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Hubert DL, Arnold KR, Greenspan ZG, Pupo A, Robinson RD, Chavarin VV, Barter TB, Djukovic D, Raftery D, Vue Z, Hinton A, McReynolds MR, Harrison BR, Phillips MA. Selection for early reproduction leads to accelerated aging and extensive metabolic remodeling in Drosophila melanogaster populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601037. [PMID: 39005259 PMCID: PMC11244849 DOI: 10.1101/2024.06.28.601037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Experimental evolution studies that feature selection on life-history characters are a proven approach for studying the evolution of aging and variation in rates of senescence. Recently, the incorporation of genomic and transcriptomic approaches into this framework has led to the identification of hundreds of genes associated with different aging patterns. However, our understanding of the specific molecular mechanisms underlying these aging patterns remains limited. Here, we incorporated extensive metabolomic profiling into this framework to generate mechanistic insights into aging patterns in Drosophila melanogaster . Specifically, we characterized metabolomic change over time associated with accelerated aging in populations of D. melanogaster under selection for early reproduction compared to their controls. Using this data we: i) evaluated the evolutionary repeatability across the metabolome; ii) evaluated the value of the metabolome as a predictor of "biological age" in this system; and iii) identified specific metabolic pathways associated with accelerated aging. Generally, our findings suggest that the metabolome is a reliable predictor of age and senescence in populations that share a recent evolutionary history. Metabolomic analysis revealed that generations of selection for early reproduction resulted in highly repeatable alterations to the metabolome. Specifically, changes in carbohydrate, amino acid, and TCA cycle-related metabolite abundances over time point to metabolic remodeling that favors rapid early reproduction with long-term consequences for carbohydrate and protein utilization.
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2
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Wodrich APK, Scott AW, Giniger E. What do we mean by "aging"? Questions and perspectives revealed by studies in Drosophila. Mech Ageing Dev 2023; 213:111839. [PMID: 37354919 PMCID: PMC10330756 DOI: 10.1016/j.mad.2023.111839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
What is the nature of aging, and how best can we study it? Here, using a series of questions that highlight differing perspectives about the nature of aging, we ask how data from Drosophila melanogaster at the organismal, tissue, cellular, and molecular levels shed light on the complex interactions among the phenotypes associated with aging. Should aging be viewed as an individual's increasing probability of mortality over time or as a progression of physiological states? Are all age-correlated changes in physiology detrimental to vigor or are some compensatory changes that maintain vigor? Why do different age-correlated functions seem to change at different rates in a single individual as it ages? Should aging be considered as a single, integrated process across the scales of biological resolution, from organismal to molecular, or must we consider each level of biological scale as a separate, distinct entity? Viewing aging from these differing perspectives yields distinct but complementary interpretations about the properties and mechanisms of aging and may offer a path through the complexities related to understanding the nature of aging.
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Affiliation(s)
- Andrew P K Wodrich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States; Interdisciplinary Program in Neuroscience, Georgetown University, Washington DC, United States; College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Andrew W Scott
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States.
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3
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Shaposhnikov MV, Gorbunova AA, Zemskaya NV, Ulyasheva NS, Pakshina NR, Yakovleva DV, Moskalev A. Simultaneous activation of the hydrogen sulfide biosynthesis genes (CBS and CSE) induces sex-specific geroprotective effects in Drosophila melanogaster. Biogerontology 2023; 24:275-292. [PMID: 36662374 DOI: 10.1007/s10522-023-10017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023]
Abstract
Hydrogen sulfide (H2S) is one of the most important gasotransmitters that affect lifespan and provide resistance to adverse environmental conditions. Here we investigated geroprotective effects of the individual and simultaneous overexpression of genes encoding key enzymes of H2S biosynthesis - cystathionine-β-synthase (CBS) and cystathionine-γ-lyase (CSE) on D. melanogaster model. Simultaneous overexpression of CBS and CSE resulted in additive (in males) and synergistic (in females) beneficial effects on median lifespan. Individual overexpression of CBS was associated with increased thermotolerance and decreased transcription level of genes encoding stress-responsive transcription factors HIF1 and Hsf, while individual overexpression of CSE was associated with increased resistance to paraquat. Simultaneous overexpression of both genes increased resistance to hyperthermia in old females or paraquat in old males. The obtained results suggest sex-specific epistatic interaction of CBS and CSE overexpression effects on longevity and stress resistance.
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Affiliation(s)
- Mikhail V Shaposhnikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation, 119991
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russian Federation, 167982
| | - Anastasia A Gorbunova
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russian Federation, 167982
| | - Nadezhda V Zemskaya
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russian Federation, 167982
| | - Natalia S Ulyasheva
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russian Federation, 167982
| | - Natalya R Pakshina
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russian Federation, 167982
| | - Daria V Yakovleva
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russian Federation, 167982
| | - Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation, 119991.
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russian Federation, 167982.
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4
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Balashova E, Trifonova O, Maslov D, Lichtenberg S, Lokhov P, Archakov A. Metabolome profiling in the study of aging processes. BIOMEDITSINSKAYA KHIMIYA 2022; 68:321-338. [DOI: 10.18097/pbmc20226805321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aging of a living organism is closely related to systemic metabolic changes. But due to the multilevel and network nature of metabolic pathways, it is difficult to understand these connections. Today, this problem is solved using one of the main approaches of metabolomics — untargeted metabolome profiling. The purpose of this publication is to systematize the results of metabolomic studies based on such profiling, both in animal models and in humans.
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Affiliation(s)
| | | | - D.L. Maslov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - P.G. Lokhov
- Institute of Biomedical Chemistry, Moscow, Russia
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5
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Balashova EE, Maslov DL, Trifonova OP, Lokhov PG, Archakov AI. Metabolome Profiling in Aging Studies. BIOLOGY 2022; 11:1570. [PMID: 36358271 PMCID: PMC9687709 DOI: 10.3390/biology11111570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 06/07/2024]
Abstract
Organism aging is closely related to systemic metabolic changes. However, due to the multilevel and network nature of metabolic pathways, it is difficult to understand these connections. Today, scientists are trying to solve this problem using one of the main approaches of metabolomics-untargeted metabolome profiling. The purpose of this publication is to review metabolomic studies based on such profiling, both in animal models and in humans. This review describes metabolites that vary significantly across age groups and include carbohydrates, amino acids, carnitines, biogenic amines, and lipids. Metabolic pathways associated with the aging process are also shown, including those associated with amino acid, lipid, and energy metabolism. The presented data reveal the mechanisms of aging and can be used as a basis for monitoring biological age and predicting age-related diseases in the early stages of their development.
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Affiliation(s)
- Elena E. Balashova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, 119121 Moscow, Russia
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6
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Kokoreva AS, Isakova EP, Tereshina VM, Klein OI, Gessler NN, Deryabina YI. The Effect of Different Substrates on the Morphological Features and Polyols Production of Endomyces magnusii Yeast during Long-Lasting Cultivation. Microorganisms 2022; 10:microorganisms10091709. [PMID: 36144311 PMCID: PMC9506286 DOI: 10.3390/microorganisms10091709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/12/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
The study on the influence of different glucose concentrations (2%, 0.5%, and 0.2%) and glycerol (1%) on the morphological and physiological features, as well as the composition of soluble carbohydrates, was performed using Endomyces magnusii yeast. Two-factor analysis of variance with repetitions to process the data of the cell size changes showed that the substrate type affected cell size the most. The cells with 2% glucose were 30–35% larger than those growing on glycerol. The decrease in the initial glucose concentration up to 0.5–0.2% slightly changed the cell length. However, even in the logarithmic growth phase pseudo-mycelium of two to four cells appeared in the cultures when using low glucose, unlike those using glycerol. Throughout the whole experiment, more than 90% of the populations remained viable on all of the substrates tested. The ability for colony formation decreased during aging. Nevertheless, at the three-week stage, upon substrate restriction (0.2% glucose), it was twice higher than those under the other conditions. The respiration rate also decreased and exceeded not more than 10% of that in the logarithmic phase. By the end of the experiment, the cyanide-sensitive respiration share decreased up to 40% for all types of substrates. The study of soluble cytosol carbohydrates showed that the cultures using 2% glucose and 1% glycerol contained mainly arabitol and mannitol, while at low glucose concentrations they were substituted for inositol. The formation of inositol is supposed to be related to pseudo-mycelium formation. The role of calorie restriction in the regulation of carbohydrate synthesis and the composition in the yeast and its biotechnological application is under consideration.
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Affiliation(s)
- Anastasia S. Kokoreva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Elena P. Isakova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
- Correspondence: ; Tel.: +7-(495)-954-4008
| | - Vera M. Tereshina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya, 7/2, 117312 Moscow, Russia
| | - Olga I. Klein
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Natalya N. Gessler
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Yulia I. Deryabina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
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7
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Guo X, Jahoor A, Jensen J, Sarup P. Metabolomic spectra for phenotypic prediction of malting quality in spring barley. Sci Rep 2022; 12:7881. [PMID: 35551263 PMCID: PMC9098465 DOI: 10.1038/s41598-022-12028-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
We investigated prediction of malting quality (MQ) phenotypes in different locations using metabolomic spectra, and compared the prediction ability of different models, and training population (TP) sizes. Data of five MQ traits was measured on 2667 individual plots of 564 malting spring barley lines from three years and two locations. A total of 24,018 metabolomic features (MFs) were measured on each wort sample. Two statistical models were used, a metabolomic best linear unbiased prediction (MBLUP) and a partial least squares regression (PLSR). Predictive ability within location and across locations were compared using cross-validation methods. For all traits, more than 90% of the total variance in MQ traits could be explained by MFs. The prediction accuracy increased with increasing TP size and stabilized when the TP size reached 1000. The optimal number of components considered in the PLSR models was 20. The accuracy using leave-one-line-out cross-validation ranged from 0.722 to 0.865 and using leave-one-location-out cross-validation from 0.517 to 0.817. In conclusion, the prediction accuracy of metabolomic prediction of MQ traits using MFs was high and MBLUP is better than PLSR if the training population is larger than 100. The results have significant implications for practical barley breeding for malting quality.
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Affiliation(s)
- Xiangyu Guo
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark. .,Danish Pig Research Centre, Danish Agriculture and Food Council, 1609, Copenhagen V, Denmark.
| | - Ahmed Jahoor
- Nordic Seed A/S, 8300, Odder, Denmark.,Department of Plant Breeding, The Swedish University of Agricultural Sciences, 2353, Alnarp, Sweden
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
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Maslov DL, Zemskaya NV, Trifonova OP, Lichtenberg S, Balashova EE, Lisitsa AV, Moskalev AA, Lokhov PG. Comparative Metabolomic Study of Drosophila Species with Different Lifespans. Int J Mol Sci 2021; 22:ijms222312873. [PMID: 34884677 PMCID: PMC8657752 DOI: 10.3390/ijms222312873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 12/19/2022] Open
Abstract
The increase in life expectancy, leading to a rise in the proportion of older people, is accompanied by a prevalence of age-related disorders among the world population, the fight against which today is one of the leading biomedical challenges. Exploring the biological insights concerning the lifespan is one of the ways to provide a background for designing an effective treatment for the increase in healthy years of life. Untargeted direct injection mass spectrometry-based metabolite profiling of 12 species of Drosophila with significant variations in natural lifespans was conducted in this research. A cross-comparison study of metabolomic profiles revealed lifespan signatures of flies. These signatures indicate that lifespan extension is associated with the upregulation of amino acids, phospholipids, and carbohydrate metabolism. Such information provides a metabolome-level view on longevity and may provide a molecular measure of organism age in age-related studies.
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Affiliation(s)
- Dmitry L. Maslov
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
- Correspondence: ; Tel.: +7-499-246-6980
| | - Nadezhda V. Zemskaya
- Laboratory of Geroprotective and Radioprotective Technologies, Komi Science Center, Institute of Biology, Russian Academy of Sciences, 167982 Syktyvkar, Russia; (N.V.Z.); (A.A.M.)
| | - Oxana P. Trifonova
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
| | - Steven Lichtenberg
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
- Metabometrics Inc., 651 N Broad Street, Suite 205 #1370, Middletown, DE 19709, USA
| | - Elena E. Balashova
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
| | - Andrey V. Lisitsa
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
| | - Alexey A. Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Komi Science Center, Institute of Biology, Russian Academy of Sciences, 167982 Syktyvkar, Russia; (N.V.Z.); (A.A.M.)
| | - Petr G. Lokhov
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
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9
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Tapia A, Palomino-Schätzlein M, Roca M, Lahoz A, Pineda-Lucena A, López del Amo V, Galindo MI. Mild Muscle Mitochondrial Fusion Distress Extends Drosophila Lifespan through an Early and Systemic Metabolome Reorganization. Int J Mol Sci 2021; 22:ijms222212133. [PMID: 34830014 PMCID: PMC8618903 DOI: 10.3390/ijms222212133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
In a global aging population, it is important to understand the factors affecting systemic aging and lifespan. Mitohormesis, an adaptive response caused by different insults affecting the mitochondrial network, triggers a response from the nuclear genome inducing several pathways that promote longevity and metabolic health. Understanding the role of mitochondrial function during the aging process could help biomarker identification and the development of novel strategies for healthy aging. Herein, we interfered the muscle expression of the Drosophila genes Marf and Opa1, two genes that encode for proteins promoting mitochondrial fusion, orthologues of human MFN2 and OPA1. Silencing of Marf and Opa1 in muscle increases lifespan, improves locomotor capacities in the long term, and maintains muscular integrity. A metabolomic analysis revealed that muscle down-regulation of Marf and Opa1 promotes a non-autonomous systemic metabolome reorganization, mainly affecting metabolites involved in the energetic homeostasis: carbohydrates, lipids and aminoacids. Interestingly, the differences are consistently more evident in younger flies, implying that there may exist an anticipative adaptation mediating the protective changes at the older age. We demonstrate that mild mitochondrial muscle disturbance plays an important role in Drosophila fitness and reveals metabolic connections between tissues. This study opens new avenues to explore the link of mitochondrial dynamics and inter-organ communication, as well as their relationship with muscle-related pathologies, or in which muscle aging is a risk factor for their appearance. Our results suggest that early intervention in muscle may prevent sarcopenia and promote healthy aging.
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Affiliation(s)
- Andrea Tapia
- Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain; (A.T.); (M.P.-S.)
| | | | - Marta Roca
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain; (M.R.); (A.L.)
| | - Agustín Lahoz
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain; (M.R.); (A.L.)
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Antonio Pineda-Lucena
- Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, Universidad de Navarra, 31008 Pamplona Spain;
| | - Víctor López del Amo
- Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA
- Correspondence: (V.L.d.A.); (M.I.G.)
| | - Máximo Ibo Galindo
- Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain; (A.T.); (M.P.-S.)
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, 46022 Valencia, Spain
- UPV-CIPF Joint Unit Disease Mechanisms and Nanomedicine, 46012 Valencia, Spain
- Correspondence: (V.L.d.A.); (M.I.G.)
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10
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Maravat M, Bertrand M, Landon C, Fayon F, Morisset-Lopez S, Sarou-Kanian V, Decoville M. Complementary Nuclear Magnetic Resonance-Based Metabolomics Approaches for Glioma Biomarker Identification in a Drosophila melanogaster Model. J Proteome Res 2021; 20:3977-3991. [PMID: 34286978 DOI: 10.1021/acs.jproteome.1c00304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human malignant gliomas are the most common type of primary brain tumor. Composed of glial cells and their precursors, they are aggressive and highly invasive, leading to a poor prognosis. Due to the difficulty of surgically removing tumors and their resistance to treatments, novel therapeutic approaches are needed to improve patient life expectancy and comfort. Drosophila melanogaster is a compelling genetic model to better understanding human neurological diseases owing to its high conservation in signaling pathways and cellular content of the brain. Here, glioma has been induced in Drosophila by co-activating the epidermal growth factor receptor and the phosphatidyl-inositol-3 kinase signaling pathways. Complementary nuclear magnetic resonance (NMR) techniques were used to obtain metabolic profiles in the third instar larvae brains. Fresh organs were directly studied by 1H high resolution-magic angle spinning (HR-MAS) NMR, and brain extracts were analyzed by solution-state 1H-NMR. Statistical analyses revealed differential metabolic signatures, impacted metabolic pathways, and glioma biomarkers. Each method was efficient to determine biomarkers. The highlighted metabolites including glucose, myo-inositol, sarcosine, glycine, alanine, and pyruvate for solution-state NMR and proline, myo-inositol, acetate, and glucose for HR-MAS show very good performances in discriminating samples according to their nature with data mining based on receiver operating characteristic curves. Combining results allows for a more complete view of induced disturbances and opens the possibility of deciphering the biochemical mechanisms of these tumors. The identified biomarkers provide a means to rebalance specific pathways through targeted metabolic therapy and to study the effects of pharmacological treatments using Drosophila as a model organism.
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Affiliation(s)
- Marion Maravat
- CNRS, CEMHTI UPR3079, Université d'Orléans, F-45071 Orléans, France
| | | | - Céline Landon
- CNRS, CBM UPR4301, Université d'Orléans, F-45071 Orléans, France
| | - Franck Fayon
- CNRS, CEMHTI UPR3079, Université d'Orléans, F-45071 Orléans, France
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11
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Rohde PD, Kristensen TN, Sarup P, Muñoz J, Malmendal A. Prediction of complex phenotypes using the Drosophila melanogaster metabolome. Heredity (Edinb) 2021; 126:717-732. [PMID: 33510469 PMCID: PMC8102504 DOI: 10.1038/s41437-021-00404-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Understanding the genotype-phenotype map and how variation at different levels of biological organization is associated are central topics in modern biology. Fast developments in sequencing technologies and other molecular omic tools enable researchers to obtain detailed information on variation at DNA level and on intermediate endophenotypes, such as RNA, proteins and metabolites. This can facilitate our understanding of the link between genotypes and molecular and functional organismal phenotypes. Here, we use the Drosophila melanogaster Genetic Reference Panel and nuclear magnetic resonance (NMR) metabolomics to investigate the ability of the metabolome to predict organismal phenotypes. We performed NMR metabolomics on four replicate pools of male flies from each of 170 different isogenic lines. Our results show that metabolite profiles are variable among the investigated lines and that this variation is highly heritable. Second, we identify genes associated with metabolome variation. Third, using the metabolome gave better prediction accuracies than genomic information for four of five quantitative traits analyzed. Our comprehensive characterization of population-scale diversity of metabolomes and its genetic basis illustrates that metabolites have large potential as predictors of organismal phenotypes. This finding is of great importance, e.g., in human medicine, evolutionary biology and animal and plant breeding.
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Affiliation(s)
- Palle Duun Rohde
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Department of Animal Science, Aarhus University, Tjele, Denmark
| | - Pernille Sarup
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- Nordic Seed A/S, Odder, Denmark
| | - Joaquin Muñoz
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anders Malmendal
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.
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12
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Mohammad K, Titorenko VI. Caloric restriction creates a metabolic pattern of chronological aging delay that in budding yeast differs from the metabolic design established by two other geroprotectors. Oncotarget 2021; 12:608-625. [PMID: 33868583 PMCID: PMC8021023 DOI: 10.18632/oncotarget.27926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
Caloric restriction and the tor1Δ mutation are robust geroprotectors in yeast and other eukaryotes. Lithocholic acid is a potent geroprotector in Saccharomycescerevisiae. Here, we used liquid chromatography coupled with tandem mass spectrometry method of non-targeted metabolomics to compare the effects of these three geroprotectors on the intracellular metabolome of chronologically aging budding yeast. Yeast cells were cultured in a nutrient-rich medium. Our metabolomic analysis identified and quantitated 193 structurally and functionally diverse water-soluble metabolites implicated in the major pathways of cellular metabolism. We show that the three different geroprotectors create distinct metabolic profiles throughout the entire chronological lifespan of S. cerevisiae. We demonstrate that caloric restriction generates a unique metabolic pattern. Unlike the tor1Δ mutation or lithocholic acid, it slows down the metabolic pathway for sulfur amino acid biosynthesis from aspartate, sulfate and 5-methyltetrahydrofolate. Consequently, caloric restriction significantly lowers the intracellular concentrations of methionine, S-adenosylmethionine and cysteine. We also noticed that the low-calorie diet, but not the tor1Δ mutation or lithocholic acid, decreases intracellular ATP, increases the ADP:ATP and AMP:ATP ratios, and rises intracellular ADP during chronological aging. We propose a model of how the specific remodeling of cellular metabolism by caloric restriction contributes to yeast chronological aging delay.
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Affiliation(s)
- Karamat Mohammad
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
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13
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Bertrand M, Decoville M, Meudal H, Birman S, Landon C. Metabolomic Nuclear Magnetic Resonance Studies at Presymptomatic and Symptomatic Stages of Huntington’s Disease on a Drosophila Model. J Proteome Res 2020; 19:4034-4045. [DOI: 10.1021/acs.jproteome.0c00335] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Marylène Bertrand
- Center for Molecular Biophysics, CBM, UPR 4301, CNRS, Rue Charles SADRON, F-45071 Orléans Cedex 02, France
| | - Martine Decoville
- Center for Molecular Biophysics, CBM, UPR 4301, CNRS, Rue Charles SADRON, F-45071 Orléans Cedex 02, France
- University of Orléans, 6 Avenue du Parc Floral, F-45100 Orléans, France
| | - Hervé Meudal
- Center for Molecular Biophysics, CBM, UPR 4301, CNRS, Rue Charles SADRON, F-45071 Orléans Cedex 02, France
| | - Serge Birman
- GCRN Team, Brain Plasticity Unit, UMR 8249, CNRS, ESPCI Paris, PSL Research University, F-75005 Paris, France
| | - Céline Landon
- Center for Molecular Biophysics, CBM, UPR 4301, CNRS, Rue Charles SADRON, F-45071 Orléans Cedex 02, France
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14
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Sessions AO, Min P, Cordes T, Weickert BJ, Divakaruni AS, Murphy AN, Metallo CM, Engler AJ. Preserved cardiac function by vinculin enhances glucose oxidation and extends health- and life-span. APL Bioeng 2018; 2. [PMID: 30105314 PMCID: PMC6086353 DOI: 10.1063/1.5019592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Despite limited regenerative capacity as we age, cardiomyocytes maintain their function in part through compensatory mechanisms, e.g., Vinculin reinforcement of intercalated discs in aged organisms. This mechanism, which is conserved from flies to non-human primates, creates a more crystalline sarcomere lattice that extends lifespan, but systemic connections between the cardiac sarcomere structure and lifespan extension are not apparent. Using the rapidly aging fly system, we found that cardiac-specific Vinculin-overexpression [Vinculin heart-enhanced (VincHE)] increases heart contractility, maximal cardiac mitochondrial respiration, and organismal fitness with age. Systemic metabolism also dramatically changed with age and VincHE; steady state sugar concentrations, as well as aerobic glucose metabolism, increase in VincHE and suggest enhanced energy substrate utilization with increased cardiac performance. When cardiac stress was induced with the complex I inhibitor rotenone, VincHE hearts sustain contractions unlike controls. This work establishes a new link between the cardiac cytoskeleton and systemic glucose utilization and protects mitochondrial function from external stress.
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Affiliation(s)
- Ayla O Sessions
- Biomedical Sciences Program, UC San Diego, La Jolla, California 92093, USA
| | - Peter Min
- Department of Bioengineering, UC San Diego, La Jolla, California 92093, USA
| | - Thekla Cordes
- Department of Bioengineering, UC San Diego, La Jolla, California 92093, USA
| | - Barry J Weickert
- Department of Bioengineering, UC San Diego, La Jolla, California 92093, USA
| | - Ajit S Divakaruni
- Department of Pharmacology, UC San Diego, La Jolla, California 92093, USA
| | - Anne N Murphy
- Department of Pharmacology, UC San Diego, La Jolla, California 92093, USA
| | | | - Adam J Engler
- Biomedical Sciences Program, UC San Diego, La Jolla, California 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, California 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, California 92037, USA
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15
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Metabolomics: State-of-the-Art Technologies and Applications on Drosophila melanogaster. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1076:257-276. [PMID: 29951824 DOI: 10.1007/978-981-13-0529-0_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Metabolomics is one of the latest "omics" technology concerned with the high-throughput identification and quantification of metabolites, the final products of cellular processes. The revealed data provide an instantaneous snapshot of an organism's metabolic pathways, which can be used to explain its phenotype or physiology. On the other hand, Drosophila has shown its power in studying metabolism and related diseases. At this stage, we have the state-of-the-art knowledge in place: a potential candidate to study cellular metabolism (Drosophila melanogaster) and a powerful methodology for metabolic network decipherer (metabolomics). Yet missing is advanced metabolomics technologies like isotope-assisted metabolomics optimized for Drosophila. In this chapter, we will discuss on the current status and future perspectives in technologies and applications of Drosophila metabolomics.
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16
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Gogna N, Sharma R, Gupta V, Dorai K, Prasad NG. Evolution of the metabolome in response to selection for increased immunity in populations of Drosophila melanogaster. PLoS One 2017; 12:e0188089. [PMID: 29149207 PMCID: PMC5693281 DOI: 10.1371/journal.pone.0188089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/31/2017] [Indexed: 11/19/2022] Open
Abstract
We used NMR-based metabolomics to test two hypotheses–(i) there will be evolved differences in the metabolome of selected and control populations even under un-infected conditions and (ii) post infection, the metabolomes of the selected and control populations will respond differently. We selected replicate populations of Drosophila melanogaster for increased survivorship (I) against a gram-negative pathogen. We subjected the selected (I) and their control populations (S) to three different treatments: (1) infected with heat-killed bacteria (i), (2) sham infected (s), and (3) untreated (u). We performed 1D and 2D NMR experiments to identify the metabolic differences. Multivariate analysis of the metabolic profiles of the untreated (Iu and Su) flies yielded higher concentrations of lipids, organic acids, sugars, amino acids, NAD and AMP in the Iu treatment as compared to the Su treatment, showing that even in the absence of infection, the metabolome of the I and S regimes was different. In the S and I regimes, post infection/injury, concentration of metabolites directly or indirectly associated with energy related pathways (lipids, organic acids, sugars) declined while the concentration of metabolites that are probably associated with immune response (amino acids) increased. However, in most cases, the I regime flies had a higher concentration of such metabolites even under un-infected conditions. The change in the metabolite concentration upon infection/injury was not always comparable between I and S regimes (in case of lactate, alanine, leucine, lysine, threonine) indicating that the I and S regimes had evolved to respond differentially to infection and to injury.
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Affiliation(s)
- Navdeep Gogna
- Department of Physical Sciences, Indian Institute of Science Education & Research IISER, Mohali, Punjab, India
| | - Rakesh Sharma
- Department of Physical Sciences, Indian Institute of Science Education & Research IISER, Mohali, Punjab, India
| | - Vanika Gupta
- Department of Biological Sciences, Indian Institute of Science Education & Research IISER, Mohali, Punjab, India
| | - Kavita Dorai
- Department of Physical Sciences, Indian Institute of Science Education & Research IISER, Mohali, Punjab, India
| | - N. G. Prasad
- Department of Biological Sciences, Indian Institute of Science Education & Research IISER, Mohali, Punjab, India
- * E-mail:
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17
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Zhou YZ, Yan ML, Gao L, Zhang JQ, Qin XM, Zhang X, Du GH. Metabonomics approach to assessing the metabolism variation and gender gap of Drosophila melanogaster in aging process. Exp Gerontol 2017; 98:110-119. [DOI: 10.1016/j.exger.2017.07.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 07/25/2017] [Accepted: 07/31/2017] [Indexed: 02/06/2023]
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18
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Colinet H, Renault D. Similar post-stress metabolic trajectories in young and old flies. Exp Gerontol 2017; 102:43-50. [PMID: 28822810 DOI: 10.1016/j.exger.2017.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/15/2017] [Indexed: 01/10/2023]
Abstract
Homeostenosis (i.e. decline in stress resistance and resilience with age) is a fundamental notion of the biogerontology and physiology of aging. Stressful situations typically challenge metabolic homeostasis and the capacity to recover from a stress-induced metabolic disorder might be particularly compromised in senescent individuals. In the present work, we report the effects of aging on low temperature stress tolerance and metabolic profiles in Drosophila melanogaster females of different ages. Adult flies aged 4, 16, 30 and 44days were subjected to acute and chronic cold stress, and data confirmed a strong decline in cold tolerance and resilience of old flies compared to young counterparts. Using quantitative target GC-MS analysis, we found distinct metabolic phenotypes between young (4day-old) and old (44day-old) flies, with glycolytic pathways being differentially affected between the two age groups. We also compared the robustness of metabolic homeostasis in young vs. old flies when exposed to cold stress using time-series metabolic analysis. In both age groups, we found evidence of strong alteration of metabolic profiles when flies were exposed to low temperature stress. Interestingly, the temporal metabolic trajectories during the recovery period were similar in young and old flies, despite strong differences in thermotolerance. In conclusion, metabolic signatures markedly changed with age and homeostenosis was observed in the phenotypic response to cold stress. However, these changes did not reflect in different temporal homeostatic response at metabolic level.
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Affiliation(s)
- Hervé Colinet
- UMR CNRS 6553 EcoBio, Université de Rennes 1, 263 Avenue du General Leclerc, CS 74205, 35042 Rennes Cedex, France.
| | - David Renault
- UMR CNRS 6553 EcoBio, Université de Rennes 1, 263 Avenue du General Leclerc, CS 74205, 35042 Rennes Cedex, France
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19
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Hoffman JM, Lyu Y, Pletcher SD, Promislow DEL. Proteomics and metabolomics in ageing research: from biomarkers to systems biology. Essays Biochem 2017; 61:379-388. [PMID: 28698311 PMCID: PMC5743054 DOI: 10.1042/ebc20160083] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 02/07/2023]
Abstract
Age is the single greatest risk factor for a wide range of diseases, and as the mean age of human populations grows steadily older, the impact of this risk factor grows as well. Laboratory studies on the basic biology of ageing have shed light on numerous genetic pathways that have strong effects on lifespan. However, we still do not know the degree to which the pathways that affect ageing in the lab also influence variation in rates of ageing and age-related disease in human populations. Similarly, despite considerable effort, we have yet to identify reliable and reproducible 'biomarkers', which are predictors of one's biological as opposed to chronological age. One challenge lies in the enormous mechanistic distance between genotype and downstream ageing phenotypes. Here, we consider the power of studying 'endophenotypes' in the context of ageing. Endophenotypes are the various molecular domains that exist at intermediate levels of organization between the genotype and phenotype. We focus our attention specifically on proteins and metabolites. Proteomic and metabolomic profiling has the potential to help identify the underlying causal mechanisms that link genotype to phenotype. We present a brief review of proteomics and metabolomics in ageing research with a focus on the potential of a systems biology and network-centric perspective in geroscience. While network analyses to study ageing utilizing proteomics and metabolomics are in their infancy, they may be the powerful model needed to discover underlying biological processes that influence natural variation in ageing, age-related disease, and longevity.
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Affiliation(s)
- Jessica M Hoffman
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd CH464, Birmingham, AL 35294, U.S.A
| | - Yang Lyu
- Department of Molecular and Integrative Physiology and Geriatrics Center, Biomedical Sciences and Research Building, University of Michigan, Ann Arbor, MI 48109, U.S.A
| | - Scott D Pletcher
- Department of Molecular and Integrative Physiology and Geriatrics Center, Biomedical Sciences and Research Building, University of Michigan, Ann Arbor, MI 48109, U.S.A
| | - Daniel E L Promislow
- Department of Pathology, University of Washington, Box 357705, 1959 NE Pacific Street, Seattle, Washington 98195, U.S.A.
- Department of Biology, University of Washington, Seattle, Washington 98195, U.S.A
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20
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Cox JE, Thummel CS, Tennessen JM. Metabolomic Studies in Drosophila. Genetics 2017; 206:1169-1185. [PMID: 28684601 PMCID: PMC5500124 DOI: 10.1534/genetics.117.200014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/25/2017] [Indexed: 01/01/2023] Open
Abstract
Metabolomic analysis provides a powerful new tool for studies of Drosophila physiology. This approach allows investigators to detect thousands of chemical compounds in a single sample, representing the combined contributions of gene expression, enzyme activity, and environmental context. Metabolomics has been used for a wide range of studies in Drosophila, often providing new insights into gene function and metabolic state that could not be obtained using any other approach. In this review, we survey the uses of metabolomic analysis since its entry into the field. We also cover the major methods used for metabolomic studies in Drosophila and highlight new directions for future research.
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Affiliation(s)
- James E Cox
- Department of Biochemistry and
- The Metabolomics Core Research Facility, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Carl S Thummel
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Jason M Tennessen
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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21
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Schou MF, Kristensen TN, Pedersen A, Karlsson BG, Loeschcke V, Malmendal A. Metabolic and functional characterization of effects of developmental temperature in Drosophila melanogaster. Am J Physiol Regul Integr Comp Physiol 2016; 312:R211-R222. [PMID: 27927623 PMCID: PMC5336569 DOI: 10.1152/ajpregu.00268.2016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 11/22/2022]
Abstract
The ability of ectotherms to respond to changes in their thermal environment through plastic mechanisms is central to their adaptive capability. However, we still lack knowledge on the physiological and functional responses by which ectotherms acclimate to temperatures during development, and in particular, how physiological stress at extreme temperatures may counteract beneficial acclimation responses at benign temperatures. We exposed Drosophila melanogaster to 10 developmental temperatures covering their entire permissible temperature range. We obtained metabolic profiles and reaction norms for several functional traits: egg-to-adult viability, developmental time, and heat and cold tolerance. Females were more heat tolerant than males, whereas no sexual dimorphism was found in cold tolerance. A group of metabolites, mainly free amino acids, had linear reaction norms. Several energy-carrying molecules, as well as some sugars, showed distinct inverted U-shaped norms of reaction across the thermal range, resulting in a positive correlation between metabolite intensities and egg-to-adult viability. At extreme temperatures, low levels of these metabolites were interpreted as a response characteristic of costs of homeostatic perturbations. Our results provide novel insights into a range of metabolites reported to be central for the acclimation response and suggest several new candidate metabolites. Low and high temperatures result in different adaptive physiological responses, but they also have commonalities likely to be a result of the failure to compensate for the physiological stress. We suggest that the regulation of metabolites that are tightly connected to the performance curve is important for the ability of ectotherms to cope with variation in temperature.
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Affiliation(s)
- Mads F Schou
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | - Torsten N Kristensen
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Anders Pedersen
- The Swedish NMR-Centre, University of Gothenburg, Gothenburg, Sweden; and
| | - B Göran Karlsson
- The Swedish NMR-Centre, University of Gothenburg, Gothenburg, Sweden; and
| | | | - Anders Malmendal
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N, Denmark
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22
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Eanes WF. New views on the selection acting on genetic polymorphism in central metabolic genes. Ann N Y Acad Sci 2016; 1389:108-123. [PMID: 27859384 DOI: 10.1111/nyas.13285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/20/2016] [Accepted: 09/29/2016] [Indexed: 12/14/2022]
Abstract
Studies of the polymorphism of central metabolic genes as a source of fitness variation in natural populations date back to the discovery of allozymes in the 1960s. The unique features of these genes and their enzymes and our knowledge base greatly facilitates the systems-level study of this group. The expectation that pathway flux control is central to understanding the molecular evolution of genes is discussed, as well as studies that attempt to place gene-specific molecular evolution and polymorphism into a context of pathway and network architecture. There is an increasingly complex picture of the metabolic genes assuming additional roles beyond their textbook anabolic and catabolic reactions. In particular, this review emphasizes the potential role of these genes as part of the energy-sensing machinery. It is underscored that the concentrations of key cellular metabolites are the reflections of cellular energy status and nutritional input. These metabolites are the top-down signaling messengers that set signaling through signaling pathways that are involved in energy economy. I propose that the polymorphisms in central metabolic genes shift metabolite concentrations and in that fashion act as genetic modifiers of the energy-state coupling to the transcriptional networks that affect physiological trade-offs with significant fitness consequences.
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Affiliation(s)
- Walter F Eanes
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York
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23
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Kapranas A, Snart CJP, Williams H, Hardy ICW, Barrett DA. Metabolomics of aging assessed in individual parasitoid wasps. Sci Rep 2016; 6:34848. [PMID: 27713504 PMCID: PMC5054366 DOI: 10.1038/srep34848] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/02/2016] [Indexed: 11/09/2022] Open
Abstract
Metabolomics studies of low-biomass organisms, such as small insects, have previously relied on the pooling of biological samples to overcome detection limits, particularly using NMR. We show that the differentiation of metabolite profiles of individual 1 mg parasitoid wasps of different ages is possible when using a modified sample preparation and a combination of untargeted NMR and LC-MS based metabolomics. Changes were observed between newly emerged and older wasps in glycerolipids, amino acids and circulatory sugars. This advance in chemical profiling has important implications for the study of the behaviour and ecology of parasitoids and many other species of small organisms because predictions and observations are typically made at the level of the individual. Thus, the metabolomic state of low-biomass individuals can now be related to their behaviour and ecological performance. We discuss specifically the utility of age-related metabolomic profiling but our new approach can be applied to a wide range of biological research.
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Affiliation(s)
| | - Charles J. P. Snart
- School of Biosciences, University of Nottingham, LE12 5RD, UK
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Huw Williams
- School of Chemistry, University of Nottingham, NG7 2RD, UK
| | - Ian C. W. Hardy
- School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - David A. Barrett
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, NG7 2RD, UK
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24
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Sarup P, Petersen SMM, Nielsen NC, Loeschcke V, Malmendal A. Mild heat treatments induce long-term changes in metabolites associated with energy metabolism in Drosophila melanogaster. Biogerontology 2016; 17:873-882. [DOI: 10.1007/s10522-016-9657-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/27/2016] [Indexed: 01/07/2023]
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25
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Abstract
Dietary restriction (DR), a moderate reduction in food intake, improves health during aging and extends life span across multiple species. Specific nutrients, rather than overall calories, mediate the effects of DR, with protein and specific amino acids (AAs) playing a key role. Modulations of single dietary AAs affect traits including growth, reproduction, physiology, health, and longevity in animals. Epidemiological data in humans also link the quality and quantity of dietary proteins to long-term health. Intricate nutrient-sensing pathways fine tune the metabolic responses to dietary AAs in a highly conserved manner. In turn, these metabolic responses can affect the onset of insulin resistance, obesity, neurodegenerative disease, and other age-related diseases. In this review we discuss how AA requirements are shaped and how ingested AAs regulate a spectrum of homeostatic processes. Finally, we highlight the resulting opportunity to develop nutritional strategies to improve human health during aging.
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Affiliation(s)
- George A Soultoukis
- Max Planck Institute for Biology of Ageing, Department of Biological Mechanisms of Ageing, Cologne 50931, Germany; ,
| | - Linda Partridge
- Max Planck Institute for Biology of Ageing, Department of Biological Mechanisms of Ageing, Cologne 50931, Germany; , .,Institute of Healthy Ageing and Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom
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26
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Levengood JM, Schaeffer DJ, Ulanov AV. Metabolite Profiles of Male and Female Humboldt Penguins. Vet Sci 2015; 2:349-362. [PMID: 29061948 PMCID: PMC5644650 DOI: 10.3390/vetsci2040349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/28/2015] [Accepted: 10/08/2015] [Indexed: 11/18/2022] Open
Abstract
We examined 185 metabolites in 30 adult Humboldt Penguins (Spheniscus humboldti) nesting at the Punta San Juan Marine Protected Area, Peru, in order to examine gender differences in metabolome profiles, particularly those involved in metabolism and energetics. The majority of the compounds identified were fatty (26% of total identified compounds), organic (19%), and amino (16%) acids. We were able to differentiate male and female penguins with 96.6% accuracy on the basis of 12 metabolites, most of which are involved in lipid and carbohydrate metabolism. These included 2-oxoglutarate, erythronic acid, GABA, mannitol, sedoheptulose 7-phosphate, and serine and six metabolites present in higher concentrations in females compared to males (2-aminoadipic acid, O-phosphorylethanolamine, glycerol 2-phosphate, glycerol 3-phosphate, pantothenic acid, and creatinine). Of these, 2-oxoglutarate and glycerol 3-phosphate were key metabolites distinguishing gender. Our results indicated that male and female Humboldt Penguins were characterized by differing metabolic states. Such differences could be important to individual and brood survival in times of environmental stress.
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Affiliation(s)
- Jeffrey M Levengood
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA.
| | - David J Schaeffer
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA.
| | - Alexander V Ulanov
- Metabolomics Center, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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27
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Laye MJ, Tran V, Jones DP, Kapahi P, Promislow DEL. The effects of age and dietary restriction on the tissue-specific metabolome of Drosophila. Aging Cell 2015; 14:797-808. [PMID: 26085309 PMCID: PMC4568967 DOI: 10.1111/acel.12358] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2015] [Indexed: 11/28/2022] Open
Abstract
Dietary restriction (DR) is a robust intervention that extends lifespan and slows the onset of age-related diseases in diverse organisms. While significant progress has been made in attempts to uncover the genetic mechanisms of DR, there are few studies on the effects of DR on the metabolome. In recent years, metabolomic profiling has emerged as a powerful technology to understand the molecular causes and consequences of natural aging and disease-associated phenotypes. Here, we use high-resolution mass spectroscopy and novel computational approaches to examine changes in the metabolome from the head, thorax, abdomen, and whole body at multiple ages in Drosophila fed either a nutrient-rich ad libitum (AL) or nutrient-restricted (DR) diet. Multivariate analysis clearly separates the metabolome by diet in different tissues and different ages. DR significantly altered the metabolome and, in particular, slowed age-related changes in the metabolome. Interestingly, we observed interacting metabolites whose correlation coefficients, but not mean levels, differed significantly between AL and DR. The number and magnitude of positively correlated metabolites was greater under a DR diet. Furthermore, there was a decrease in positive metabolite correlations as flies aged on an AL diet. Conversely, DR enhanced these correlations with age. Metabolic set enrichment analysis identified several known (e.g., amino acid and NAD metabolism) and novel metabolic pathways that may affect how DR effects aging. Our results suggest that network structure of metabolites is altered upon DR and may play an important role in preventing the decline of homeostasis with age.
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Affiliation(s)
| | - ViLinh Tran
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA USA
- Department of Medicine Clinical Biomarkers Laboratory Emory University Atlanta GA USA
| | - Dean P. Jones
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA USA
- Department of Medicine Clinical Biomarkers Laboratory Emory University Atlanta GA USA
| | | | - Daniel E. L. Promislow
- Department of Pathology University of Washington Seattle WA USA
- Department of Biology University of Washington Seattle WA USA
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28
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Jové M, Maté I, Naudí A, Mota-Martorell N, Portero-Otín M, De la Fuente M, Pamplona R. Human Aging Is a Metabolome-related Matter of Gender. J Gerontol A Biol Sci Med Sci 2015; 71:578-85. [DOI: 10.1093/gerona/glv074] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/30/2015] [Indexed: 11/13/2022] Open
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29
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Gogna N, Singh VJ, Sheeba V, Dorai K. NMR-based investigation of the Drosophila melanogaster metabolome under the influence of daily cycles of light and temperature. MOLECULAR BIOSYSTEMS 2015; 11:3305-15. [DOI: 10.1039/c5mb00386e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This work presents an NMR-based metabolomic approach to study metabolic processes inD. melanogasterthat exhibit a diurnal rhythm.
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Affiliation(s)
- Navdeep Gogna
- Indian Institute of Science Education & Research (IISER) Mohali
- Manauli 140306
- India
| | | | - Vasu Sheeba
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru
- India
| | - Kavita Dorai
- Indian Institute of Science Education & Research (IISER) Mohali
- Manauli 140306
- India
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30
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Santoro MM. Zebrafish as a model to explore cell metabolism. Trends Endocrinol Metab 2014; 25:546-54. [PMID: 24997878 DOI: 10.1016/j.tem.2014.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/04/2014] [Accepted: 06/10/2014] [Indexed: 12/20/2022]
Abstract
Cell metabolism plays a key role in many essential biological processes. The recent availability of novel technologies and organisms to model cell metabolism in vivo is expanding current knowledge of cell metabolism. In this context, the zebrafish (Danio rerio) is emerging as a valuable model system to learn about the metabolic routes critical for cellular homeostasis. Here, the most recent methods and studies on cell metabolism are summarized, which support the overall value for the zebrafish model system not only to study metabolism but also metabolic disease states. It is envisioned that this small vertebrate system will help in the understanding of pathogenesis for numerous metabolic-related disorders in humans and in the identification of their therapeutic treatments.
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Affiliation(s)
- Massimo M Santoro
- Laboratory of Endothelial Molecular Biology, Vesalius Research Center, Department of Oncology, University of Leuven, Leuven, B-3000, Belgium; Laboratory of Endothelial Molecular Biology, Vesalius Research Center, VIB, Leuven, B-3000, Belgium.
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31
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Clendinen C, Lee-McMullen B, Williams CM, Stupp GS, Vandenborne K, Hahn DA, Walter GA, Edison AS. ¹³C NMR metabolomics: applications at natural abundance. Anal Chem 2014; 86:9242-50. [PMID: 25140385 PMCID: PMC4165451 DOI: 10.1021/ac502346h] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/20/2014] [Indexed: 12/30/2022]
Abstract
(13)C NMR has many advantages for a metabolomics study, including a large spectral dispersion, narrow singlets at natural abundance, and a direct measure of the backbone structures of metabolites. However, it has not had widespread use because of its relatively low sensitivity compounded by low natural abundance. Here we demonstrate the utility of high-quality (13)C NMR spectra obtained using a custom (13)C-optimized probe on metabolomic mixtures. A workflow was developed to use statistical correlations between replicate 1D (13)C and (1)H spectra, leading to composite spin systems that can be used to search publicly available databases for compound identification. This was developed using synthetic mixtures and then applied to two biological samples, Drosophila melanogaster extracts and mouse serum. Using the synthetic mixtures we were able to obtain useful (13)C-(13)C statistical correlations from metabolites with as little as 60 nmol of material. The lower limit of (13)C NMR detection under our experimental conditions is approximately 40 nmol, slightly lower than the requirement for statistical analysis. The (13)C and (1)H data together led to 15 matches in the database compared to just 7 using (1)H alone, and the (13)C correlated peak lists had far fewer false positives than the (1)H generated lists. In addition, the (13)C 1D data provided improved metabolite identification and separation of biologically distinct groups using multivariate statistical analysis in the D. melanogaster extracts and mouse serum.
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Affiliation(s)
- Chaevien
S. Clendinen
- Department of Biochemistry & Molecular Biology, Department of Entomology and Nematology, Department of Physical
Therapy, Department of Physiology and Functional Genomics, and Southeast Center for Integrated
Metabolomics, University of Florida, Gainesville, Florida 32610-0245, United States
| | - Brittany Lee-McMullen
- Department of Biochemistry & Molecular Biology, Department of Entomology and Nematology, Department of Physical
Therapy, Department of Physiology and Functional Genomics, and Southeast Center for Integrated
Metabolomics, University of Florida, Gainesville, Florida 32610-0245, United States
| | - Caroline M. Williams
- Department of Biochemistry & Molecular Biology, Department of Entomology and Nematology, Department of Physical
Therapy, Department of Physiology and Functional Genomics, and Southeast Center for Integrated
Metabolomics, University of Florida, Gainesville, Florida 32610-0245, United States
| | - Gregory S. Stupp
- Department of Biochemistry & Molecular Biology, Department of Entomology and Nematology, Department of Physical
Therapy, Department of Physiology and Functional Genomics, and Southeast Center for Integrated
Metabolomics, University of Florida, Gainesville, Florida 32610-0245, United States
| | - Krista Vandenborne
- Department of Biochemistry & Molecular Biology, Department of Entomology and Nematology, Department of Physical
Therapy, Department of Physiology and Functional Genomics, and Southeast Center for Integrated
Metabolomics, University of Florida, Gainesville, Florida 32610-0245, United States
| | - Daniel A. Hahn
- Department of Biochemistry & Molecular Biology, Department of Entomology and Nematology, Department of Physical
Therapy, Department of Physiology and Functional Genomics, and Southeast Center for Integrated
Metabolomics, University of Florida, Gainesville, Florida 32610-0245, United States
| | - Glenn A. Walter
- Department of Biochemistry & Molecular Biology, Department of Entomology and Nematology, Department of Physical
Therapy, Department of Physiology and Functional Genomics, and Southeast Center for Integrated
Metabolomics, University of Florida, Gainesville, Florida 32610-0245, United States
| | - Arthur S. Edison
- Department of Biochemistry & Molecular Biology, Department of Entomology and Nematology, Department of Physical
Therapy, Department of Physiology and Functional Genomics, and Southeast Center for Integrated
Metabolomics, University of Florida, Gainesville, Florida 32610-0245, United States
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32
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An PNT, Yamaguchi M, Bamba T, Fukusaki E. Metabolome analysis of Drosophila melanogaster during embryogenesis. PLoS One 2014; 9:e99519. [PMID: 25121768 PMCID: PMC4133167 DOI: 10.1371/journal.pone.0099519] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 05/15/2014] [Indexed: 02/02/2023] Open
Abstract
The Drosophila melanogaster embryo has been widely utilized as a model for genetics and developmental biology due to its small size, short generation time, and large brood size. Information on embryonic metabolism during developmental progression is important for further understanding the mechanisms of Drosophila embryogenesis. Therefore, the aim of this study is to assess the changes in embryos’ metabolome that occur at different stages of the Drosophila embryonic development. Time course samples of Drosophila embryos were subjected to GC/MS-based metabolome analysis for profiling of low molecular weight hydrophilic metabolites, including sugars, amino acids, and organic acids. The results showed that the metabolic profiles of Drosophila embryo varied during the course of development and there was a strong correlation between the metabolome and different embryonic stages. Using the metabolome information, we were able to establish a prediction model for developmental stages of embryos starting from their high-resolution quantitative metabolite composition. Among the important metabolites revealed from our model, we suggest that different amino acids appear to play distinct roles in different developmental stages and an appropriate balance in trehalose-glucose ratio is crucial to supply the carbohydrate source for the development of Drosophila embryo.
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Affiliation(s)
- Phan Nguyen Thuy An
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Insect Biomedical Research Center, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
| | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- * E-mail:
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33
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Hoffman JM, Soltow QA, Li S, Sidik A, Jones DP, Promislow DEL. Effects of age, sex, and genotype on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. Aging Cell 2014; 13:596-604. [PMID: 24636523 PMCID: PMC4116462 DOI: 10.1111/acel.12215] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2014] [Indexed: 12/24/2022] Open
Abstract
Researchers have used whole-genome sequencing and gene expression profiling to identify genes associated with age, in the hope of understanding the underlying mechanisms of senescence. But there is a substantial gap from variation in gene sequences and expression levels to variation in age or life expectancy. In an attempt to bridge this gap, here we describe the effects of age, sex, genotype, and their interactions on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. Among the 6800 features analyzed, we found that over one-quarter of all metabolites were significantly associated with age, sex, genotype, or their interactions, and multivariate analysis shows that individual metabolomic profiles are highly predictive of these traits. Using a metabolomic equivalent of gene set enrichment analysis, we identified numerous metabolic pathways that were enriched among metabolites associated with age, sex, and genotype, including pathways involving sugar and glycerophospholipid metabolism, neurotransmitters, amino acids, and the carnitine shuttle. Our results suggest that high-sensitivity metabolomic studies have excellent potential not only to reveal mechanisms that lead to senescence, but also to help us understand differences in patterns of aging among genotypes and between males and females.
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Affiliation(s)
| | - Quinlyn A. Soltow
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA 30322USA
- Department of Medicine Clinical Biomarkers Laboratory Emory University Atlanta GA 30322USA
- ClinMet Inc. 3210 Merryfield Row San Diego CA 92121USA
| | - Shuzhao Li
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA 30322USA
| | - Alfire Sidik
- Department of Genetics University of Georgia Athens GA 30602USA
| | - Dean P. Jones
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA 30322USA
- Department of Medicine Clinical Biomarkers Laboratory Emory University Atlanta GA 30322USA
- Center for Health Discovery & Well Being Emory University Atlanta GA 30322 USA
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34
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Boehm AM, Rosenstiel P, Bosch TCG. Stem cells and aging from a quasi-immortal point of view. Bioessays 2013; 35:994-1003. [PMID: 24037777 DOI: 10.1002/bies.201300075] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Understanding aging and how it affects an organism's lifespan is a fundamental problem in biology. A hallmark of aging is stem cell senescence, the decline of functionality, and number of somatic stem cells, resulting in an impaired regenerative capacity and reduced tissue function. In addition, aging is characterized by profound remodeling of the immune system and a quantitative decline of adequate immune responses, a phenomenon referred to as immune-senescence. Yet, what is causing stem cell and immune-senescence? This review discusses experimental studies of potentially immortal Hydra which have made contributions to answering this question. Hydra transcription factor FoxO has been shown to modulate both stem cell proliferation and innate immunity, lending strong support to a role of FoxO as critical rate-of-aging regulator from Hydra to human. Constructing a model of how FoxO responds to diverse environmental factors provides a framework for how stem cell factors might contribute to aging.
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Affiliation(s)
- Anna-Marei Boehm
- Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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35
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Metabolomic analysis of the selection response of Drosophila melanogaster to environmental stress: are there links to gene expression and phenotypic traits? Naturwissenschaften 2013; 100:417-27. [DOI: 10.1007/s00114-013-1040-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 03/19/2013] [Accepted: 03/21/2013] [Indexed: 12/25/2022]
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36
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Wit J, Sarup P, Lupsa N, Malte H, Frydenberg J, Loeschcke V. Longevity for free? Increased reproduction with limited trade-offs in Drosophila melanogaster selected for increased life span. Exp Gerontol 2013; 48:349-57. [DOI: 10.1016/j.exger.2013.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 01/11/2013] [Accepted: 01/16/2013] [Indexed: 10/27/2022]
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