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genome scale metabolic modeling

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https://www.readbyqxmd.com/read/28092686/epigenomic-reprogramming-during-pancreatic-cancer-progression-links-anabolic-glucose-metabolism-to-distant-metastasis
#1
Oliver G McDonald, Xin Li, Tyler Saunders, Rakel Tryggvadottir, Samantha J Mentch, Marc O Warmoes, Anna E Word, Alessandro Carrer, Tal H Salz, Sonoko Natsume, Kimberly M Stauffer, Alvin Makohon-Moore, Yi Zhong, Hao Wu, Kathryn E Wellen, Jason W Locasale, Christine A Iacobuzio-Donahue, Andrew P Feinberg
During the progression of pancreatic ductal adenocarcinoma (PDAC), heterogeneous subclonal populations emerge that drive primary tumor growth, regional spread, distant metastasis, and patient death. However, the genetics of metastases largely reflects that of the primary tumor in untreated patients, and PDAC driver mutations are shared by all subclones. This raises the possibility that an epigenetic process might operate during metastasis. Here we report large-scale reprogramming of chromatin modifications during the natural evolution of distant metastasis...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28088694/metabolic-network-modeling-with-model-organisms
#2
REVIEW
L Safak Yilmaz, Albertha Jm Walhout
Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases...
January 12, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28072816/systematic-analysis-of-transcriptional-and-post-transcriptional-regulation-of-metabolism-in-yeast
#3
Emanuel Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrao, Julio Saez-Rodriguez
Cells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data. Here we acquired time-resolved metabolomics measurements in yeast under salt and pheromone stimulation and developed a machine learning approach to explore regulatory associations between metabolism and signal transduction. Existing phosphoproteomics measurements under the same conditions and kinase-substrate regulatory interactions were used to in silico estimate the enzymatic activity of signalling kinases...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28065897/trfba-an-algorithm-to-integrate-genome-scale-metabolic-and-transcriptional-regulatory-networks-with-incorporation-of-expression-data
#4
Ehsan Motamedian, Maryam Mohammadi, Seyed Abbas Shojaosadati, Mona Heydari
MOTIVATION: Integration of different biological networks and data-types has been a major challenge in systems biology. The present study introduces the transcriptional regulated flux balance analysis (TRFBA) algorithm that integrates transcriptional regulatory and metabolic models using a set of expression data for various perturbations. RESULTS: TRFBA considers the expression levels of genes as a new continuous variable and introduces two new linear constraints...
January 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28062460/large-scale-transposition-mutagenesis-of-streptomyces-coelicolor-identifies-hundreds-of-genes-influencing-antibiotic-biosynthesis
#5
Zhong Xu, Yemin Wang, Keith F Chater, Hong-Yu Ou, H Howard Xu, Zixin Deng, Meifeng Tao
: Gram-positive Streptomyces bacteria produce thousands of bioactive secondary metabolites including antibiotics. To systematically investigate genes affecting secondary metabolism, we developed a hyperactive transposase-based Tn5 transposition system and employed it to mutagenize the model species Streptomyces coelicolor, leading to the identification of 51,443 transposition insertions. These insertions were distributed randomly along the chromosome except for some preferred regions associated with relatively low GC content in the chromosomal core...
January 6, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28049424/a-mixed-integer-linear-programming-approach-to-the-reduction-of-genome-scale-metabolic-networks
#6
Annika Röhl, Alexander Bockmayr
BACKGROUND: Constraint-based analysis has become a widely used method to study metabolic networks. While some of the associated algorithms can be applied to genome-scale network reconstructions with several thousands of reactions, others are limited to small or medium-sized models. In 2015, Erdrich et al. introduced a method called NetworkReducer, which reduces large metabolic networks to smaller subnetworks, while preserving a set of biological requirements that can be specified by the user...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28045126/ecolicore2-a-reference-network-model-of-the-central-metabolism-of-escherichia-coli-and-relationships-to-its-genome-scale-parent-model
#7
Oliver Hädicke, Steffen Klamt
Genome-scale metabolic modeling has become an invaluable tool to analyze properties and capabilities of metabolic networks and has been particularly successful for the model organism Escherichia coli. However, for several applications, smaller metabolic (core) models are needed. Using a recently introduced reduction algorithm and the latest E. coli genome-scale reconstruction iJO1366, we derived EColiCore2, a model of the central metabolism of E. coli. EColiCore2 is a subnetwork of iJO1366 and preserves predefined phenotypes including optimal growth on different substrates...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043922/reconstruction-of-a-genome-scale-metabolic-model-and-in-silico-analysis-of-the-polymalic-acid-producer-aureobasidium-pullulans-cctcc-m2012223
#8
Jun Feng, Jing Yang, Xiaorong Li, Meijin Guo, Bochu Wang, Shang-Tian Yang, Xiang Zou
Aureobasidium pullulans is a yeast-like fungus used for producing biopolymers e.g. polymalic acid (PMA) and pullulan. A high PMA producing strain, A. pullulans CCTCC M2012223, was isolated and sequenced in our previous study. To understand its metabolic performance, a genome-scale metabolic model, iZX637, consisting of 637 genes, 1347 reactions and 1133 metabolites, was reconstructed based on genome annotation and literature mining studies. The iZX637 model was validated by simulating cell growth, utilization of carbon and nitrogen sources, and gene essentiality analysis in A...
December 30, 2016: Gene
https://www.readbyqxmd.com/read/28035338/human-gut-microbiota-and-healthy-aging-recent-developments-and-future-prospective
#9
REVIEW
Manish Kumar, Parizad Babaei, Boyang Ji, Jens Nielsen
The human gut microbiota alters with the aging process. In the first 2-3 years of life, the gut microbiota varies extensively in composition and metabolic functions. After this period, the gut microbiota demonstrates adult-like more stable and diverse microbial species. However, at old age, deterioration of physiological functions of the human body enforces the decrement in count of beneficial species (e.g. Bifidobacteria) in the gut microbiota, which promotes various gut-related diseases (e.g. inflammatory bowel disease)...
October 27, 2016: Nutr Healthy Aging
https://www.readbyqxmd.com/read/28032403/a-unique-large-scale-undergraduate-research-experience-in-molecular-systems-biology-for-non-mathematics-majors
#10
Ulrike Kappler, Susan L Rowland, Rhianna K Pedwell
Systems biology is frequently taught with an emphasis on mathematical modeling approaches. This focus effectively excludes most biology, biochemistry, and molecular biology students, who are not mathematics majors. The mathematical focus can also present a misleading picture of systems biology, which is a multi-disciplinary pursuit requiring collaboration between biochemists, bioinformaticians, and mathematicians. This article describes an authentic large-scale undergraduate research experience (ALURE) in systems biology that incorporates proteomics, bacterial genomics, and bioinformatics in the one exercise...
December 28, 2016: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28028815/metabolic-systems-biology-a-brief-primer
#11
REVIEW
Lindsay M Edwards
In the early to mid 20(th) Century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig Von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome...
December 28, 2016: Journal of Physiology
https://www.readbyqxmd.com/read/28025204/novel-probabilistic-models-of-spatial-genetic-ancestry-with-applications-to-stratification-correction-in-genome-wide-association-studies
#12
Anand Bhaskar, Adel Javanmard, Thomas A Courtade, David Tse
MOTIVATION: Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure...
December 25, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28012908/flux-balance-analysis-of-photoautotrophic-metabolism-uncovering-new-biological-details-of-subsystems-involved-in-cyanobacterial-photosynthesis
#13
Xiao Qian, Min Kyung Kim, G Kenchappa Kumaraswamy, Ananya Agarwal, Desmond S Lun, G Charles Dismukes
We have constructed and experimentally tested a comprehensive genome-scale model of photoautotrophic growth, denoted iSyp821, for the cyanobacterium Synechococcus sp. PCC 7002. iSyp821 incorporates a variable biomass objective function (vBOF), in which stoichiometries of the major biomass components vary according to light intensity. The vBOF was constrained to fit the measured cellular carbohydrate/protein content under different light intensities. iSyp821 provides rigorous agreement with experimentally measured cell growth rates and inorganic carbon uptake rates as a function of light intensity...
December 21, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27996047/a-genome-scale-escherichia-coli-kinetic-metabolic-model-k-ecoli457-satisfying-flux-data-for-multiple-mutant-strains
#14
Ali Khodayari, Costas D Maranas
Kinetic models of metabolism at a genome scale that faithfully recapitulate the effect of multiple genetic interventions would be transformative in our ability to reliably design novel overproducing microbial strains. Here, we introduce k-ecoli457, a genome-scale kinetic model of Escherichia coli metabolism that satisfies fluxomic data for wild-type and 25 mutant strains under different substrates and growth conditions. The k-ecoli457 model contains 457 model reactions, 337 metabolites and 295 substrate-level regulatory interactions...
December 20, 2016: Nature Communications
https://www.readbyqxmd.com/read/27993779/recon2neo4j-applying-graph-database-technologies-for-managing-comprehensive-genome-scale-networks
#15
Irina Balaur, Alexander Mazein, Mansoor Saqi, Artem Lysenko, Christopher J Rawlings, Charles Auffray
: The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest...
December 19, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27992644/a-genome-scale-modeling-approach-to-quantify-biofilm-component-growth-of-salmonella-typhimurium
#16
Nicholas Ribaudo, Xianhua Li, Brett Davis, Thomas K Wood, Zuyi Jacky Huang
Salmonella typhimurium (S. typhimurium) is an extremely dangerous foodborne bacterium that infects both animal and human subjects, causing fatal diseases around the world. Salmonella's robust virulence, antibiotic-resistant nature, and capacity to survive under harsh conditions are largely due to its ability to form resilient biofilms. Multiple genome-scale metabolic models have been developed to study the complex and diverse nature of this organism's metabolism; however, none of these models fully integrated the reactions and mechanisms required to study the influence of biofilm formation...
January 2017: Journal of Food Science
https://www.readbyqxmd.com/read/27987175/pathway-analysis-and-omics-data-visualization-using-pathway-genome-databases-fragariacyc-a-case-study
#17
Sushma Naithani, Pankaj Jaiswal
The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to various extrinsic (e.g. developmental and differentiation) and/or extrinsic signals (e.g. pathogens and abiotic stresses) from the surrounding environment. Using FragariaCyc, a pathway database for the diploid strawberry Fragaria vesca, we show (1) the basic navigation across a PGDB; (2) a case study of pathway comparison across plant species; and (3) an example of RNA-Seq data analysis using Omics Viewer tool...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27986597/literature-mining-supports-a-next-generation-modeling-approach-to-predict-cellular-byproduct-secretion
#18
Zachary A King, Edward J O'Brien, Adam M Feist, Bernhard O Palsson
The metabolic byproducts secreted by growing cells can be easily measured and provide a window into the state of a cell; they have been essential to the development of microbiology, cancer biology, and biotechnology. Progress in computational modeling of cells has made it possible to predict metabolic byproduct secretion with bottom-up reconstructions of metabolic networks. However, owing to a lack of data, it has not been possible to validate these predictions across a wide range of strains and conditions...
January 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/27973705/metabolic-engineering-of-mannheimia-succiniciproducens-for-succinic-acid-production-based-on-elementary-mode-analysis-with-clustering
#19
Won Jun Kim, Jung Ho Ahn, Hyun Uk Kim, Tae Yong Kim, Sang Yup Lee
Mannheimia succiniciproducens, a capnophilic gram-negative rumen bacterium, has been employed for the efficient production of succinic acid. Although M. succiniciproducens metabolism was previously studied using a genome-scale metabolic model, more metabolic characteristics are to be understood. To this end, we used elementary mode analysis accompanied with clustering ('EMC' analysis) to gain further insights on metabolic characteristics of M. succiniciproducens allowing efficient succinic acid production. Elementary modes (EMs) generated from the central carbon metabolic network of M...
December 14, 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27965696/modeling-rice-metabolism-from-elucidating-environmental-effects-on-cellular-phenotype-to-guiding-crop-improvement
#20
REVIEW
Meiyappan Lakshmanan, C Y Maurice Cheung, Bijayalaxmi Mohanty, Dong-Yup Lee
Crop productivity is severely limited by various biotic and abiotic stresses. Thus, it is highly needed to understand the underlying mechanisms of environmental stress response and tolerance in plants, which could be addressed by systems biology approach. To this end, high-throughput omics profiling and in silico modeling can be considered to explore the environmental effects on phenotypic states and metabolic behaviors of rice crops at the systems level. Especially, the advent of constraint-based metabolic reconstruction and analysis paves a way to characterize the plant cellular physiology under various stresses by combining the mathematical network models with multi-omics data...
2016: Frontiers in Plant Science
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