway and how the flow of substrate through this step might be assessed by giving a "metaprobe" is developed. The specific and desirable structural requirements of the metaprobe are considered. A number of examples are given that further exploit the concepts of "underground" metabolism and of metabolic "hijackers." It is our view that we are on the verge of a new era where, for the many pragmatic and exciting reasons discussed, stable isotope probes will find and increasing use in the practice of clinical medicine and in the preventive and public health areas.
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Affiliation(s)
- V R Young
- Laboratory of Human Nutrition and Clinical Research Center, Massachusetts Institute of Technology, Cambridge 02139, USA
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Young VR, Ajami A. The Rudolf Schoenheimer Centenary Lecture. Isotopes in nutrition research. Proc Nutr Soc 1999; 58:15-32. [PMID: 10343336 DOI: 10.1079/pns19990004] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The present lecture begins with a brief overview of the professional and scientific journey taken by Rudolf Schoenheimer, before turning to a discussion of the power of isotopic tracers in nutrition research. Schoenheimer's remarkable contributions to the study of intermediary metabolism and the turnover of body constituents, based initially on compounds tagged with 2H and later with 15N, spanned a mere decade. It is difficult, however, to overestimate the enormous impact of Schoenheimer's research on the evolution of biological science. After a relative hiatus, following Schoenheimer's death in 1941, in the use of stable nuclides as tracers in metabolism and nutrition, especially in human subjects, there is now an expanded and exciting range of techniques, experimental protocols and stable-isotope tracer compounds that are helping to probe the dynamic aspects of the metabolism of the major energy-yielding substrates, amino acids and other N-containing compounds, vitamins and mineral elements in human subjects. Various aspects of the contemporary applications of these tracers in nutrition research are covered in the present lecture.
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Affiliation(s)
- V R Young
- Laboratory of Human Nutrition, School of Science, Massachusetts Institute of Technology, Cambridge 02139, USA.
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de Meer K, Roef MJ, Kulik W, Jakobs C. In vivo research with stable isotopes in biochemistry, nutrition and clinical medicine: an overview. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 1999; 35:19-37. [PMID: 10902535 DOI: 10.1080/10256019908234077] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Tracers and kinetic modelling provide the opportunity to follow the movement and to quantify the metabolic fates of biological compounds in vivo. For studies in children and for repeated studies in adults, the use of stable isotopically labelled substrates are preferable and safe. Measurement of isotopic enrichment in biological molecules is highly specific and can be extremely precise. This allows the development of models of biological system dynamics in cells and organs that are otherwise inaccessible for sampling. Applications in biochemistry, nutrition and clinical medicine show the potential of stable isotopes in vivo. Methodology is of paramount importance and includes the choice of bolus studies, (primed) continuous infusions, use of multiple tracers and use of isotopomer information and intrinsic labels. There is no limit to the number and kind of compounds that can be traced. Topics include intermediate metabolism (lipids, proteins and carbohydrates) using hydrogen, carbon and nitrogen labels. In clinical medicine, 13C-breath tests are available for detection of Helicobacter pylori ([13C]urea breath test), and for assessment of a variety of gastro-intestinal and hepatic functions (e.g. [13C]octanoate and mixed [13C]triglyceride breath tests for studies of gastric emptying and fat absorption, respectively). Because theoretical, methodological, physiological and practical aspects are intertwined, in vivo research with stable isotopes demands close collaboration between the clinical researcher and the chemist responsible for the mass spectrometry.
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Affiliation(s)
- K de Meer
- University Hospital Vrije Universiteit, Department of Clinical Chemistry, Amsterdam, The Netherlands
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Abstract
Protein synthesis is crucial for the survival of a living system, and any derangement of this process can cause large imbalances and deficiencies in humans. The measurement of whole body protein turnover in humans was a significant advance on simple nitrogen balance studies. Until recently, however, the advantages of focusing on the measurement of synthesis at the tissue or specific protein level have been overwhelmed by the difficulties. The advent of powerful new methods of mass spectrometry and stable isotope tracer methodology along with effective purification techniques enabled the measurement of protein synthesis at the tissue (liver, gut and muscle), specific protein fraction (mitochondrial and sarcoplasmic) and individual protein (myosin heavy chain, albumin and fibrinogen) levels in humans. This offers better insight into the underlying mechanisms of protein synthesis in disease and health conditions.
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Affiliation(s)
- P Balagopal
- Nemours Children's Clinic, Jacksonville, FL 32207, USA.
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