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https://www.readbyqxmd.com/read/28424673/genome-scale-reconstruction-of-the-metabolic-network-in-oenococcus-oeni-to-assess-wine-malolactic-fermentation
#1
Sebastián N Mendoza, Pablo M Cañón, Ángela Contreras, Magdalena Ribbeck, Eduardo Agosín
Oenococcus oeni is the main responsible agent for malolactic fermentation in wine, an unpredictable and erratic process in winemaking. To address this, we have constructed and exhaustively curated the first genome-scale metabolic model of Oenococcus oeni, comprising 660 reactions, 536 metabolites and 454 genes. In silico experiments revealed that nutritional requirements are predicted with an accuracy of 93%, while 14 amino acids were found to be essential for the growth of this bacterial species. When the model was applied to determine the non-growth associated maintenance, results showed that O...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28419089/erroneous-energy-generating-cycles-in-published-genome-scale-metabolic-networks-identification-and-removal
#2
Claus Jonathan Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J Lercher
Energy metabolism is central to cellular biology. Thus, genome-scale models of heterotrophic unicellular species must account appropriately for the utilization of external nutrients to synthesize energy metabolites such as ATP. However, metabolic models designed for flux-balance analysis (FBA) may contain thermodynamically impossible energy-generating cycles: without nutrient consumption, these models are still capable of charging energy metabolites (such as ADP→ATP or NADP+→NADPH). Here, we show that energy-generating cycles occur in over 85% of metabolic models without extensive manual curation, such as those contained in the ModelSEED and MetaNetX databases; in contrast, such cycles are rare in the manually curated models of the BiGG database...
April 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28396843/clostridioides-difficile-630%C3%AE-erm-in-silico-and-in-vivo-quantitative-growth-and-extensive-polysaccharide-secretion
#3
Henning Dannheim, Sabine E Will, Dietmar Schomburg, Meina Neumann-Schaal
Antibiotic-associated infections with Clostridioides difficile are a severe and often lethal risk for hospitalized patients, and can also affect populations without these classical risk factors. For a rational design of therapeutical concepts, a better knowledge of the metabolism of the pathogen is crucial. Metabolic modeling can provide a simulation of quantitative growth and usage of metabolic pathways, leading to a deeper understanding of the organism. Here, we present an elaborate genome-scale metabolic model of C...
April 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28389638/imgmd-a-platform-for-the-integration-and-standardisation-of-in-silico-microbial-genome-scale-metabolic-models
#4
Chao Ye, Nan Xu, Chuan Dong, Yuannong Ye, Xuan Zou, Xiulai Chen, Fengbiao Guo, Liming Liu
Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28385593/a-genome-scale-model-of-geobacillus-thermoglucosidasius-c56-ys93-reveals-its-biotechnological-potential-on-rice-straw-hydrolysate
#5
Ahmad Ahmad, Hassan B Hartman, S Krishnakumar, David A Fell, Mark G Poolman, Shireesh Srivastava
Rice straw is a major crop residue which is burnt in many countries, creating significant air pollution. Thus, alternative routes for disposal of rice straw are needed. Biotechnological treatment of rice straw hydrolysate has potential to convert this agriculture waste into valuable biofuel(s) and platform chemicals. Geobacillus thermoglucosidasius is a thermophile with properties specially suited for use as a biocatalyst in lignocellulosic bioprocesses, such as high optimal temperature and tolerance to high levels of ethanol...
April 4, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28385592/genome-scale-metabolic-modelling-common-cofactors-metabolism-in-microorganisms
#6
Nan Xu, Chao Ye, Xiulai Chen, Jia Liu, Liming Liu
The common cofactors ATP/ADP, NAD(P)(H), and acetyl-CoA/CoA are indispensable participants in biochemical reactions in industrial microbes. To systematically explore the effects of these cofactors on cell growth and metabolic phenotypes, the first genome-scale cofactor metabolic model, icmNX6434, including 6434 genes, 1782 metabolites, and 6877 reactions, was constructed from 14 genome-scale metabolic models of 14 industrial strains. The origin, consumption, and interactions of these common cofactors in microbial cells were elucidated by the icmNX6434 model, and they played important roles in cell growth...
April 4, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28382331/a-genome-scale-model-of-shewanella-piezotolerans-simulates-mechanisms-of-metabolic-diversity-and-energy-conservation
#7
Keith Dufault-Thompson, Huahua Jian, Ruixue Cheng, Jiefu Li, Fengping Wang, Ying Zhang
Shewanella piezotolerans strain WP3 belongs to the group 1 branch of the Shewanella genus and is a piezotolerant and psychrotolerant species isolated from the deep sea. In this study, a genome-scale model was constructed for WP3 using a combination of genome annotation, ortholog mapping, and physiological verification. The metabolic reconstruction contained 806 genes, 653 metabolites, and 922 reactions, including central metabolic functions that represented nonhomologous replacements between the group 1 and group 2 Shewanella species...
March 2017: MSystems
https://www.readbyqxmd.com/read/28381205/the-jbei-quantitative-metabolic-modeling-library-jqmm-a-python-library-for-modeling-microbial-metabolism
#8
Garrett W Birkel, Amit Ghosh, Vinay S Kumar, Daniel Weaver, David Ando, Tyler W H Backman, Adam P Arkin, Jay D Keasling, Héctor García Martín
BACKGROUND: Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the circumstantial ones, bounding the outcomes of experiments and guiding engineering approaches. Among different modeling schemes, the quantification of intracellular metabolic fluxes (i.e. the rate of each reaction in cellular metabolism) is of particular interest for metabolic engineering because it describes how carbon and energy flow throughout the cell...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28379466/mackinac-a-bridge-between-modelseed-and-cobrapy-to-generate-and-analyze-genome-scale-metabolic-models
#9
Michael Mundy, Helena Mendes-Soares, Nicholas Chia
Summary: Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Here we describe Mackinac, a Python package that combines ModelSEED's ability to automatically reconstruct metabolic models with COBRApy's advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms...
August 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28367990/systems-approach-to-characterize-the-metabolism-of-liver-cancer-stem-cells-expressing-cd133
#10
Wonhee Hur, Jae Yong Ryu, Hyun Uk Kim, Sung Woo Hong, Eun Byul Lee, Sang Yup Lee, Seung Kew Yoon
Liver cancer stem cells (LCSCs) have attracted attention because they cause therapeutic resistance in hepatocellular carcinoma (HCC). Understanding the metabolism of LCSCs can be a key to developing therapeutic strategy, but metabolic characteristics have not yet been studied. Here, we systematically analyzed and compared the global metabolic phenotype between LCSCs and non-LCSCs using transcriptome and metabolome data. We also reconstructed genome-scale metabolic models (GEMs) for LCSC and non-LCSC to comparatively examine differences in their metabolism at genome-scale...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28367572/a-systematic-reconstruction-and-constraint-based-analysis-of-leishmania-donovani-metabolic-network-identification-of-potential-antileishmanial-drug-targets
#11
Mahesh Sharma, Naeem Shaikh, Shailendra Yadav, Sushma Singh, Prabha Garg
Visceral leishmaniasis, a lethal parasitic disease, is caused by the protozoan parasite Leishmania donovani. The absence of an effective vaccine, drug toxicity and parasite resistance necessitates the identification of novel drug targets. Reconstruction of genome-scale metabolic models and their simulation has been established as an important tool for systems-level understanding of a microorganism's metabolism. In this work, amalgamating the tools and techniques of computational systems biology with rigorous manual curation, a constraint-based metabolic model for Leishmania donovani BPK282A1 has been developed...
April 3, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28361704/comparison-of-tissue-disease-specific-integrated-networks-using-directed-graphlet-signatures
#12
Arzu Burcak Sonmez, Tolga Can
BACKGROUND: Analysis of integrated genome-scale networks is a challenging problem due to heterogeneity of high-throughput data. There are several topological measures, such as graphlet counts, for characterization of biological networks. RESULTS: In this paper, we present methods for counting small sub-graph patterns in integrated genome-scale networks which are modeled as labeled multidigraphs. We have obtained physical, regulatory, and metabolic interactions between H...
March 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28361242/optimal-resource-allocation-enables-mathematical-exploration-of-microbial-metabolic-configurations
#13
Laurent Tournier, Anne Goelzer, Vincent Fromion
Central to the functioning of any living cell, the metabolic network is a complex network of biochemical reactions. It may also be viewed as an elaborate production system, integrating a diversity of internal and external signals in order to efficiently produce the energy and the biochemical precursors to ensure all cellular functions. Even in simple organisms like bacteria, it shows a striking level of coordination, adapting to very different growth media. Constraint-based models constitute an efficient mathematical framework to compute optimal metabolic configurations, at the scale of a whole genome...
March 30, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28358919/beware-batch-culture-seasonality-and-niche-construction-predicted-to-favor-bacterial-adaptive-diversification
#14
Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider, Guillaume Beslon
Metabolic cross-feeding interactions between microbial strains are common in nature, and emerge during evolution experiments in the laboratory, even in homogeneous environments providing a single carbon source. In sympatry, when the environment is well-mixed, the reasons why emerging cross-feeding interactions may sometimes become stable and lead to monophyletic genotypic clusters occupying specific niches, named ecotypes, remain unclear. As an alternative to evolution experiments in the laboratory, we developed Evo2Sim, a multi-scale model of in silico experimental evolution, equipped with the whole tool case of experimental setups, competition assays, phylogenetic analysis, and, most importantly, allowing for evolvable ecological interactions...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28355531/using-a-genome-scale-metabolic-network-model-to-elucidate-the-mechanism-of-chloroquine-action-in-plasmodium-falciparum
#15
Shivendra G Tewari, Sean T Prigge, Jaques Reifman, Anders Wallqvist
Chloroquine, long the default first-line treatment against malaria, is now abandoned in large parts of the world because of widespread drug-resistance in Plasmodium falciparum. In spite of its importance as a cost-effective and efficient drug, a coherent understanding of the cellular mechanisms affected by chloroquine and how they influence the fitness and survival of the parasite remains elusive. Here, we used a systems biology approach to integrate genome-scale transcriptomics to map out the effects of chloroquine, identify targeted metabolic pathways, and translate these findings into mechanistic insights...
March 22, 2017: International Journal for Parasitology, Drugs and Drug Resistance
https://www.readbyqxmd.com/read/28338129/prediction-of-metabolic-fluxes-from-gene-expression-data-with-huber-penalty-convex-optimization-function
#16
Shao-Wu Zhang, Wang-Long Gou, Yan Li
As one of the critical parameters of a metabolic pathway, the metabolic flux in a metabolic network serves as an essential role in physiology and pathology. Constraint-based metabolic models are the widely used frameworks for predicting metabolic fluxes in genome-scale metabolic networks. Integrating the transcriptomic data into the constraint-based metabolic models can effectively predict context-specific fluxes across different conditions. However, these methods always need user-defined thresholds to identify the expression levels of metabolic genes or restrain the rate of biomass production, and the predictive results are sensitive to the thresholds...
March 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28334407/organismal-and-spatial-partitioning-of-energy-and-macronutrient-transformations-within-a-hypersaline-mat
#17
Jennifer M Mobberley, Stephen R Lindemann, Hans C Bernstein, James J Moran, Ryan S Renslow, Jerome Babauta, Dehong Hu, Haluk Beyenal, William C Nelson
Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms; however, little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity and metabolic gradient measurements...
April 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28333921/bioenergetics-based-modeling-of-plasmodium-falciparum-metabolism-reveals-its-essential-genes-nutritional-requirements-and-thermodynamic-bottlenecks
#18
Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis
Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this complexity and allow integrative analyses of cell metabolism. In this study, we present a genome-scale metabolic model (iPfa) of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA). Using previous absolute concentration data of the intraerythrocytic parasite, we applied TFA to iPfa and predicted up to 63 essential genes and 26 essential pairs of genes...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28325918/robust-analysis-of-fluxes-in-genome-scale-metabolic-pathways
#19
Michael MacGillivray, Amy Ko, Emily Gruber, Miranda Sawyer, Eivind Almaas, Allen Holder
Constraint-based optimization, such as flux balance analysis (FBA), has become a standard systems-biology computational method to study cellular metabolisms that are assumed to be in a steady state of optimal growth. The methods are based on optimization while assuming (i) equilibrium of a linear system of ordinary differential equations, and (ii) deterministic data. However, the steady-state assumption is biologically imperfect, and several key stoichiometric coefficients are experimentally inferred from situations of inherent variation...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28323032/metabolic-re-wiring-of-isogenic-breast-epithelial-cell-lines-following-epithelial-to-mesenchymal-transition
#20
Skarphedinn Halldorsson, Neha Rohatgi, Manuela Magnusdottir, Kumari Sonal Choudhary, Thorarinn Gudjonsson, Erik Knutsen, Anna Barkovskaya, Bylgja Hilmarsdottir, Maria Perander, Gunhild M Mælandsmo, Steinn Gudmundsson, Óttar Rolfsson
Epithelial to mesenchymal transition (EMT) has implications in tumor progression and metastasis. Metabolic alterations have been described in cancer development but studies focused on the metabolic re-wiring that takes place during EMT are still limited. We performed metabolomics profiling of a breast epithelial cell line and its EMT derived mesenchymal phenotype to create genome-scale metabolic models descriptive of both cell lines. Glycolysis and OXPHOS were higher in the epithelial phenotype while amino acid anaplerosis and fatty acid oxidation fueled the mesenchymal phenotype...
March 18, 2017: Cancer Letters
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