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Article
Open AccessAn analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
Metabolic fluxes provide invaluable insight on the integrated response of a cell to environmental stimuli or genetic modifications. Current computational methods for estimating the metabolic fluxes from 13C isoto...
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Article
Open AccessOxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A
The yeast Saccharomyces cerevisiae is able to adjust to external oxygen availability by utilizing both respirative and fermentative metabolic modes. Adjusting the metabolic mode involves alteration of the intrace...
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Article
Open Access13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose
The filamentous fungus Trichoderma reesei is an important host organism for industrial enzyme production. It is adapted to nutrient poor environments where it is capable of producing large amounts of hydrolytic e...
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Article
Open AccessInferring branching pathways in genome-scale metabolic networks
A central problem in computational metabolic modelling is how to find biochemically plausible pathways between metabolites in a metabolic network. Two general, complementary frameworks have been utilized to fi...
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Article
Open AccessReconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation
Several protein-protein interaction studies have been performed for the yeast Saccharomyces cerevisiae using different high-throughput experimental techniques. All these results are collected in the BioGRID datab...
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Article
Open AccessA multi-level study of recombinant Pichia pastoris in different oxygen conditions
Yeasts are attractive expression platforms for many recombinant proteins, and there is evidence for an important interrelation between the protein secretion machinery and environmental stresses. While adaptive...
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Article
Open AccessCorrelation of gene expression and protein production rate - a system wide study
Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on Sac...
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Article
Open AccessMetabolic flux profiling of recombinant protein secreting Pichia pastoris growing on glucose:methanol mixtures
The methylotrophic yeast Pichia pastoris has emerged as one of the most promising yeast hosts for the production of heterologous proteins. Mixed feeds of methanol and a multicarbon source instead of methanol as s...
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Chapter
Anaerobic Carbon Metabolism of Saccharomyces cerevisiae
The yeast Saccharomyces cerevisiae is a facultative anaerobic organism able to grow in the absence of oxygen. Oxygenation is one of the major costs in biotechnical production processes, and the anaerobic performa...
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Protocol
Labelling Analysis for 13C MFA Using NMR Spectroscopy
NMR spectroscopy is an efficient method for analyzing 13C labelling of cellular metabolites. The strength of it is especially the ability to provide direct quantitative positional information on the 13C labelling...
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Article
Open AccessIntegration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae
Saccharomyces cerevisiae is able to adapt to a wide range of external oxygen conditions. Previously, oxygen-dependent phenotypes have been studied individually at the transcriptional, metabolite, and flux level....
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Article
Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures
Xylose is present with glucose in lignocellulosic streams available for valorisation to biochemicals. Saccharomyces cerevisiae has excellent characteristics as a host for the bioconversion, except that it strongl...
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Article
Open AccessYeast metabolic chassis designs for diverse biotechnological products
The diversity of industrially important molecules for which microbial production routes have been experimentally demonstrated is rapidly increasing. The development of economically viable producer cells is, ho...
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Article
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies
Bacterial metabolism plays a fundamental role in gut microbiota ecology and host–microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth charac...
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Chapter
Yeast Genome-Scale Metabolic Models for Simulating Genotype–Phenotype Relations
Understanding genotype–phenotype dependency is a universal aim for all life sciences. While the complete genotype–phenotype relations remain challenging to resolve, metabolic phenotypes are moving within the r...
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Article
Open AccessPHB production from cellobiose with Saccharomyces cerevisiae
Replacement of petrochemical-based materials with microbially produced biodegradable alternatives calls for industrially attractive fermentation processes. Lignocellulosic materials offer non-edible alternativ...
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Article
Open AccessGenome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts
Use of alternative non-Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce t...
