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genome scale metabolic modeling

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https://www.readbyqxmd.com/read/29160039/fine-tuning-the-p-pastoris-imt1026-genome-scale-metabolic-model-for-improved-prediction-of-growth-on-methanol-or-glycerol-as-sole-carbon-sources
#1
Màrius Tomàs-Gamisans, Pau Ferrer, Joan Albiol
The methylotrophic yeast Pichia pastoris (Komagataella spp.) is widely used as cell factory for recombinant protein production. In the past recent years, important breakthroughs in the systems-level quantitative analysis of its physiology have been achieved. This wealth of information has allowed the development of genome-scale metabolic models, which make new approaches possible for host cell and bioprocess engineering. Nevertheless, the predictive accuracy of the previous consensus model required to be upgraded and validated with new experimental data sets for P...
November 21, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/29157227/metabolic-adaptation-of-two-in-silico-mutants-of-mycobacterium-tuberculosis-during-infection
#2
Víctor A López-Agudelo, Andres Baena, Howard Ramirez-Malule, Silvia Ochoa, Luis F Barrera, Rigoberto Ríos-Estepa
BACKGROUND: Up to date, Mycobacterium tuberculosis (Mtb) remains as the worst intracellular killer pathogen. To establish infection, inside the granuloma, Mtb reprograms its metabolism to support both growth and survival, keeping a balance between catabolism, anabolism and energy supply. Mtb knockouts with the faculty of being essential on a wide range of nutritional conditions are deemed as target candidates for tuberculosis (TB) treatment. Constraint-based genome-scale modeling is considered as a promising tool for evaluating genetic and nutritional perturbations on Mtb metabolic reprogramming...
November 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29151887/an-accurate-description-of-aspergillus-niger-organic-acid-batch-fermentation-through-dynamic-metabolic-modelling
#3
Daniel J Upton, Simon J McQueen-Mason, A Jamie Wood
Background: Aspergillus niger fermentation has provided the chief source of industrial citric acid for over 50 years. Traditional strain development of this organism was achieved through random mutagenesis, but advances in genomics have enabled the development of genome-scale metabolic modelling that can be used to make predictive improvements in fermentation performance. The parent citric acid-producing strain of A. niger, ATCC 1015, has been described previously by a genome-scale metabolic model that encapsulates its response to ambient pH...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29147021/genome-scale-modeling-and-transcriptome-analysis-of-leuconostoc-mesenteroides-unravel-the-redox-governed-metabolic-states-in-obligate-heterofermentative-lactic-acid-bacteria
#4
Lokanand Koduru, Yujin Kim, Jeongsu Bang, Meiyappan Lakshmanan, Nam Soo Han, Dong-Yup Lee
Obligate heterofermentative lactic acid bacteria (LAB) are well-known for their beneficial health effects in humans. To delineate the incompletely characterized metabolism that currently limits their exploitation, at systems-level, we developed a genome-scale metabolic model of the representative obligate heterofermenting LAB, Leuconostoc mesenteroides (iLME620). Constraint-based flux analysis was then used to simulate several qualitative and quantitative phenotypes of L. mesenteroides, thereby evaluating the model validity...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146901/genome-driven-evolutionary-game-theory-helps-understand-the-rise-of-metabolic-interdependencies-in-microbial-communities
#5
Ali R Zomorrodi, Daniel Segrè
Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29134060/modelling-pyruvate-dehydrogenase-under-hypoxia-and-its-role-in-cancer-metabolism
#6
Filmon Eyassu, Claudio Angione
Metabolism is the only biological system that can be fully modelled at genome scale. As a result, metabolic models have been increasingly used to study the molecular mechanisms of various diseases. Hypoxia, a low-oxygen tension, is a well-known characteristic of many cancer cells. Pyruvate dehydrogenase (PDH) controls the flux of metabolites between glycolysis and the tricarboxylic acid cycle and is a key enzyme in metabolic reprogramming in cancer metabolism. Here, we develop and manually curate a constraint-based metabolic model to investigate the mechanism of pyruvate dehydrogenase under hypoxia...
October 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/29131817/characterizing-steady-states-of-genome-scale-metabolic-networks-in-continuous-cell-cultures
#7
Jorge Fernandez-de-Cossio-Diaz, Kalet Leon, Roberto Mulet
In the continuous mode of cell culture, a constant flow carrying fresh media replaces culture fluid, cells, nutrients and secreted metabolites. Here we present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct accumulation. We provide a method to determine the steady states of this system that is tractable for metabolic networks of arbitrary complexity...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29123506/challenges-and-advances-for-genetic-engineering-of-non-model-bacteria-and-uses-in-consolidated-bioprocessing
#8
REVIEW
Qiang Yan, Stephen S Fong
Metabolic diversity in microorganisms can provide the basis for creating novel biochemical products. However, most metabolic engineering projects utilize a handful of established model organisms and thus, a challenge for harnessing the potential of novel microbial functions is the ability to either heterologously express novel genes or directly utilize non-model organisms. Genetic manipulation of non-model microorganisms is still challenging due to organism-specific nuances that hinder universal molecular genetic tools and translatable knowledge of intracellular biochemical pathways and regulatory mechanisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29113935/predicting-age-by-mining-electronic-medical-records-with-deep-learning-characterizes-differences-between-chronological-and-physiological-age
#9
Zichen Wang, Li Li, Benjamin S Glicksberg, Ariel Israel, Joel T Dudley, Avi Ma'ayan
Determining the discrepancy between chronological and physiological age of patients is central to preventative and personalized care. Electronic medical records (EMR) provide rich information about the patient physiological state, but it is unclear whether such information can be predictive of chronological age. Here we present a deep learning model the uses vital signs and lab tests contained within the EMR of Mount Sinai Health System (MSHS) to predict chronological age. The model is trained on 377,686 EMR from patients of ages 18-85 years old...
November 4, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29105249/mimicking-microbial-interactions-under-nitrate-reducing-conditions-in-an-anoxic-bioreactor-enrichment-of-novel-nitrospirae-bacteria-distantly-related-to-thermodesulfovibrio
#10
Arslan Arshad, Paula Dalcin Martins, Jeroen Frank, Mike S M Jetten, Huub J M Op den Camp, Cornelia U Welte
Microorganisms are main drivers of the sulfur, nitrogen and carbon biogeochemical cycles. These element cycles are interconnected by the activity of different guilds in e.g. sediments or wastewater treatment systems. Here, we investigated a nitrate-reducing microbial community in a laboratory-scale bioreactor model that closely mimicked estuary or brackish sediment conditions. The bioreactor simultaneously consumed sulfide, methane and ammonium at the expense of nitrate. Ammonium oxidation occurred solely by the activity of anammox bacteria identified as Candidatus Scalindua brodae and Ca...
November 3, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29089935/design-optimization-and-application-of-small-molecule-biosensor-in-metabolic-engineering
#11
REVIEW
Yang Liu, Ye Liu, Meng Wang
The development of synthetic biology and metabolic engineering has painted a great future for the bio-based economy, including fuels, chemicals, and drugs produced from renewable feedstocks. With the rapid advance of genome-scale modeling, pathway assembling and genome engineering/editing, our ability to design and generate microbial cell factories with various phenotype becomes almost limitless. However, our lack of ability to measure and exert precise control over metabolite concentration related phenotypes becomes a bottleneck in metabolic engineering...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29078384/framework-and-resource-for-more-than-11-000-gene-transcript-protein-reaction-associations-in-human-metabolism
#12
Jae Yong Ryu, Hyun Uk Kim, Sang Yup Lee
Alternative splicing plays important roles in generating different transcripts from one gene, and consequently various protein isoforms. However, there has been no systematic approach that facilitates characterizing functional roles of protein isoforms in the context of the entire human metabolism. Here, we present a systematic framework for the generation of gene-transcript-protein-reaction associations (GeTPRA) in the human metabolism. The framework in this study generated 11,415 GeTPRA corresponding to 1,106 metabolic genes for both principal and nonprincipal transcripts (PTs and NPTs) of metabolic genes...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29069611/metabolic-modeling-helps-interpret-transcriptomic-changes-during-malaria
#13
Yan Tang, Anuj Gupta, Swetha Garimalla, Mary R Galinski, Mark P Styczynski, Luis L Fonseca, Eberhard O Voit
Disease represents a specific case of malfunctioning within a complex system. Whereas it is often feasible to observe and possibly treat the symptoms of a disease, it is much more challenging to identify and characterize its molecular root causes. Even in infectious diseases that are caused by a known parasite, it is often impossible to pinpoint exactly which molecular profiles of components or processes are directly or indirectly altered. However, a deep understanding of such profiles is a prerequisite for rational, efficacious treatments...
October 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29062956/development-of-fungal-cell-factories-for-the-production-of-secondary-metabolites-linking-genomics-and-metabolism
#14
REVIEW
Jens Christian Nielsen, Jens Nielsen
The genomic era has revolutionized research on secondary metabolites and bioinformatics methods have in recent years revived the antibiotic discovery process after decades with only few new active molecules being identified. New computational tools are driven by genomics and metabolomics analysis, and enables rapid identification of novel secondary metabolites. To translate this increased discovery rate into industrial exploitation, it is necessary to integrate secondary metabolite pathways in the metabolic engineering process...
March 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29059321/confronting-the-catalytic-dark-matter-encoded-by-sequenced-genomes
#15
Kenneth W Ellens, Nils Christian, Charandeep Singh, Venkata P Satagopam, Patrick May, Carole L Linster
The post-genomic era has provided researchers with a deluge of protein sequences. However, a significant fraction of the proteins encoded by sequenced genomes remains without an identified function. Here, we aim at determining how many enzymes of uncertain or unknown function are still present in the Saccharomyces cerevisiae and human proteomes. Using information available in the Swiss-Prot, BRENDA and KEGG databases in combination with a Hidden Markov Model-based method, we estimate that >600 yeast and 2000 human proteins (>30% of their proteins of unknown function) are enzymes whose precise function(s) remain(s) to be determined...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29057718/escherichia-coli-genome-scale-metabolic-gene-knockout-of-lactate-dehydrogenase-ldha-increases-succinate-production-from-glycerol
#16
Bashir Sajo Mienda
Genome-scale metabolic model (GEM) of Escherichia coli has been published with applications in predicting metabolic engineering capabilities on different carbon sources and directing biological discovery. The use of glycerol as an alternative carbon source is economically viable in bio-refinery. The use of GEM for predicting metabolic gene deletion of lactate dehydrogenase (ldhA) for increasing succinate production in E. coli from glycerol carbon source remained largely unexplored. Here I hypothesized that metabolic gene knockout of ldhA in E...
October 23, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29040409/towards-dynamic-genome-scale-models
#17
David Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr
The analysis of the dynamic behaviour of genome-scale models of metabolism (GEMs) currently presents considerable challenges because of the difficulties of simulating such large and complex networks. Bacterial GEMs can comprise about 5000 reactions and metabolites, and encode a huge variety of growth conditions; such models cannot be used without sophisticated tool support. This article is intended to aid modellers, both specialist and non-specialist in computerized methods, to identify and apply a suitable combination of tools for the dynamic behaviour analysis of large-scale metabolic designs...
October 13, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29038751/combining-graph-and-flux-based-structures-to-decipher-phenotypic-essential-metabolites-within-metabolic-networks
#18
Julie Laniau, Clémence Frioux, Jacques Nicolas, Caroline Baroukh, Maria-Paz Cortes, Jeanne Got, Camille Trottier, Damien Eveillard, Anne Siegel
BACKGROUND: The emergence of functions in biological systems is a long-standing issue that can now be addressed at the cell level with the emergence of high throughput technologies for genome sequencing and phenotyping. The reconstruction of complete metabolic networks for various organisms is a key outcome of the analysis of these data, giving access to a global view of cell functioning. The analysis of metabolic networks may be carried out by simply considering the architecture of the reaction network or by taking into account the stoichiometry of reactions...
2017: PeerJ
https://www.readbyqxmd.com/read/29036557/standardizing-biomass-reactions-and-ensuring-complete-mass-balance-in-genome-scale-metabolic-models
#19
Siu H J Chan, Jingyi Cai, Lin Wang, Margaret N Simons-Senftle, Costas D Maranas
Motivation: In a genome-scale metabolic model, the biomass produced is defined to have a molecular weight (MW) of 1 g mmol-1. This is critical for correctly predicting growth yields, contrasting multiple models and more importantly modeling microbial communities. However, the standard is rarely verified in the current practice and the chemical formulae of biomass components such as proteins, nucleic acids and lipids are often represented by undefined side groups (e.g. X, R). Results: We introduced a systematic procedure for checking the biomass weight and ensuring complete mass balance of a model...
November 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29030275/metabolite-damage-and-repair-in-metabolic-engineering-design
#20
REVIEW
Jiayi Sun, James G Jeffryes, Christopher S Henry, Steven D Bruner, Andrew D Hanson
The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it...
October 10, 2017: Metabolic Engineering
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