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Article
Open AccessWhole-genome metabolic model of Trichoderma reesei built by comparative reconstruction
Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of ...
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Article
Characterization and mutagenesis of two novel iron–sulphur cluster pentonate dehydratases
We describe here the identification and characterization of two novel enzymes belonging to the IlvD/EDD protein family, the D-xylonate dehydratase from Caulobacter crescentus, Cc XyDHT, (EC 4.2.1.82), and the L-a...
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Article
Open AccessPloidy influences the functional attributes of de novo lager yeast hybrids
The genomes of hybrid organisms, such as lager yeast (Saccharomyces cerevisiae × Saccharomyces eubayanus), contain orthologous genes, the functionality and effect of which may differ depending on their origin and...
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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 AccessA novel aldose-aldose oxidoreductase for co-production of D-xylonate and xylitol from D-xylose with Saccharomyces cerevisiae
An open reading frame CC1225 from the Caulobacter crescentus CB15 genome sequence belongs to the Gfo/Idh/MocA protein family and has 47 % amino acid sequence identity with the glucose-fructose oxidoreductase from...
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Article
l-Arabinose/d-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of l-arabinose to l-arabonate with Saccharomyces cerevisiae
Four potential dehydrogenases identified through literature and bioinformatic searches were tested for l-arabonate production from l-arabinose in the yeast Saccharomyces cerevisiae. The most efficient enzyme, ann...
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Article
Open AccessComparison of intracellular and secretion-based strategies for production of human α-galactosidase A in the filamentous fungus Trichoderma reesei
Trichoderma reesei is known as a good producer of industrial proteins but has hitherto been less successful in the production of therapeutic proteins. In order to elucidate the bottlenecks of heterologous protein...
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Article
Open AccessTranscriptome of Saccharomyces cerevisiae during production of D-xylonate
Production of D-xylonate by the yeast S. cerevisiae provides an example of bioprocess development for sustainable production of value-added chemicals from cheap raw materials or side streams. Production of D-xylo...
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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
Open AccessRe-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates
Trichoderma reesei is a soft rot Ascomycota fungus utilised for industrial production of secreted enzymes, especially lignocellulose degrading enzymes. About 30 carbohydrate active enzymes (CAZymes) of T. reesei ...
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Article
Open AccessArray comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties
Trichoderma reesei is the main industrial producer of cellulases and hemicellulases that are used to depolymerize biomass in a variety of biotechnical applications. Many of the production strains currently in use...
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Article
Open AccessMethods for estimating human endogenous retrovirus activities from EST databases
Human endogenous retroviruses (HERVs) are surviving traces of ancient retrovirus infections and now reside within the human DNA. Recently HERV expression has been detected in both normal tissues and diseased p...
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Chapter and Conference Paper
In Silico Expression Profiles of Human Endogenous Retroviruses
Human endogenous retroviruses (HERVs) are remnants of ancient retrovirus infections and now reside within the human DNA. Recently HERV expression has been detected in both normal and diseased tissues. However,...
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Chapter
Exploratory Clustering of Gene Expression Profiles of Mutated Yeast Strains
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Article
Open AccessTrustworthiness and metrics in visualizing similarity of gene expression
Conventionally, the first step in analyzing the large and high-dimensional data sets measured by microarrays is visual exploration. Dendrograms of hierarchical clustering, self-organizing maps (SOMs), and mult...
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Chapter
Exploratory Clustering of Gene Expression Profiles of Mutated Yeast Strains
