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van Zyl CDW, van Reenen M, Osthoff G, du Preez I. Evaluation of BAYESIL for automated annotation of 1H NMR data using limited sample volumes: application to African elephant serum. Metabolomics 2023; 19:31. [PMID: 36995481 PMCID: PMC10063514 DOI: 10.1007/s11306-023-02001-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/22/2023] [Indexed: 03/31/2023]
Abstract
INTRODUCTION Technological advancements enabled the analyses of limited sample volumes on 1H NMR. Manual spectral profiling of the data is, however, complex, and timely. OBJECTIVE To evaluate the performance of BAYESIL for automated identification and quantification of 1H NMR spectra of limited volume samples. METHOD Aliquots of a pooled African elephant serum sample were analyzed using standard and reduced volumes. Performance was evaluated on confidence scores, non-detects and laboratory CV. RESULTS Of the 47 compounds detected, 28 had favorable performances. The approach could differentiate samples based on biological variation. CONCLUSIONS BAYESIL is valuable for limited sample 1H NMR data analyses.
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Affiliation(s)
| | - Mari van Reenen
- Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Gernot Osthoff
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - Ilse du Preez
- Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa.
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Ensminger DC, Salvador-Pascual A, Arango BG, Allen KN, Vázquez-Medina JP. Fasting ameliorates oxidative stress: A review of physiological strategies across life history events in wild vertebrates. Comp Biochem Physiol A Mol Integr Physiol 2021; 256:110929. [PMID: 33647461 DOI: 10.1016/j.cbpa.2021.110929] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/17/2021] [Accepted: 02/21/2021] [Indexed: 02/06/2023]
Abstract
Fasting is a component of many species' life history due to environmental factors or behavioral patterns that limit access to food. Despite metabolic and physiological challenges associated with these life history stages, fasting-adapted wild vertebrates exhibit few if any signs of oxidative stress, suggesting that fasting promotes redox homeostasis. Here we review mammalian, avian, reptilian, amphibian, and piscine examples of animals undergoing fasting during prolonged metabolic suppression (e.g. hibernation and estivation) or energetically demanding processes (e.g. migration and breeding) to better understand the mechanisms underlying fasting tolerance in wild vertebrates. These studies largely show beneficial effects of fasting on redox balance via limited oxidative damage. Though some species exhibit signs of oxidative stress due to energetically or metabolically extreme processes, fasting wild vertebrates largely buffer themselves from the negative consequences of oxidative damage through specific strategies such as elevating antioxidants, selectively maintaining redox balance in critical tissues, or modifying behavioral patterns. We conclude with suggestions for future research to better elucidate the protective effects of fasting on oxidative stress as well as disentangle the impacts from other life history stages. Further research in these areas will facilitate our understanding of the mechanisms wild vertebrates use to mitigate the negative impacts associated with metabolically-extreme life history stages as well as potential translation into therapeutic interventions in non-fasting-adapted species including humans.
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Affiliation(s)
- David C Ensminger
- Department of Integrative Biology, University of California, Berkeley, USA
| | | | - B Gabriela Arango
- Department of Integrative Biology, University of California, Berkeley, USA
| | - Kaitlin N Allen
- Department of Integrative Biology, University of California, Berkeley, USA
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Weitzner EL, Fanter CE, Hindle AG. Pinniped Ontogeny as a Window into the Comparative Physiology and Genomics of Hypoxia Tolerance. Integr Comp Biol 2020; 60:1414-1424. [PMID: 32559283 DOI: 10.1093/icb/icaa083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Diving physiology has received considerable scientific attention as it is a central element of the extreme phenotype of marine mammals. Many scientific discoveries have illuminated physiological mechanisms supporting diving, such as massive, internally bound oxygen stores and dramatic cardiovascular regulation. However, the cellular and molecular mechanisms that support the diving phenotype remain mostly unexplored as logistic and legal restrictions limit the extent of scientific manipulation possible. With next-generation sequencing (NGS) tools becoming more widespread and cost-effective, there are new opportunities to explore the diving phenotype. Genomic investigations come with their own challenges, particularly those including cross-species comparisons. Studying the regulatory pathways that underlie diving mammal ontogeny could provide a window into the comparative physiology of hypoxia tolerance. Specifically, in pinnipeds, which shift from terrestrial pups to elite diving adults, there is potential to characterize the transcriptional, epigenetic, and posttranslational differences between contrasting phenotypes while leveraging a common genome. Here we review the current literature detailing the maturation of the diving phenotype in pinnipeds, which has primarily been explored via biomarkers of metabolic capability including antioxidants, muscle fiber typing, and key aerobic and anaerobic metabolic enzymes. We also discuss how NGS tools have been leveraged to study phenotypic shifts within species through ontogeny, and how this approach may be applied to investigate the biochemical and physiological mechanisms that develop as pups become elite diving adults. We conclude with a specific example of the Antarctic Weddell seal by overlapping protein biomarkers with gene regulatory microRNA datasets.
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Affiliation(s)
- Emma L Weitzner
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Cornelia E Fanter
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Allyson G Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
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Camps-Bossacoma M, Garcia-Aloy M, Saldaña-Ruiz S, Cambras T, González-Domínguez R, Franch À, Pérez-Cano FJ, Andres-Lacueva C, Castell M. Role of Theobromine in Cocoa's Metabolic Properties in Healthy Rats. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3605-3614. [PMID: 30855143 DOI: 10.1021/acs.jafc.8b07248] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cocoa is rich in polyphenols and methylxanthines, and it has been reported that its consumption, among other properties, has beneficial effects on metabolism. This study aimed to investigate the role of theobromine in cocoa's metabolic properties in healthy rats. In addition to morphometric measurements, biochemical markers of lipids and glucose metabolism and gene expression of molecules related to immune cells in adipose and hepatic tissues were assessed after 7 or 18 days of diet. Additionally, a metabolomic analysis was carried out at day 7. This study revealed the presence of six discriminant metabolites in plasma due to the diets. Moreover, the results showed that theobromine is the main responsible factor for cocoa's effects on body weight gain as well as on lipid and glucose metabolism. The effects on body weight and lipids appeared as early as after 7 days of diet, whereas those affecting glucose metabolism required a longer intervention.
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Affiliation(s)
- Mariona Camps-Bossacoma
- Secció de Fisiologia, Departament de Bioquímica i Fisiologia, Facultat de Farmàcia i Ciències de l'Alimentació; Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB) , Universitat de Barcelona (UB) , Barcelona 08028 , Spain
| | - Mar Garcia-Aloy
- Biomarkers and Nutrimetabolomics Laboratory, Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, XaRTA, INSA-UB, Facultat de Farmàcia i Ciències de l'Alimentació, UB, Barcelona; CIBER de Fragilidad y Envejecimiento (CIBERFES) , Instituto de Salud Carlos III , Madrid 28029 , Spain
| | - Sandra Saldaña-Ruiz
- Secció de Fisiologia, Departament de Bioquímica i Fisiologia, Facultat de Farmàcia i Ciències de l'Alimentació; Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB) , Universitat de Barcelona (UB) , Barcelona 08028 , Spain
| | - Trinitat Cambras
- Secció de Fisiologia, Departament de Bioquímica i Fisiologia, Facultat de Farmàcia i Ciències de l'Alimentació; Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB) , Universitat de Barcelona (UB) , Barcelona 08028 , Spain
| | - Raúl González-Domínguez
- Biomarkers and Nutrimetabolomics Laboratory, Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, XaRTA, INSA-UB, Facultat de Farmàcia i Ciències de l'Alimentació, UB, Barcelona; CIBER de Fragilidad y Envejecimiento (CIBERFES) , Instituto de Salud Carlos III , Madrid 28029 , Spain
| | - Àngels Franch
- Secció de Fisiologia, Departament de Bioquímica i Fisiologia, Facultat de Farmàcia i Ciències de l'Alimentació; Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB) , Universitat de Barcelona (UB) , Barcelona 08028 , Spain
| | - Francisco J Pérez-Cano
- Secció de Fisiologia, Departament de Bioquímica i Fisiologia, Facultat de Farmàcia i Ciències de l'Alimentació; Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB) , Universitat de Barcelona (UB) , Barcelona 08028 , Spain
| | - Cristina Andres-Lacueva
- Biomarkers and Nutrimetabolomics Laboratory, Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, XaRTA, INSA-UB, Facultat de Farmàcia i Ciències de l'Alimentació, UB, Barcelona; CIBER de Fragilidad y Envejecimiento (CIBERFES) , Instituto de Salud Carlos III , Madrid 28029 , Spain
| | - Margarida Castell
- Secció de Fisiologia, Departament de Bioquímica i Fisiologia, Facultat de Farmàcia i Ciències de l'Alimentació; Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB) , Universitat de Barcelona (UB) , Barcelona 08028 , Spain
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Gas chromatography-mass spectrometry profiles of urinary organic acids in healthy captive cheetahs ( Acinonyx jubatus ). J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1049-1050:8-15. [DOI: 10.1016/j.jchromb.2017.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 02/12/2017] [Accepted: 02/14/2017] [Indexed: 12/24/2022]
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Oxidative stress in northern elephant seals: Integration of omics approaches with ecological and experimental studies. Comp Biochem Physiol A Mol Integr Physiol 2016; 200:94-103. [DOI: 10.1016/j.cbpa.2016.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/16/2016] [Accepted: 02/18/2016] [Indexed: 01/28/2023]
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Chicco AJ, Le CH, Schlater AE, Nguyen AD, Kaye SD, Beals JW, Scalzo RL, Bell C, Gnaiger E, Costa DP, Crocker DE, Kanatous SB. High fatty acid oxidation capacity and phosphorylation control despite elevated leak and reduced respiratory capacity in northern elephant seal muscle mitochondria. J Exp Biol 2014; 217:2947-55. [DOI: 10.1242/jeb.105916] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Northern elephant seals (Mirounga angustirostris) are extreme, hypoxia-adapted endotherms that rely largely on aerobic metabolism during extended breath-hold dives in near freezing water temperatures. While many aspects of their physiology have been characterized to account for these remarkable feats, the contribution of adaptations in the aerobic powerhouses of muscle cells, the mitochondria, are unknown. In the present study, the ontogeny and comparative physiology of elephant seal muscle mitochondrial respiratory function was investigated under a variety of substrate conditions and respiratory states. Intact mitochondrial networks were studied by high-resolution respirometry in saponin-permeabilized fiber bundles obtained from primary swimming muscles of pup, juvenile, and adult seals, and compared to fibers from adult human vastus laterais. Results indicate that seal muscle maintains a high capacity for fatty acid oxidation despite a progressive decrease in total respiratory capacity as animals mature from pups to adults. This is explained by a progressive increase in phosphorylation control and fatty acid utilization over pyruvate in adult seals compared to humans and seal pups. Interestingly, despite higher indices of oxidative phosphorylation efficiency, juvenile and adult seals also exhibit a ~50% greater capacity for respiratory leak compared to humans and pups. The ontogeny of this phenotype suggests it is an adaptation of muscle to the prolonged breath-hold exercise and highly variable ambient temperatures experienced by mature elephant seals. These studies highlight the remarkable plasticity of mammalian mitochondria to meet the demands for both efficient ATP production and endothermy in a cold, oxygen-limited environment.
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Champagne CD, Boaz SM, Fowler MA, Houser DS, Costa DP, Crocker DE. A profile of carbohydrate metabolites in the fasting northern elephant seal. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2013; 8:141-51. [PMID: 23542762 DOI: 10.1016/j.cbd.2013.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/23/2013] [Accepted: 02/25/2013] [Indexed: 02/05/2023]
Abstract
Northern elephant seals endure prolonged periods of food deprivation at multiple life-history stages and simultaneous with energetically costly activities-including reproduction and development. Most mammals decrease their energy expenditure while fasting, with simultaneous reductions in gluconeogenesis and circulating glucose concentration. Paradoxically, elephant seals maintain high rates of both energy expenditure and gluconeogenesis, and high blood glucose concentrations throughout fasting. We therefore characterized the suite of changes that occur in carbohydrate metabolites during fasting in northern elephant seals. Using a broad-based metabolomics platform we investigated fasting during two states-lactation in adult females and the post-weaning developmental period in pups. A total of 227 metabolites were detected in seal plasma; 31 associated with carbohydrate metabolism were analyzed in the present study. Several compounds showed similar responses during lactation and the post-weaning fast (e.g. glycerol and mesaconate) whereas other compounds displayed quite different abundances between groups (e.g. citrate and pyruvate). This work found that, while the changes that occur with fasting were frequently similar in lactating females and developing pups, the relative abundance of compounds often varied markedly. These differences suggest that the metabolic strategies used to endure prolonged fasts are influenced by life-history or nutrient constraints.
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Affiliation(s)
- Cory D Champagne
- Dept. of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA.
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Vázquez-Medina JP, Zenteno-Savín T, Elsner R, Ortiz RM. Coping with physiological oxidative stress: a review of antioxidant strategies in seals. J Comp Physiol B 2012; 182:741-50. [PMID: 22327141 DOI: 10.1007/s00360-012-0652-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/25/2012] [Accepted: 01/28/2012] [Indexed: 12/30/2022]
Abstract
While diving, seals are exposed to apnea-induced hypoxemia and repetitive cycles of ischemia/reperfusion. While on land, seals experience sleep apnea, as well as prolonged periods of food and water deprivation. Prolonged fasting, sleep apnea, hypoxemia and ischemia/reperfusion increase oxidant production and oxidative stress in terrestrial mammals. In seals, however, neither prolonged fasting nor apnea-induced hypoxemia or ischemia/reperfusion increase systemic or local oxidative damage. The strategies seals evolved to cope with increased oxidant production are reviewed in the present manuscript. Among these strategies, high antioxidant capacity and the oxidant-mediated activation of hormetic responses against hypoxia and oxidative stress are discussed. In addition to expanding our knowledge of the evolution of antioxidant defenses and adaptive responses to oxidative stress, understanding the mechanisms that naturally allow mammals to avoid oxidative damage has the potential to advance our knowledge of oxidative stress-induced pathologies and to enhance the translative value of biomedical therapies in the long term.
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Affiliation(s)
- José Pablo Vázquez-Medina
- School of Natural Sciences, University of California Merced, 5200 N Lake Road, Merced, CA 95343, USA.
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