Modeling cellular compartmentation in one‐carbon metabolism

Scotti, Marco; Stella, Lorenzo; Shearer, Emily; Stover, Patrick J.

doi:10.1002/wsbm.1209

Cited by 46 publications

(44 citation statements)

References 156 publications

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“…The folate cycle completes when 5-methyl-THF is demethylated to produce methionine and THF. This model is composed of 7 species and 13 enzymatic reactions where their rates are modelled by the Michaelis-Menten kinetics 30,31 .…”

Section: A Rssa Formulations Performance On Large Modelsmentioning

confidence: 99%

On the rejection-based algorithm for simulation and analysis of large-scale reaction networks

Thanh

Zunino

Priami

2015

The Journal of Chemical Physics

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Stochastic simulation for in-silico studies of large biochemical networks requires a great amount of computational time. We recently proposed a new exact simulation algorithm, called the rejection-based stochastic simulation algorithm (RSSA) [J. Chem. Phys. 141(13):134116 (2014)], to improve simulation performance by postponing and collapsing as much as possible the propensity updates. In this paper, we analyze the performance of this algorithm in detail, and improve it for simulating large-scale biochemical reaction networks. We also present a new algorithm, called simultaneous RSSA (SRSSA), which generates many independent trajectories simultaneously for the analysis of the biochemical behavior. SRSSA improves simulation performance by utilizing a single data structure across simulations to select reaction firings and forming trajectories. The memory requirement for building and storing the data structure is thus independent of the number of trajectories. The updating of the data structure when needed is performed collectively in a single operation across the simulations. The trajectories generated by SRSSA are exact and independent of each other by exploiting the rejection-based mechanism. We test our new improvement on real biological systems with a wide range of reaction networks to demonstrate its applicability and efficiency.

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Section: A Rssa Formulations Performance On Large Modelsmentioning

confidence: 99%

On the rejection-based algorithm for simulation and analysis of large-scale reaction networks

Thanh

Zunino

Priami

2015

The Journal of Chemical Physics

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“…However, neither pathway nor system maps provide causal explanations for a phenotype. Biomarkers predicted or discovered by system analysis need to be validated in order to inform preventive or therapeutic treatments (Nijhout et al 2008; and to set dietary reference intakes for essential nutrients (Scotti et al 2013). A variety of different statistical and computational methods are used or developed to address this experimental data complexity of system biology (Scotti et al 2013).…”

Section: Genetic and Epigenetic Variability: Molecular Phenotypingmentioning

confidence: 99%

The genomics of micronutrient requirements

2015

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Healthy nutrition is accepted as a cornerstone of public health strategies for reducing the risk of noncommunicable conditions such as obesity, cardiovascular disease, and related morbidities. However, many research studies continue to focus on single or at most a few factors that may elicit a metabolic effect. These reductionist approaches resulted in: (1) exaggerated claims for nutrition as a cure or prevention of disease; (2) the wide use of empirically based dietary regimens, as if one fits all; and (3) frequent disappointment of consumers, patients, and healthcare providers about the real impact nutrition can make on medicine and health. Multiple factors including environment, host and microbiome genetics, social context, the chemical form of the nutrient, its (bio)availability, and chemical and metabolic interactions among nutrients all interact to result in nutrient requirement and in health outcomes. Advances in laboratory methodologies, especially in analytical and separation techniques, are making the chemical dissection of foods and their availability in physiological tissues possible in an unprecedented manner. These omics technologies have opened opportunities for extending knowledge of micronutrients and of their metabolic and endocrine roles. While these technologies are crucial, more holistic approaches to the analysis of physiology and environment, novel experimental designs, and more sophisticated computational methods are needed to advance our understanding of how nutrition influences health of individuals.

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“…Folic acid (not found in food) is the fully oxidized monoglutamate form (pteroylmonoglutamate) of the folate vitamin that is used in fortified foods and dietary supplements. Folate plays an essential role in asssociation with B 12 and B 6 vitamins in nucleotide synthesis, methionine regeneration in DNA methylation, oxidation and reduction of onecarbon units required for normal metabolism and regulation (Scotti et al 2013). Folate defeciency causes severe abnormalities in one-carbon metabolism, resulting in DNA hypomethylation, which cause certain types of chronic diseases and developmental disorders, including neural tube defects (Williams et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Relative bioavailability of folate from the traditional food plant Moringa oleifera L. as evaluated in a rat model

et al. 2015

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Moringa oleifera is an affordable and rich source of dietary folate. Quantification of folate by HPLC showed that 5-formyl-5,6,7,8-tetrahydrofolic acid (502.1 μg/100 g DW) and 5,6,7,8-tetrahydrofolic acid (223.9 μg/100 g DW) as the most dominant forms of folate in M. oleifera leaves. The bioavailability of folate and the effects of folate depletion and repletion on biochemical and molecular markers of folate status were investigated in Wistar rats. Folate deficiency was induced by keeping the animals on a folate deficient diet with 1 % succinyl sulfathiazole (w/w). After the depletion period, animals were repleted with different levels of folic acid and M. oleifera leaves as a source of folate. Feeding the animals on a folate deficient diet for 7 weeks caused a significant (3.4-fold) decrease in serum folate content, compared to non-depleted control animals. Relative bioavailability of folate from dehydrated leaves of M. oleifera was 81.9 %. During folate depletion and repletion, no significant changes in liver glycine N-methyl transferase and 5-methyltetrahydrofolatehomocysteine methyltransferase expression were recorded. In RDA calculations, only 50 % of natural folate is assumed to be bioavailable. Therefore, the bioavailability of folate from Moringa is much higher, suggesting that M. oleifera based food can be used as a significant source of folate.

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Modeling cellular compartmentation in one‐carbon metabolism

Cited by 46 publications

References 156 publications

On the rejection-based algorithm for simulation and analysis of large-scale reaction networks

On the rejection-based algorithm for simulation and analysis of large-scale reaction networks

The genomics of micronutrient requirements

Relative bioavailability of folate from the traditional food plant Moringa oleifera L. as evaluated in a rat model

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