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Srivastava R. Applications of artificial intelligence multiomics in precision oncology. J Cancer Res Clin Oncol 2023; 149:503-510. [PMID: 35796775 DOI: 10.1007/s00432-022-04161-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/17/2022] [Indexed: 02/06/2023]
Abstract
Cancer is the second leading worldwide disease that depends on oncogenic mutations and non-mutated genes for survival. Recent advancements in next-generation sequencing (NGS) have transformed the health care sector with big data and machine learning (ML) approaches. NGS data are able to detect the abnormalities and mutations in the oncogenes. These multi-omics analyses are used for risk prediction, early diagnosis, accurate prognosis, and identification of biomarkers in cancer patients. The availability of these cancer data and their analysis may provide insights into the biology of the disease, which can be used for the personalized treatment of cancer patients. Bioinformatics tools are delivering this promise by managing, integrating, and analyzing these complex datasets. The clinical outcomes of cancer patients are improved by the use of various innovative methods implicated particularly for diagnosis and therapeutics. ML-based artificial intelligence (AI) applications are solving these issues to a great extent. AI techniques are used to update the patients on a personalized basis about their treatment procedures, progress, recovery, therapies used, dietary changes in lifestyles patterns along with the survival summary of previously recovered cancer patients. In this way, the patients are becoming more aware of their diseases and the entire clinical treatment procedures. Though the technology has its own advantages and disadvantages, we hope that the day is not so far when AI techniques will provide personalized treatment to cancer patients tailored to their needs in much quicker ways.
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Affiliation(s)
- Ruby Srivastava
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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2
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Modeling Metabolism and Finding New Antibiotics. Bioinformatics 2023. [DOI: 10.1007/978-3-662-65036-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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3
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Multi-omics strategies for personalized and predictive medicine: past, current, and future translational opportunities. Emerg Top Life Sci 2022; 6:215-225. [PMID: 35234253 DOI: 10.1042/etls20210244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/13/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Precision medicine is driven by the paradigm shift of empowering clinicians to predict the most appropriate course of action for patients with complex diseases and improve routine medical and public health practice. It promotes integrating collective and individualized clinical data with patient specific multi-omics data to develop therapeutic strategies, and knowledgebase for predictive and personalized medicine in diverse populations. This study is based on the hypothesis that understanding patient's metabolomics and genetic make-up in conjunction with clinical data will significantly lead to determining predisposition, diagnostic, prognostic and predictive biomarkers and optimal paths providing personalized care for diverse and targeted chronic, acute, and infectious diseases. This study briefs emerging significant, and recently reported multi-omics and translational approaches aimed to facilitate implementation of precision medicine. Furthermore, it discusses current grand challenges, and the future need of Findable, Accessible, Intelligent, and Reproducible (FAIR) approach to accelerate diagnostic and preventive care delivery strategies beyond traditional symptom-driven, disease-causal medical practice.
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4
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Ahmed Z. Precision medicine with multi-omics strategies, deep phenotyping, and predictive analysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 190:101-125. [DOI: 10.1016/bs.pmbts.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Metabolic Modeling with MetaFlux. Methods Mol Biol 2021. [PMID: 34718999 DOI: 10.1007/978-1-0716-1585-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The MetaFlux software supports creating, executing, and solving quantitative metabolic flux models using flux balance analysis (FBA). MetaFlux offers four modes of operation: (1) solving mode executes an FBA model for an individual organism or for an organism community, (2) gene knockout mode executes an FBA model with one or many gene knockouts, (3) development mode assists the user in creating and improving FBA models, and (4) flux variability analysis mode generates a report of the robustness of an FBA model. MetaFlux also solves dynamic FBA (dFBA) for both individual organisms and communities of organisms. MetaFlux can be used in two different environments: on your local computer, which requires the installation of the Pathway Tools software, or through the web, which does not require installation of Pathway Tools. On your local computer, MetaFlux offers all four modes of operation, whereas the web environment provides only the solving mode.Several visualization tools are available to analyze model solutions. The Cellular Overview tool graphically shows the reaction fluxes on an organism's metabolic map once a model is solved. The Omics Dashboard provides a hierarchical approach to visualizing reaction fluxes, organized by metabolic subsystems. For a community of organisms, plotting of accumulated biomasses and metabolites can be performed using the Gnuplot tool.In this chapter, we present eight methods using MetaFlux. Five solving mode methods illustrate execution of models for individual organisms and for organism communities. One method illustrates the gene knockout mode. Two methods for the development mode illustrate steps for developing new metabolic models.
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6
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Hari A, Lobo D. Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks. Nucleic Acids Res 2020; 48:W427-W435. [PMID: 32442279 PMCID: PMC7319574 DOI: 10.1093/nar/gkaa409] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/20/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing has paved the way for the reconstruction of genome-scale metabolic networks as a powerful tool for understanding metabolic circuits in any organism. However, the visualization and extraction of knowledge from these large networks comprising thousands of reactions and metabolites is a current challenge in need of user-friendly tools. Here we present Fluxer (https://fluxer.umbc.edu), a free and open-access novel web application for the computation and visualization of genome-scale metabolic flux networks. Any genome-scale model based on the Systems Biology Markup Language can be uploaded to the tool, which automatically performs Flux Balance Analysis and computes different flux graphs for visualization and analysis. The major metabolic pathways for biomass growth or for biosynthesis of any metabolite can be interactively knocked-out, analyzed and visualized as a spanning tree, dendrogram or complete graph using different layouts. In addition, Fluxer can compute and visualize the k-shortest metabolic paths between any two metabolites or reactions to identify the main metabolic routes between two compounds of interest. The web application includes >80 whole-genome metabolic reconstructions of diverse organisms from bacteria to human, readily available for exploration. Fluxer enables the efficient analysis and visualization of genome-scale metabolic models toward the discovery of key metabolic pathways.
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Affiliation(s)
- Archana Hari
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
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7
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Practicing precision medicine with intelligently integrative clinical and multi-omics data analysis. Hum Genomics 2020; 14:35. [PMID: 33008459 PMCID: PMC7530549 DOI: 10.1186/s40246-020-00287-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022] Open
Abstract
Precision medicine aims to empower clinicians to predict the most appropriate course of action for patients with complex diseases like cancer, diabetes, cardiomyopathy, and COVID-19. With a progressive interpretation of the clinical, molecular, and genomic factors at play in diseases, more effective and personalized medical treatments are anticipated for many disorders. Understanding patient’s metabolomics and genetic make-up in conjunction with clinical data will significantly lead to determining predisposition, diagnostic, prognostic, and predictive biomarkers and paths ultimately providing optimal and personalized care for diverse, and targeted chronic and acute diseases. In clinical settings, we need to timely model clinical and multi-omics data to find statistical patterns across millions of features to identify underlying biologic pathways, modifiable risk factors, and actionable information that support early detection and prevention of complex disorders, and development of new therapies for better patient care. It is important to calculate quantitative phenotype measurements, evaluate variants in unique genes and interpret using ACMG guidelines, find frequency of pathogenic and likely pathogenic variants without disease indicators, and observe autosomal recessive carriers with a phenotype manifestation in metabolome. Next, ensuring security to reconcile noise, we need to build and train machine-learning prognostic models to meaningfully process multisource heterogeneous data to identify high-risk rare variants and make medically relevant predictions. The goal, today, is to facilitate implementation of mainstream precision medicine to improve the traditional symptom-driven practice of medicine, and allow earlier interventions using predictive diagnostics and tailoring better-personalized treatments. We strongly recommend automated implementation of cutting-edge technologies, utilizing machine learning (ML) and artificial intelligence (AI) approaches for the multimodal data aggregation, multifactor examination, development of knowledgebase of clinical predictors for decision support, and best strategies for dealing with relevant ethical issues.
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8
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Ahmed Z, Zeeshan S, Foran DJ, Kleinman LC, Wondisford FE, Dong X. Integrative clinical, genomics and metabolomics data analysis for mainstream precision medicine to investigate COVID-19. ACTA ACUST UNITED AC 2020. [DOI: 10.1136/bmjinnov-2020-000444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite significant scientific and medical discoveries, the genetics of novel infectious diseases like COVID-19 remains far from understanding. SARS-CoV-2 is a single-stranded RNA respiratory virus that causes COVID-19 by binding to the ACE2 receptor in the lung and other organs. Understanding its clinical presentation and metabolomic and genetic profile will lead to the discovery of diagnostic, prognostic and predictive biomarkers, which may lead to more effective medical therapy. It is important to investigate correlations and overlap between reported diagnoses of a patient with COVID-19 in clinical data with identified germline and somatic mutations, and highly expressed genes from genomics data analysis. Timely model clinical, genomics and metabolomics data to find statistical patterns across millions of features to identify underlying biological pathways, modifiable risk factors and actionable information that supports early detection and prevention of COVID-19, and development of new therapies for better patient care. Next, ensuring security reconcile noise, need to build and train machine learning prognostic models to find actionable information that supports early detection and prevention of COVID-19. Based on the myriad data, applying appropriate machine learning algorithms to stratify patients, understand scenarios, optimise decision-making, identify high-risk rare variants (including ACE2, TMPRSS2) and making medically relevant predictions. Innovative and intelligent solutions are required to improve the traditional symptom-driven practice, and allow earlier interventions using predictive diagnostics and tailor better personalised treatments, when confronted with the challenges of pandemic situations.
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9
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Grim CM, Luu GT, Sanchez LM. Staring into the void: demystifying microbial metabolomics. FEMS Microbiol Lett 2020; 366:5519856. [PMID: 31210257 DOI: 10.1093/femsle/fnz135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/14/2019] [Indexed: 12/18/2022] Open
Abstract
Metabolites give us a window into the chemistry of microbes and are split into two subclasses: primary and secondary. Primary metabolites are required for life whereas secondary metabolites have historically been classified as those appearing after exponential growth and are not necessarily needed for survival. Many microbial species are estimated to produce hundreds of metabolites and can be affected by differing nutrients. Using various analytical techniques, metabolites can be directly detected in order to elucidate their biological significance. Currently, a single experiment can produce anywhere from megabytes to terabytes of data. This big data has motivated scientists to develop informatics tools to help target specific metabolites or sets of metabolites. Broadly, it is imperative to identify clear biological questions before embarking on a study of metabolites (metabolomics). For instance, studying the effect of a transposon insertion on phenazine biosynthesis in Pseudomonas is a very different from asking what molecules are present in a specific banana-derived strain of Pseudomonas. This review is meant to serve as a primer for a 'choose your own adventure' approach for microbiologists with limited mass spectrometry expertise, with a strong focus on liquid chromatography mass spectrometry based workflows developed or optimized within the past five years.
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Affiliation(s)
- Cynthia M Grim
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
| | - Gordon T Luu
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
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10
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Abstract
Bacteria are prime cell factories that can efficiently convert carbon and nitrogen sources into a large diversity of intracellular and extracellular biopolymers, such as polysaccharides, polyamides, polyesters, polyphosphates, extracellular DNA and proteinaceous components. Bacterial polymers have important roles in pathogenicity, and their varied chemical and material properties make them suitable for medical and industrial applications. The same biopolymers when produced by pathogenic bacteria function as major virulence factors, whereas when they are produced by non-pathogenic bacteria, they become food ingredients or biomaterials. Interdisciplinary research has shed light on the molecular mechanisms of bacterial polymer synthesis, identified new targets for antibacterial drugs and informed synthetic biology approaches to design and manufacture innovative materials. This Review summarizes the role of bacterial polymers in pathogenesis, their synthesis and their material properties as well as approaches to design cell factories for production of tailor-made bio-based materials suitable for high-value applications.
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Affiliation(s)
- M Fata Moradali
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia.
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11
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Ahmed Z, Zeeshan S, Mendhe D, Dong X. Human gene and disease associations for clinical-genomics and precision medicine research. Clin Transl Med 2020; 10:297-318. [PMID: 32508008 PMCID: PMC7240856 DOI: 10.1002/ctm2.28] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/15/2022] Open
Abstract
We are entering the era of personalized medicine in which an individual's genetic makeup will eventually determine how a doctor can tailor his or her therapy. Therefore, it is becoming critical to understand the genetic basis of common diseases, for example, which genes predispose and rare genetic variants contribute to diseases, and so on. Our study focuses on helping researchers, medical practitioners, and pharmacists in having a broad view of genetic variants that may be implicated in the likelihood of developing certain diseases. Our focus here is to create a comprehensive database with mobile access to all available, authentic and actionable genes, SNPs, and classified diseases and drugs collected from different clinical and genomics databases worldwide, including Ensembl, GenCode, ClinVar, GeneCards, DISEASES, HGMD, OMIM, GTR, CNVD, Novoseek, Swiss-Prot, LncRNADisease, Orphanet, GWAS Catalog, SwissVar, COSMIC, WHO, and FDA. We present a new cutting-edge gene-SNP-disease-drug mobile database with a smart phone application, integrating information about classified diseases and related genes, germline and somatic mutations, and drugs. Its database includes over 59 000 protein-coding and noncoding genes; over 67 000 germline SNPs and over a million somatic mutations reported for over 19 000 protein-coding genes located in over 1000 regions, published with over 3000 articles in over 415 journals available at the PUBMED; over 80 000 ICDs; over 123 000 NDCs; and over 100 000 classified gene-SNP-disease associations. We present an application that can provide new insights into the information about genetic basis of human complex diseases and contribute to assimilating genomic with phenotypic data for the availability of gene-based designer drugs, precise targeting of molecular fingerprints for tumor, appropriate drug therapy, predicting individual susceptibility to disease, diagnosis, and treatment of rare illnesses are all a few of the many transformations expected in the decade to come.
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Affiliation(s)
- Zeeshan Ahmed
- Institute for Health, Health Care Policy and Aging Research, RutgersThe State University of New JerseyNew BrunswickNew JerseyUSA
- Department of Medicine, Rutgers Robert Wood Johnson Medical SchoolRutgers Biomedical and Health SciencesNew BrunswickNew JerseyUSA
| | - Saman Zeeshan
- Rutgers Cancer Institute of New Jersey, RutgersThe State University of New JerseyNew BrunswickNew JerseyUSA
| | - Dinesh Mendhe
- Institute for Health, Health Care Policy and Aging Research, RutgersThe State University of New JerseyNew BrunswickNew JerseyUSA
| | - XinQi Dong
- Institute for Health, Health Care Policy and Aging Research, RutgersThe State University of New JerseyNew BrunswickNew JerseyUSA
- Department of Medicine, Rutgers Robert Wood Johnson Medical SchoolRutgers Biomedical and Health SciencesNew BrunswickNew JerseyUSA
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12
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Srivastava M, Bencurova E, Gupta SK, Weiss E, Löffler J, Dandekar T. Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle. Front Cell Infect Microbiol 2019; 9:168. [PMID: 31192161 PMCID: PMC6540932 DOI: 10.3389/fcimb.2019.00168] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Dendritic cells (DCs) are antigen presenting cells which serve as a passage between the innate and the acquired immunity. Aspergillosis is a major lethal condition in immunocompromised patients caused by the adaptable saprophytic fungus Aspergillus fumigatus. The healthy human immune system is capable to ward off A. fumigatus infections however immune-deficient patients are highly vulnerable to invasive aspergillosis. A. fumigatus can persist during infection due to its ability to survive the immune response of human DCs. Therefore, the study of the metabolism specific to the context of infection may allow us to gain insight into the adaptation strategies of both the pathogen and the immune cells. We established a metabolic model of A. fumigatus central metabolism during infection of DCs and calculated the metabolic pathway (elementary modes; EMs). Transcriptome data were used to identify pathways activated when A. fumigatus is challenged with DCs. In particular, amino acid metabolic pathways, alternative carbon metabolic pathways and stress regulating enzymes were found to be active. Metabolic flux modeling identified further active enzymes such as alcohol dehydrogenase, inositol oxygenase and GTP cyclohydrolase participating in different stress responses in A. fumigatus. These were further validated by qRT-PCR from RNA extracted under these different conditions. For DCs, we outlined the activation of metabolic pathways in response to the confrontation with A. fumigatus. We found the fatty acid metabolism plays a crucial role, along with other metabolic changes. The gene expression data and their analysis illuminate additional regulatory pathways activated in the DCs apart from interleukin regulation. In particular, Toll-like receptor signaling, NOD-like receptor signaling and RIG-I-like receptor signaling were active pathways. Moreover, we identified subnetworks and several novel key regulators such as UBC, EGFR, and CUL3 of DCs to be activated in response to A. fumigatus. In conclusion, we analyze the metabolic and regulatory responses of A. fumigatus and DCs when confronted with each other.
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Affiliation(s)
- Mugdha Srivastava
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Shishir K Gupta
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Esther Weiss
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Jürgen Löffler
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,EMBL Heidelberg, Structural and Computational Biology, Heidelberg, Germany
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Cordes T, Metallo CM. Quantifying Intermediary Metabolism and Lipogenesis in Cultured Mammalian Cells Using Stable Isotope Tracing and Mass Spectrometry. Methods Mol Biol 2019; 1978:219-241. [PMID: 31119666 DOI: 10.1007/978-1-4939-9236-2_14] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Metabolism plays a central role in virtually all diseases, including diabetes, cancer, and neurodegeneration. Detailed analysis is required to identify the specific metabolic pathways dysregulated in the context of a given disease or biological perturbation. Measurement of metabolite concentrations can provide some insights into altered pathway activity or enzyme function, but since most biochemicals are metabolized by various enzymes in distinct pathways within cells and tissues, these approaches are somewhat limited. By applying metabolic tracers to a biological system, one can visualize pathway-specific information depending on the tracer used and analytes measured. To this end, stable isotope tracers and mass spectrometry are emerging as important tools for the examination of metabolic pathways and fluxes in cultured mammalian cells and other systems. Here, we describe a detailed workflow for quantifying metabolic processes in mammalian cell cultures using stable isotopes and gas chromatography coupled to mass spectrometry (GC-MS). As a case study, we apply 13C isotopic labeled glucose and glutamine to a cancer cell line to quantify substrate utilization for TCA metabolism and lipogenesis. Guidelines are also provided for interpretation of data and considerations for application to other cell systems. Ultimately, this approach provides a robust and precise method for quantifying stable isotope labeling in metabolite pools that can be applied to diverse biological systems.
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Affiliation(s)
- Thekla Cordes
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
- Diabetes and Endocrinology Research Center, University of California San Diego, La Jolla, CA, USA.
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
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14
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Identification of Antifungal Targets Based on Computer Modeling. J Fungi (Basel) 2018; 4:jof4030081. [PMID: 29973534 PMCID: PMC6162656 DOI: 10.3390/jof4030081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/24/2018] [Accepted: 06/29/2018] [Indexed: 01/07/2023] Open
Abstract
Aspergillus fumigatus is a saprophytic, cosmopolitan fungus that attacks patients with a weak immune system. A rational solution against fungal infection aims to manipulate fungal metabolism or to block enzymes essential for Aspergillus survival. Here we discuss and compare different bioinformatics approaches to analyze possible targeting strategies on fungal-unique pathways. For instance, phylogenetic analysis reveals fungal targets, while domain analysis allows us to spot minor differences in protein composition between the host and fungi. Moreover, protein networks between host and fungi can be systematically compared by looking at orthologs and exploiting information from host⁻pathogen interaction databases. Further data—such as knowledge of a three-dimensional structure, gene expression data, or information from calculated metabolic fluxes—refine the search and rapidly put a focus on the best targets for antimycotics. We analyzed several of the best targets for application to structure-based drug design. Finally, we discuss general advantages and limitations in identification of unique fungal pathways and protein targets when applying bioinformatics tools.
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15
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Bedaso Y, Bergmann FT, Choi K, Medley K, Sauro HM. A portable structural analysis library for reaction networks. Biosystems 2018; 169-170:20-25. [PMID: 29857031 DOI: 10.1016/j.biosystems.2018.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/30/2018] [Accepted: 05/28/2018] [Indexed: 09/30/2022]
Abstract
The topology of a reaction network can have a significant influence on the network's dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the network configuration and are important considerations before any dynamical analysis is made. Most established simulation software tools usually carry out some kind of structural analysis of a network before any attempt is made at dynamic simulation. In this paper, we describe a portable software library, libStructural, that can carry out a variety of popular structural analyses that includes conservation analysis, flux dependency analysis and enumerating elementary modes. The library employs robust algorithms that allow it to be used on large networks with more than a two thousand nodes. The library accepts either a raw or fully labeled stoichiometry matrix or models written in SBML format. The software is written in standard C/C++ and comes with extensive on-line documentation and a test suite. The software is available for Windows, Mac OS X, and can be compiled easily on any Linux operating system. A language binding for Python is also available through the pip package manager making it simple to install on any standard Python distribution. The bulk of the source code is licensed under the open source BSD license with other parts using as either the MIT license or more simply public domain. All source is available on GitHub (https://github.com/sys-bio/Libstructural).
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Affiliation(s)
- Yosef Bedaso
- Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA.
| | | | - Kiri Choi
- Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA.
| | - Kyle Medley
- Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA
| | - Herbert M Sauro
- Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA.
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16
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Constraint-based modeling in microbial food biotechnology. Biochem Soc Trans 2018; 46:249-260. [PMID: 29588387 PMCID: PMC5906707 DOI: 10.1042/bst20170268] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 12/19/2022]
Abstract
Genome-scale metabolic network reconstruction offers a means to leverage the value of the exponentially growing genomics data and integrate it with other biological knowledge in a structured format. Constraint-based modeling (CBM) enables both the qualitative and quantitative analyses of the reconstructed networks. The rapid advancements in these areas can benefit both the industrial production of microbial food cultures and their application in food processing. CBM provides several avenues for improving our mechanistic understanding of physiology and genotype–phenotype relationships. This is essential for the rational improvement of industrial strains, which can further be facilitated through various model-guided strain design approaches. CBM of microbial communities offers a valuable tool for the rational design of defined food cultures, where it can catalyze hypothesis generation and provide unintuitive rationales for the development of enhanced community phenotypes and, consequently, novel or improved food products. In the industrial-scale production of microorganisms for food cultures, CBM may enable a knowledge-driven bioprocess optimization by rationally identifying strategies for growth and stability improvement. Through these applications, we believe that CBM can become a powerful tool for guiding the areas of strain development, culture development and process optimization in the production of food cultures. Nevertheless, in order to make the correct choice of the modeling framework for a particular application and to interpret model predictions in a biologically meaningful manner, one should be aware of the current limitations of CBM.
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17
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Wu X, Yao H, Liu Q, Zheng Z, Cao L, Mu D, Wang H, Jiang S, Li X. Producing Acetic Acid of Acetobacter pasteurianus by Fermentation Characteristics and Metabolic Flux Analysis. Appl Biochem Biotechnol 2018; 186:217-232. [PMID: 29552715 DOI: 10.1007/s12010-018-2732-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/28/2018] [Indexed: 02/07/2023]
Abstract
The acetic acid bacterium Acetobacter pasteurianus plays an important role in acetic acid fermentation, which involves oxidation of ethanol to acetic acid through the ethanol respiratory chain under specific conditions. In order to obtain more suitable bacteria for the acetic acid industry, A. pasteurianus JST-S screened in this laboratory was compared with A. pasteurianus CICC 20001, a current industrial strain in China, to determine optimal fermentation parameters under different environmental stresses. The maximum total acid content of A. pasteurianus JST-S was 57.14 ± 1.09 g/L, whereas that of A. pasteurianus CICC 20001 reached 48.24 ± 1.15 g/L in a 15-L stir stank. Metabolic flux analysis was also performed to compare the reaction byproducts. Our findings revealed the potential value of the strain in improvement of industrial vinegar fermentation.
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Affiliation(s)
- Xuefeng Wu
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Hongli Yao
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
| | - Qing Liu
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
| | - Zhi Zheng
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Lili Cao
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Dongdong Mu
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
| | - Hualin Wang
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Shaotong Jiang
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Xingjiang Li
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China.
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China.
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18
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Monk J, Bosi E. Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences. Methods Mol Biol 2018; 1716:151-175. [PMID: 29222753 DOI: 10.1007/978-1-4939-7528-0_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genome-scale metabolic reconstructions are powerful resources that allow translation biological knowledge and genomic information to phenotypical predictions using a number of constraint-based methods. This approach has been applied in recent years to gain deep insights into the cellular phenotype role of the genes at a systems-level, driving the design of targeted experiments and paving the way for knowledge-based synthetic biology.The identification of genetic determinants underlying the variability at the phenotypical level is crucial to understand the evolutionary trajectories of a bacterial species. Recently, genome-scale metabolic models of different strains have been assembled to highlight the intra-species diversity at the metabolic level. The strain-specific metabolic capabilities and auxotrophies can be used to identify factors related to the lifestyle diversity of a bacterial species.In this chapter, we present the computational steps to perform genome-scale metabolic modeling in the context of comparative genomics, and the different challenges related to this task.
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Affiliation(s)
- Jonathan Monk
- Department of Bioengineering, University of California, La Jolla, CA, USA
| | - Emanuele Bosi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
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19
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Wu X, Yao H, Cao L, Zheng Z, Chen X, Zhang M, Wei Z, Cheng J, Jiang S, Pan L, Li X. Improving Acetic Acid Production by Over-Expressing PQQ-ADH in Acetobacter pasteurianus. Front Microbiol 2017; 8:1713. [PMID: 28932219 PMCID: PMC5592214 DOI: 10.3389/fmicb.2017.01713] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/24/2017] [Indexed: 11/24/2022] Open
Abstract
Pyrroquinoline quinone-dependent alcohol dehydrogenase (PQQ-ADH) is a key enzyme in the ethanol oxidase respiratory chain of acetic acid bacteria (AAB). To investigate the effect of PQQ-ADH on acetic acid production by Acetobacter pasteurianus JST-S, subunits I (adhA) and II (adhB) of PQQ-ADH were over-expressed, the fermentation parameters and the metabolic flux analysis were compared in the engineered strain and the original one. The acetic acid production was improved by the engineered strain (61.42 g L−1) while the residual ethanol content (4.18 g L−1) was decreased. Analysis of 2D maps indicated that 19 proteins were differently expressed between the two strains; of these, 17 were identified and analyzed by mass spectrometry and two-dimensional gel electrophoresis. With further investigation of metabolic flux analysis (MFA) of the pathway from ethanol and glucose, the results reveal that over-expression of PQQ-ADH is an effective way to improve the ethanol oxidation respiratory chain pathway and these can offer theoretical references for potential mechanism of metabolic regulation in AAB and researches with its acetic acid resistance.
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Affiliation(s)
- Xuefeng Wu
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China.,Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of TechnologyHefei, China
| | - Hongli Yao
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China
| | - Lili Cao
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China.,Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of TechnologyHefei, China
| | - Zhi Zheng
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China.,Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of TechnologyHefei, China
| | - Xiaoju Chen
- School of Chemical Engineering and Life Sciences, Chaohu UniversityHefei, China
| | - Min Zhang
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China
| | - Zhaojun Wei
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China
| | - Jieshun Cheng
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China.,Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of TechnologyHefei, China
| | - Shaotong Jiang
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China.,Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of TechnologyHefei, China
| | - Lijun Pan
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China.,Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of TechnologyHefei, China
| | - Xingjiang Li
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China.,Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of TechnologyHefei, China
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20
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Ma F, Jazmin LJ, Young JD, Allen DK. Isotopically Nonstationary Metabolic Flux Analysis (INST-MFA) of Photosynthesis and Photorespiration in Plants. Methods Mol Biol 2017; 1653:167-194. [PMID: 28822133 DOI: 10.1007/978-1-4939-7225-8_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Photorespiration is a central component of photosynthesis; however to better understand its role it should be viewed in the context of an integrated metabolic network rather than a series of individual reactions that operate independently. Isotopically nonstationary 13C metabolic flux analysis (INST-MFA), which is based on transient labeling studies at metabolic steady state, offers a comprehensive platform to quantify plant central metabolism. In this chapter, we describe the application of INST-MFA to investigate metabolism in leaves. Leaves are an autotrophic tissue, assimilating CO2 over a diurnal period implying that the metabolic steady state is limited to less than 12 h and thus requiring an INST-MFA approach. This strategy results in a comprehensive unified description of photorespiration, Calvin cycle, sucrose and starch synthesis, tricarboxylic acid (TCA) cycle, and amino acid biosynthetic fluxes. We present protocols of the experimental aspects for labeling studies: transient 13CO2 labeling of leaf tissue, sample quenching and extraction, mass spectrometry (MS) analysis of isotopic labeling data, measurement of sucrose and amino acids in vascular exudates, and provide details on the computational flux estimation using INST-MFA.
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Affiliation(s)
- Fangfang Ma
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Lara J Jazmin
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, USA.
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21
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Pfau T, Pacheco MP, Sauter T. Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. Brief Bioinform 2016; 17:1060-1069. [PMID: 26615025 PMCID: PMC5142010 DOI: 10.1093/bib/bbv100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Genome-scale metabolic network reconstructions provide a basis for the investigation of the metabolic properties of an organism. There are reconstructions available for multiple organisms, from prokaryotes to higher organisms and methods for the analysis of a reconstruction. One example is the use of flux balance analysis to improve the yields of a target chemical, which has been applied successfully. However, comparison of results between existing reconstructions and models presents a challenge because of the heterogeneity of the available reconstructions, for example, of standards for presenting gene-protein-reaction associations, nomenclature of metabolites and reactions or selection of protonation states. The lack of comparability for gene identifiers or model-specific reactions without annotated evidence often leads to the creation of a new model from scratch, as data cannot be properly matched otherwise. In this contribution, we propose to improve the predictive power of metabolic models by switching from gene-protein-reaction associations to transcript-isoform-reaction associations, thus taking advantage of the improvement of precision in gene expression measurements. To achieve this precision, we discuss available databases that can be used to retrieve this type of information and point at issues that can arise from their neglect. Further, we stress issues that arise from non-standardized building pipelines, like inconsistencies in protonation states. In addition, problems arising from the use of non-specific cofactors, e.g. artificial futile cycles, are discussed, and finally efforts of the metabolic modelling community to unify model reconstructions are highlighted.
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22
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Sugimoto M. Metabolomic pathway visualization tool outsourcing editing function. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2016; 2015:7659-62. [PMID: 26738066 DOI: 10.1109/embc.2015.7320166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Recent rapid improvements of measuring instrument enables us to perform various omics studies to simultaneous profile multiple molecules, which provides a holistic view of various molecular interactions, such as signal transaction, protein interactions, and metabolic pathways. Metabolomics is recently emerged omics that can identify and quantify low weight metabolites usually defined as organic molecules whose size is <; 1500 Da. In comparison to the other omics, the development of software tools to deal with metabolomic data is not matured. Conventional pathway drawing and visualization tool provide tool-specific unique functions, however, such user interface requires users to learn the usage and prevention for the use of these tools. Here, we developed a more generic pathway visualization tool. This tool incorporate pathway data yielded by common drawing tools, e.g. MS PowerPoint, and visualize the quantified values on the pathways. The statistical results also can be overlaid on each metabolite. The developed tools facilitate the interpreting metabolomic data in pathway forms.
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23
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Cordes T, Metallo CM. Tracing insights into human metabolism using chemical engineering approaches. Curr Opin Chem Eng 2016; 14:72-81. [PMID: 28480159 DOI: 10.1016/j.coche.2016.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolism coordinates the conversion of available nutrients toward energy, biosynthetic intermediates, and signaling molecules to mediate virtually all biological functions. Dysregulation of metabolic pathways contributes to many diseases, so a detailed understanding of human metabolism has significant therapeutic implications. Over the last decade major technological advances in the areas of analytical chemistry, computational estimation of intracellular fluxes, and biological engineering have improved our ability to observe and engineer metabolic pathways. These approaches are reminiscent of the design, operation, and control of industrial chemical plants. Immune cells have emerged as an intriguing system in which metabolism influences diverse biological functions. Application of metabolic flux analysis and related approaches to macrophages and T cells offers great therapeutic opportunities to biochemical engineers.
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Affiliation(s)
- Thekla Cordes
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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24
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Oxidative modifications of glyceraldehyde 3-phosphate dehydrogenase regulate metabolic reprogramming of stored red blood cells. Blood 2016; 128:e32-42. [PMID: 27405778 DOI: 10.1182/blood-2016-05-714816] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/08/2016] [Indexed: 02/07/2023] Open
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) plays a key regulatory function in glucose oxidation by mediating fluxes through glycolysis or the pentose phosphate pathway (PPP) in an oxidative stress-dependent fashion. Previous studies documented metabolic reprogramming in stored red blood cells (RBCs) and oxidation of GAPDH at functional residues upon exposure to pro-oxidants diamide and H2O2 Here we hypothesize that routine storage of erythrocyte concentrates promotes metabolic modulation of stored RBCs by targeting functional thiol residues of GAPDH. Progressive increases in PPP/glycolysis ratios were determined via metabolic flux analysis after spiking (13)C1,2,3-glucose in erythrocyte concentrates stored in Additive Solution-3 under blood bank conditions for up to 42 days. Proteomics analyses revealed a storage-dependent oxidation of GAPDH at functional Cys152, 156, 247, and His179. Activity loss by oxidation occurred with increasing storage duration and was progressively irreversible. Irreversibly oxidized GAPDH accumulated in stored erythrocyte membranes and supernatants through storage day 42. By combining state-of-the-art ultra-high-pressure liquid chromatography-mass spectrometry metabolic flux analysis with redox and switch-tag proteomics, we identify for the first time ex vivo functionally relevant reversible and irreversible (sulfinic acid; Cys to dehydroalanine) oxidations of GAPDH without exogenous supplementation of excess pro-oxidant compounds in clinically relevant blood products. Oxidative and metabolic lesions, exacerbated by storage under hyperoxic conditions, were ameliorated by hypoxic storage. Storage-dependent reversible oxidation of GAPDH represents a mechanistic adaptation in stored erythrocytes to promote PPP activation and generate reducing equivalents. Removal of irreversibly oxidized, functionally compromised GAPDH identifies enhanced vesiculation as a self-protective mechanism in ex vivo aging erythrocytes.
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25
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Bayer T, Milker S, Wiesinger T, Rudroff F, Mihovilovic MD. Designer Microorganisms for Optimized Redox Cascade Reactions - Challenges and Future Perspectives. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500202] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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26
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Ravikrishnan A, Raman K. Critical assessment of genome-scale metabolic networks: the need for a unified standard. Brief Bioinform 2015; 16:1057-68. [PMID: 25725218 DOI: 10.1093/bib/bbv003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Indexed: 12/17/2022] Open
Abstract
Genome-scale metabolic networks have been reconstructed for several organisms. These metabolic networks provide detailed information about the metabolism inside the cells, coupled with the genomic, proteomic and thermodynamic information. These networks are widely simulated using 'constraint-based' modelling techniques and find applications ranging from strain improvement for metabolic engineering to prediction of drug targets in pathogenic organisms. Components of these metabolic networks are represented in multiple file formats and also using different markup languages, with varying levels of annotations; this leads to inconsistencies and increases the complexities in comparing and analysing reconstructions on multiple platforms. In this work, we critically examine nearly 100 published genome-scale metabolic networks and their corresponding constraint-based models and discuss various issues with respect to model quality. One of the major concerns is the lack of annotations using standard identifiers that can uniquely describe several components such as metabolites, genes, proteins and reactions. We also find that many models do not have complete information regarding constraints on reactions fluxes and objective functions for carrying out simulations. Overall, our analysis highlights the need for a widely acceptable standard for representing constraint-based models. A rigorous standard can help in streamlining the process of reconstruction and improve the quality of reconstructed metabolic models.
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27
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Hartmann A, Schreiber F. Integrative analysis of metabolic models - from structure to dynamics. Front Bioeng Biotechnol 2015; 2:91. [PMID: 25674560 PMCID: PMC4306315 DOI: 10.3389/fbioe.2014.00091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/30/2014] [Indexed: 01/09/2023] Open
Abstract
The characterization of biological systems with respect to their behavior and functionality based on versatile biochemical interactions is a major challenge. To understand these complex mechanisms at systems level modeling approaches are investigated. Different modeling formalisms allow metabolic models to be analyzed depending on the question to be solved, the biochemical knowledge and the availability of experimental data. Here, we describe a method for an integrative analysis of the structure and dynamics represented by qualitative and quantitative metabolic models. Using various formalisms, the metabolic model is analyzed from different perspectives. Determined structural and dynamic properties are visualized in the context of the metabolic model. Interaction techniques allow the exploration and visual analysis thereby leading to a broader understanding of the behavior and functionality of the underlying biological system. The System Biology Metabolic Model Framework (SBM (2) - Framework) implements the developed method and, as an example, is applied for the integrative analysis of the crop plant potato.
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Affiliation(s)
- Anja Hartmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Falk Schreiber
- Monash University, Melbourne, VIC, Australia
- Martin-Luther-University Halle-Wittenberg, Halle, Germany
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28
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Abstract
Bacterial metabolism is an important source of novel products/processes for everyday life and strong efforts are being undertaken to discover and exploit new usable substances of microbial origin. Computational modeling and in silico simulations are powerful tools in this context since they allow the exploration and a deeper understanding of bacterial metabolic circuits. Many approaches exist to quantitatively simulate chemical reaction fluxes within the whole microbial metabolism and, regardless of the technique of choice, metabolic model reconstruction is the first step in every modeling pipeline. Reconstructing a metabolic network consists in drafting the list of the biochemical reactions that an organism can carry out together with information on cellular boundaries, a biomass assembly reaction, and exchange fluxes with the external environment. Building up models able to represent the different functional cellular states is universally recognized as a tricky task that requires intensive manual effort and much additional information besides genome sequence. In this chapter we present a general protocol for metabolic reconstruction in bacteria and the main challenges encountered during this process.
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Affiliation(s)
- Marco Fondi
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence, Italy,
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29
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Dräger A, Palsson BØ. Improving collaboration by standardization efforts in systems biology. Front Bioeng Biotechnol 2014; 2:61. [PMID: 25538939 PMCID: PMC4259112 DOI: 10.3389/fbioe.2014.00061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/14/2014] [Indexed: 11/17/2022] Open
Abstract
Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology.
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Affiliation(s)
- Andreas Dräger
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Cognitive Systems, Center for Bioinformatics Tübingen (ZBIT), Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Bernhard Ø. Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
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30
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Narang P, Khan S, Hemrom AJ, Lynn AM. MetaNET--a web-accessible interactive platform for biological metabolic network analysis. BMC SYSTEMS BIOLOGY 2014; 8:130. [PMID: 25779921 PMCID: PMC4267457 DOI: 10.1186/s12918-014-0130-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022]
Abstract
Background Metabolic reactions have been extensively studied and compiled over the last century. These have provided a theoretical base to implement models, simulations of which are used to identify drug targets and optimize metabolic throughput at a systemic level. While tools for the perturbation of metabolic networks are available, their applications are limited and restricted as they require varied dependencies and often a commercial platform for full functionality. We have developed MetaNET, an open source user-friendly platform-independent and web-accessible resource consisting of several pre-defined workflows for metabolic network analysis. Result MetaNET is a web-accessible platform that incorporates a range of functions which can be combined to produce different simulations related to metabolic networks. These include (i) optimization of an objective function for wild type strain, gene/catalyst/reaction knock-out/knock-down analysis using flux balance analysis. (ii) flux variability analysis (iii) chemical species participation (iv) cycles and extreme paths identification and (v) choke point reaction analysis to facilitate identification of potential drug targets. The platform is built using custom scripts along with the open-source Galaxy workflow and Systems Biology Research Tool as components. Pre-defined workflows are available for common processes, and an exhaustive list of over 50 functions are provided for user defined workflows. Conclusion MetaNET, available at http://metanet.osdd.net, provides a user-friendly rich interface allowing the analysis of genome-scale metabolic networks under various genetic and environmental conditions. The framework permits the storage of previous results, the ability to repeat analysis and share results with other users over the internet as well as run different tools simultaneously using pre-defined workflows, and user-created custom workflows.
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Affiliation(s)
- Pankaj Narang
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India,
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31
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Weaver DS, Keseler IM, Mackie A, Paulsen IT, Karp PD. A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC SYSTEMS BIOLOGY 2014; 8:79. [PMID: 24974895 PMCID: PMC4086706 DOI: 10.1186/1752-0509-8-79] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 06/19/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND Constraint-based models of Escherichia coli metabolic flux have played a key role in computational studies of cellular metabolism at the genome scale. We sought to develop a next-generation constraint-based E. coli model that achieved improved phenotypic prediction accuracy while being frequently updated and easy to use. We also sought to compare model predictions with experimental data to highlight open questions in E. coli biology. RESULTS We present EcoCyc-18.0-GEM, a genome-scale model of the E. coli K-12 MG1655 metabolic network. The model is automatically generated from the current state of EcoCyc using the MetaFlux software, enabling the release of multiple model updates per year. EcoCyc-18.0-GEM encompasses 1445 genes, 2286 unique metabolic reactions, and 1453 unique metabolites. We demonstrate a three-part validation of the model that breaks new ground in breadth and accuracy: (i) Comparison of simulated growth in aerobic and anaerobic glucose culture with experimental results from chemostat culture and simulation results from the E. coli modeling literature. (ii) Essentiality prediction for the 1445 genes represented in the model, in which EcoCyc-18.0-GEM achieves an improved accuracy of 95.2% in predicting the growth phenotype of experimental gene knockouts. (iii) Nutrient utilization predictions under 431 different media conditions, for which the model achieves an overall accuracy of 80.7%. The model's derivation from EcoCyc enables query and visualization via the EcoCyc website, facilitating model reuse and validation by inspection. We present an extensive investigation of disagreements between EcoCyc-18.0-GEM predictions and experimental data to highlight areas of interest to E. coli modelers and experimentalists, including 70 incorrect predictions of gene essentiality on glucose, 80 incorrect predictions of gene essentiality on glycerol, and 83 incorrect predictions of nutrient utilization. CONCLUSION Significant advantages can be derived from the combination of model organism databases and flux balance modeling represented by MetaFlux. Interpretation of the EcoCyc database as a flux balance model results in a highly accurate metabolic model and provides a rigorous consistency check for information stored in the database.
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Affiliation(s)
- Daniel S Weaver
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave., 94025 Menlo Park, CA, USA
| | - Ingrid M Keseler
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave., 94025 Menlo Park, CA, USA
| | - Amanda Mackie
- Department of Chemistry and Biomolecular Science, Macquarie University, Balaclava Rd, North Ryde NSW 2109, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Science, Macquarie University, Balaclava Rd, North Ryde NSW 2109, Australia
| | - Peter D Karp
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave., 94025 Menlo Park, CA, USA
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32
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Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon JL. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res 2014; 42:W389-94. [PMID: 24792156 PMCID: PMC4086079 DOI: 10.1093/nar/gku362] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As metabolic engineering and synthetic biology progress toward reaching the goal of a more sustainable use of biological resources, the need of increasing the number of value-added chemicals that can be produced in industrial organisms becomes more imperative. Exploring, however, the vast possibility of pathways amenable to engineering through heterologous genes expression in a chassis organism is complex and unattainable manually. Here, we present XTMS, a web-based pathway analysis platform available at http://xtms.issb.genopole.fr, which provides full access to the set of pathways that can be imported into a chassis organism such as Escherichia coli through the application of an Extended Metabolic Space modeling framework. The XTMS approach consists on determining the set of biochemical transformations that can potentially be processed in vivo as modeled by molecular signatures, a specific coding system for derivation of reaction rules for metabolic reactions and enumeration of all the corresponding substrates and products. Most promising routes are described in terms of metabolite exchange, maximum allowable pathway yield, toxicity and enzyme efficiency. By answering such critical design points, XTMS not only paves the road toward the rationalization of metabolic engineering, but also opens new processing possibilities for non-natural metabolites and novel enzymatic transformations.
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Affiliation(s)
- Pablo Carbonell
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
| | - Pierre Parutto
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
| | - Joan Herisson
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
| | | | - Jean-Loup Faulon
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
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Fernández-Castané A, Fehér T, Carbonell P, Pauthenier C, Faulon JL. Computer-aided design for metabolic engineering. J Biotechnol 2014; 192 Pt B:302-13. [PMID: 24704607 DOI: 10.1016/j.jbiotec.2014.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 03/18/2014] [Accepted: 03/24/2014] [Indexed: 12/20/2022]
Abstract
The development and application of biotechnology-based strategies has had a great socio-economical impact and is likely to play a crucial role in the foundation of more sustainable and efficient industrial processes. Within biotechnology, metabolic engineering aims at the directed improvement of cellular properties, often with the goal of synthesizing a target chemical compound. The use of computer-aided design (CAD) tools, along with the continuously emerging advanced genetic engineering techniques have allowed metabolic engineering to broaden and streamline the process of heterologous compound-production. In this work, we review the CAD tools available for metabolic engineering with an emphasis, on retrosynthesis methodologies. Recent advances in genetic engineering strategies for pathway implementation and optimization are also reviewed as well as a range of bionalytical tools to validate in silico predictions. A case study applying retrosynthesis is presented as an experimental verification of the output from Retropath, the first complete automated computational pipeline applicable to metabolic engineering. Applying this CAD pipeline, together with genetic reassembly and optimization of culture conditions led to improved production of the plant flavonoid pinocembrin. Coupling CAD tools with advanced genetic engineering strategies and bioprocess optimization is crucial for enhanced product yields and will be of great value for the development of non-natural products through sustainable biotechnological processes.
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Affiliation(s)
- Alfred Fernández-Castané
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
| | - Tamás Fehér
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
| | - Pablo Carbonell
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
| | - Cyrille Pauthenier
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
| | - Jean-Loup Faulon
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
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Ahmed Z, Zeeshan S, Dandekar T. Developing sustainable software solutions for bioinformatics by the " Butterfly" paradigm. F1000Res 2014; 3:71. [PMID: 25383181 PMCID: PMC4215756 DOI: 10.12688/f1000research.3681.2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/01/2014] [Indexed: 11/29/2022] Open
Abstract
Software design and sustainable software engineering are essential for the long-term development of bioinformatics software. Typical challenges in an academic environment are short-term contracts, island solutions, pragmatic approaches and loose documentation. Upcoming new challenges are big data, complex data sets, software compatibility and rapid changes in data representation. Our approach to cope with these challenges consists of iterative intertwined cycles of development (“
Butterfly” paradigm) for key steps in scientific software engineering. User feedback is valued as well as software planning in a sustainable and interoperable way. Tool usage should be easy and intuitive. A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently. We validated the approach of our own software development and compared the different design paradigms in various software solutions.
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Affiliation(s)
- Zeeshan Ahmed
- Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Wuerzburg, 97074, Germany ; Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, 97074, Germany
| | - Saman Zeeshan
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, 97074, Germany
| | - Thomas Dandekar
- EMBL, Structural and Computational Biology Unit, Heidelberg, 69117, Germany
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Gelius-Dietrich G, Desouki AA, Fritzemeier CJ, Lercher MJ. Sybil--efficient constraint-based modelling in R. BMC SYSTEMS BIOLOGY 2013; 7:125. [PMID: 24224957 PMCID: PMC3843580 DOI: 10.1186/1752-0509-7-125] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 11/01/2013] [Indexed: 12/17/2022]
Abstract
Background Constraint-based analyses of metabolic networks are widely used to simulate the properties of genome-scale metabolic networks. Publicly available implementations tend to be slow, impeding large scale analyses such as the genome-wide computation of pairwise gene knock-outs, or the automated search for model improvements. Furthermore, available implementations cannot easily be extended or adapted by users. Results Here, we present sybil, an open source software library for constraint-based analyses in R; R is a free, platform-independent environment for statistical computing and graphics that is widely used in bioinformatics. Among other functions, sybil currently provides efficient methods for flux-balance analysis (FBA), MOMA, and ROOM that are about ten times faster than previous implementations when calculating the effect of whole-genome single gene deletions in silico on a complete E. coli metabolic model. Conclusions Due to the object-oriented architecture of sybil, users can easily build analysis pipelines in R or even implement their own constraint-based algorithms. Based on its highly efficient communication with different mathematical optimisation programs, sybil facilitates the exploration of high-dimensional optimisation problems on small time scales. Sybil and all its dependencies are open source. Sybil and its documentation are available for download from the comprehensive R archive network (CRAN).
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Affiliation(s)
| | | | | | - Martin J Lercher
- Institute for Computer Science, Heinrich-Heine-University, Universitätsstr 1, 40225 Düsseldorf, Germany.
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Sims JK, Manteiga S, Lee K. Towards high resolution analysis of metabolic flux in cells and tissues. Curr Opin Biotechnol 2013; 24:933-9. [PMID: 23906926 DOI: 10.1016/j.copbio.2013.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/05/2013] [Indexed: 12/22/2022]
Abstract
Metabolism extracts chemical energy from nutrients, uses this energy to form building blocks for biosynthesis, and interconverts between various small molecules that coordinate the activities of cellular pathways. The metabolic state of a cell is increasingly recognized to determine the phenotype of not only metabolically active cell types such as liver, muscle, and adipose, but also other specialized cell types such as neurons and immune cells. This review focuses on methods to quantify intracellular reaction flux as a measure of cellular metabolic activity, with emphasis on studies involving cells of mammalian tissue. Two key areas are highlighted for future development, single cell metabolomics and noninvasive imaging, which could enable spatiotemporally resolved analysis and thereby overcome issues of heterogeneity, a distinctive feature of tissue metabolism.
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Affiliation(s)
- James K Sims
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States
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Ahmed Z, Zeeshan S, Huber C, Hensel M, Schomburg D, Münch R, Eisenreich W, Dandekar T. Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling. BMC Bioinformatics 2013; 14:218. [PMID: 23837681 PMCID: PMC3720290 DOI: 10.1186/1471-2105-14-218] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 06/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution. RESULTS The open-source software "Least Square Mass Isotopomer Analyzer" (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman's least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed. CONCLUSIONS The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.
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Affiliation(s)
- Zeeshan Ahmed
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Department of Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Saman Zeeshan
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hanover, Germany
| | - Claudia Huber
- Lehrstuhl für Biochemie, Technische Universität München, München, Germany
| | - Michael Hensel
- Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technical University Braunschweig, Braunschweig, Germany
| | - Richard Münch
- Institute for Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | | | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- EMBL, Structural and Computational Biology Unit, Heidelberg, Germany
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