ArticleProceedings of the National Academy of Sciences of the United States of America2004
A modular minimal cell model: purine and pyrimidine transport and metabolism.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT04802707 (A Phase II, Monocenter, Single Arm Study To Assess The Safety and Efficacy Of Combination Deoxycytidine and Deoxythymidine For Mitochondrial Depletion Disorders), which is not on this map. Cited by 15 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
A Phase II, Monocenter, Single Arm Study To Assess The Safety and Efficacy Of Combination Deoxycytidine and Deoxythymidine For Mitochondrial Depletion Disorders
Who cites it
15 citing papers in PubMed.
- Data integration strategies for whole-cell modeling.FEMS yeast research · 2024Review
- Effect of Sodium Selenite on the Metabolite Profile of Epichloë sp. Mycelia from Festuca sinensis in Solid Culture.Biological trace element research · 2022Article
- Dynamic carbon flux network of a diverse marine microbial community.ISME communications · 2021Article
- Transforming the study of organisms: Phenomic data models and knowledge bases.PLoS computational biology · 2020Review
- Toward a genome scale sequence specific dynamic model of cell-free protein synthesis inMetabolic engineering communications · 2020Article
- Circadian clock helps cyanobacteria manage energy in coastal and high latitude ocean.The ISME journal · 2020Article
- Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.Frontiers in bioengineering and biotechnology · 2020Article
- NMR-based metabolomics reveals the metabolite profiles of Vibrio parahaemolyticus under ferric iron stimulation.Journal of microbiology (Seoul, Korea) · 2017Article
- From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality.Frontiers in microbiology · 2017Review
- A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network.Scientific reports · 2016Article
- Systems biology perspectives on minimal and simpler cells.Microbiology and molecular biology reviews : MMBR · 2014Review
- Article
- The dawn of virtual cell biology.Cell · 2012Article
- Stochastic simulations of minimal self-reproducing cellular systems.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2007Article
- OptStrain: a computational framework for redesign of microbial production systems.Genome research · 2004Article
Corrections and comments
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A more complete understanding of the relationship of cell physiology to genomic structure is desirable. Because of the intrinsic complexity of biological organisms, only the simplest cells will allow complete definition of all components and their interactions. The theoretical and experimental construction of a minimal cell has been suggested as a tool to develop such an understanding. Our ultimate goal is to convert a "coarse-grain" lumped parameter computer model of Escherichia coli into a genetically and chemically detailed model of a "minimal cell." The base E. coli model has been converted into a generalized model of a heterotrophic bacterium. This coarse-grain minimal cell model is functionally complete, with growth rate, composition, division, and changes in cell morphology as natural outputs from dynamic simulations where only the initial composition of the cell and of the medium are specified. A coarse-grain model uses pseudochemical species (or modules) that are aggregates of distinct chemical species that share similar chemistry and metabolic dynamics. This model provides a framework in which these modules can be "delumped" into chemical and genetic descriptions while maintaining connectivity to all other functional elements. Here we demonstrate that a detailed description of nucleotide precursors transport and metabolism is successfully integrated into the whole-cell model. This nucleotide submodel requires fewer (12) genes than other theoretical predictions in minimal cells. The demonstration of modularity suggests the possibility of developing modules in parallel and recombining them into a fully functional chemically and genetically detailed model of a prokaryote cell.
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