Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue

The fruit fly D. melanogaster is increasingly used as a model organism for studying acute hypoxia tolerance and for studying aging, but the interactions between these two factors are not well known. Here we show that hypoxia tolerance degrades with age in post-hypoxic recovery of whole-body movement, heart rate and ATP content. We previously used 1H NMR metabolomics and a constraint-based model of ATP-generating metabolism to discover the end products of hypoxic metabolism in flies and generate hypotheses for the biological mechanisms. We expand the reactions in the model using tissue- and age-specific microarray data from the literature, and then examine metabolomic profiles of thoraxes after 4 hours at 0.5% O2 and after 5 minutes of recovery in 40- versus 3-day-old flies. Model simulations were constrained to fluxes calculated from these data. Simulations suggest that the decreased ATP production during reoxygenation seen in aging flies can be attributed to reduced recovery of mitochondrial respiration pathways and concomitant over-dependence on the acetate production pathway as an energy source.Comment: 30 page

Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysis

BACKGROUND: Cellular hypoxia is a component of many diseases, but mechanisms of global hypoxic adaptation and resistance are not completely understood. Previously, a population of Drosophila flies was experimentally selected over several generations to survive a chronically hypoxic environment. NMR-based metabolomics, combined with flux-balance simulations of genome-scale metabolic networks, can generate specific hypotheses for global reaction fluxes within the cell. We applied these techniques to compare metabolic activity during acute hypoxia in muscle tissue of adapted versus "naïve" control flies. RESULTS: Metabolic profiles were gathered for adapted and control flies after exposure to acute hypoxia using (1)H NMR spectroscopy. Principal Component Analysis suggested that the adapted flies are tuned to survive a specific oxygen level. Adapted flies better tolerate acute hypoxic stress, and we explored the mechanisms of this tolerance using a flux-balance model of central metabolism. In the model, adapted flies produced more ATP per glucose and created fewer protons than control flies, had lower pyruvate carboxylase flux, and had greater usage of Complex I over Complex II. CONCLUSION: We suggest a network-level hypothesis of metabolic regulation in hypoxia-adapted flies, in which lower baseline rates of biosynthesis in adapted flies draws less anaplerotic flux, resulting in lower rates of glycolysis, less acidosis, and more efficient use of substrate during acute hypoxic stress. In addition we suggest new specific hypothesis, which were found to be consistent with existing data

Search algorithms as a framework for the optimization of drug combinations

Combination therapies are often needed for effective clinical outcomes in the management of complex diseases, but presently they are generally based on empirical clinical experience. Here we suggest a novel application of search algorithms, originally developed for digital communication, modified to optimize combinations of therapeutic interventions. In biological experiments measuring the restoration of the decline with age in heart function and exercise capacity in Drosophila melanogaster, we found that search algorithms correctly identified optimal combinations of four drugs with only one third of the tests performed in a fully factorial search. In experiments identifying combinations of three doses of up to six drugs for selective killing of human cancer cells, search algorithms resulted in a highly significant enrichment of selective combinations compared with random searches. In simulations using a network model of cell death, we found that the search algorithms identified the optimal combinations of 6-9 interventions in 80-90% of tests, compared with 15-30% for an equivalent random search. These findings suggest that modified search algorithms from information theory have the potential to enhance the discovery of novel therapeutic drug combinations. This report also helps to frame a biomedical problem that will benefit from an interdisciplinary effort and suggests a general strategy for its solution.Comment: 36 pages, 10 figures, revised versio

Synthesis and biological activity of heterocycles and heptapeptide derivatives related to microcin B17 : potential leads for new herbicides and antibiotics

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Results of flux-balance analysis on the model of ATP-generating metabolism

<p><b>Copyright information:</b></p><p>Taken from "Flexibility in energy metabolism supports hypoxia tolerance in flight muscle: metabolomic and computational systems analysis"</p><p></p><p>Molecular Systems Biology 2007;3():99-99.</p><p>Published online 17 Apr 2007</p><p>PMCID:PMC1865581.</p><p>Copyright © 2007, EMBO and Nature Publishing Group</p> () Proton production increases but then levels off at low oxygen levels as pyruvate begins to be fermented to alanine, acetate, and lactate. Glucose uptake is decreased during restricted oxygen. () When pyruvate is only allowed to be converted to lactate (pseudo-mammalian), proton production is much higher and glucose uptake remains constant during hypoxia, whereas () ATP production remains the same or better. Abbreviations: ac: acetate accumulation; ala: alanine accumulation; atp: ATP production; CO: CO production; glc: glucose uptake; h: proton production and lac: lactate accumulation

Molecular karyotyping in human constitutional cytogenetics

International audienc

La CGH microarray : principe et applications en pathologie constitutionnelle

International audienc