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Development of tools for quantitative intracellular metabolomics of Aspergillus niger chemostat cultures

Lameiras, F. (author), Heijnen, J.J. (author), Van Gulik, W.M. (author)

In view of the high citric acid production capacity of Aspergillus niger, it should be well suited as a cell factory for the production of other relevant acids as succinic, fumaric, itaconic and malic. Quantitative metabolomics is an important omics tool in a synthetic biology approach to develop A. niger for the production of these acids. Such...

journal article 2015

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Feasibility study of an alkaline-based chemical treatment for the purification of polyhydroxybutyrate produced by a mixed enriched culture

Jiang, Y. (author), Mikova, G. (author), Kleerebezem, R. (author), Van der Wielen, L.A.M. (author), Cuellar Soares, M.C. (author)

This study focused on investigating the feasibility of purifying polyhydroxybutyrate (PHB) from mixed culture biomass by alkaline-based chemical treatment. The PHB-containing biomass was enriched on acetate under non-sterile conditions. Alkaline treatment (0.2 M NaOH) together with surfactant SDS (0.2 w/v% SDS) could reach 99% purity, with more...

journal article 2015

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Effect and behaviour of different substrates in relation to the formation of aerobic granular sludge

Pronk, M. (author), Abbas, B. (author), Al-zuhairy, S.H.K. (author), Kraan, R. (author), Kleerebezem, R. (author), Van Loosdrecht, M.C.M. (author)

When aerobic granular sludge is applied for industrial wastewater treatment, different soluble substrates can be present. For stable granular sludge formation on volatile fatty acids (e.g. acetate), production of storage polymers under anaerobic feeding conditions has been shown to be important. This prevents direct aerobic growth on readily...

journal article 2015

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Electron Tunneling Rates in Respiratory Complex?I Are Tuned for Efficient Energy Conversion

De Vries, S. (author), Dörner, K. (author), Strampraad, M.J.F. (author), Friedrich, T. (author)

Respiratory complex I converts the free energy of ubiquinone reduction by NADH into a proton motive force, a redox reaction catalyzed by flavin mononucleotide(FMN) and a chain of seven iron–sulfur centers. Electron transfer rates between the centers were determined by ultrafast freeze-quenching and analysis by EPR and UV/Vis spectroscopy. The...

journal article 2015

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Die Elektronentunnelraten im Atmungskettenkomplex I sind auf eine effiziente Energiewandlung abgestimmt

De Vries, S. (author), Dörner, K. (author), Strampraad, M.J.F. (author), Friedrich, T. (author)

Der Atmungskettenkomplex I wandelt die freie Energie, die bei der Reduktion von Ubichinon durch NADH frei wird, in einen Protonengradienten über die Membran um. Die biologische Redoxreaktion wird von einem Flavinmononukleotid und einer Kette von sieben Eisen-Schwefel-Zentren katalysiert. Die Elektronentransfergeschwindigkeiten zwischen den...

journal article 2015

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Enantioselective Michael Addition of Water

Chen, B.S. (author), Resch, V. (author), Otten, L.G. (author), Hanefeld, U. (author)

The enantioselective Michael addition using water as both nucleophile and solvent has to date proved beyond the ability of synthetic chemists. Herein, the direct, enantioselective Michael addition of water in water to prepare important ?-hydroxy carbonyl compounds using whole cells of Rhodococcus strains is described. Good yields and excellent...

journal article 2014

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MS approaches to select peptides with post-translational modifications from amphibian defense secretions prior to full sequence elucidation

Pinkse, M.W.H. (author), Evaristo, G. (author), Pieterse, M.M. (author), Yu, Y. (author), Verhaert, P.D.E.M. (author)

Peptide families are characterized by structural motifs, which often comprise specific post-translational modifications (PTMs) required for biological activity. In conventional bioactivity-based peptidomics studies natural peptide mixtures are chromatographically separated and the bioactive fractions purified to homogeneity, prior to structural...

journal article 2014

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Rethinking Sustainable Development: Considering How Different Worldviews Envision “Development” and “Quality of Life”

Hedlund-de Witt, A. (author)

The concept of sustainable development does not articulate what needs to be sustained, developed, or how, and is consequently intersubjective and intercultural. I therefore argue that it is essential to consider different worldviews when discussing sustainable development, and I offer broad, provisional suggestions as to how we can begin doing...

journal article 2014

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Engineering acetyl coenzyme A supply: Functional expression of a bacterial pyruvate dehydrogenase complex in the cytosol of Saccharomyces cerevisiae

Kozak, B.U. (author), Van Rossum, M.H. (author), Luttik, M.A. (author), Akeroyd, M. (author), Benjamin, K.R. (author), Wu, L. (author), De Vries, S. (author), Daran, J.M. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)

The energetic (ATP) cost of biochemical pathways critically determines the maximum yield of metabolites of vital or commercial relevance. Cytosolic acetyl coenzyme A (acetyl-CoA) is a key precursor for biosynthesis in eukaryotes and for many industrially relevant product pathways that have been introduced into Saccharomyces cerevisiae, such as...

journal article 2014

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Editorial: The EuPA Company Club: Status, report, developments and perspectives

Verhaert, P. (author)

The high-temperature phase diagram of the UO2–ThO2 system has been experimentally revisited in the present study for the first time since 1970, using a laser heating approach combined with fast pyrometry in a thermal arrest method. The melting/solidification temperature, which is of fundamental information for a reactor design was studied here....

journal article 2014

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Recombinant micro-organism for use in method with increased product yield

Van Maris, A.J.A. (author), Pronk, J.T. (author), Guadalupe Medina, V.G. (author), Wisselink, H.W. (author)

The invention relates to a recombinant yeast cell, in particular a transgenic yeast cell, functionally expressing one or more recombinant, in particular heterologous, nucleic acid sequences encoding ribulose-1,5-biphosphate carboxylase oxygenase (Rubisco) and phosphoribulokinase (PRK). The invention further relates to the use of carbon dioxide...

patent 2014

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Process for the treatment of manure

Van Spronsen, J. (author), Witkamp, G.J. (author), Evers, J.A. (author), De Graaff, B. (author), Van Kaathoven, H. (author)

patent 2014

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Engineering a fungal peroxidase that degrades lignin at very acidic pH

Fernandez-Fueyo, E. (author), Ruiz-Duenas, F.J. (author), Martinez, A.T. (author)

Background Ligninolytic peroxidases are divided into three families: manganese peroxidases (MnPs), lignin peroxidases (LiPs), and versatile peroxidases (VPs). The latter two are able to degrade intact lignins, as shown using nonphenolic lignin model compounds, with VP oxidizing the widest range of recalcitrant substrates. One of the main...

journal article 2014

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An alternative, arginase-independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme

Romagnoli, G. (author), Verhoeven, M.D. (author), Mans, R. (author), Fleury Rey, Y. (author), Bel-Rhlid, R. (author), Van den Broek, M. (author), Maleki Seifar, R. (author), Ten Pierick, A. (author), Thompson, M. (author), Müller, V. (author), Wahl, S.A. (author), Pronk, J.T. (author), Daran, J.M. (author)

Most available knowledge on fungal arginine metabolism is derived from studies on Saccharomyces cerevisiae, in which arginine catabolism is initiated by releasing urea via the arginase reaction. Orthologues of the S. cerevisiae genes encoding the first three enzymes in the arginase pathway were cloned from Kluyveromyces lactis and shown to...

journal article 2014

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Stable acetate production in extreme-thermophilic (70ºC) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens

Zhang, F. (author), Zhang, Y. (author), Ding, J. (author), Dai, K. (author), Van Loosdrecht, M.C.M. (author), Zeng, R.J. (author)

The control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in extreme-thermophilic (706C) mixed culture fermentation....

journal article 2014

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The emergence of peptides in the pharmaceutical business: From exploration to exploitation

Uhlig, T. (author), Kyprianou, T.D. (author), Martinelli, F.G. (author), Oppici, C.A. (author), Heiligers, D. (author), Hills, D.R.J. (author), Calvo, X.R. (author), Verhaert, P.D.E.M. (author)

This minireview touches upon the challenges and opportunities peptides experience on the track to become an approved pharmaceutical. Peptide attributes originally considered troublesome with respect to drug development may now turn out to be more convenient rather than unfavourable. Besides characteristic high target affinity, biological...

journal article 2014

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Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site

Suzuki, S. (author), Kuenen, J.G. (author), Schipper, K. (author), Van der Velde, S. (author), Ishii, S. (author), Wu, A. (author), Sorokin, D.Y. (author), Tenney, A. (author), Meng, X.Y. (author), Morrill, P.L. (author), Kamagata, Y. (author), Muyzer, G. (author), Nealson, K.H. (author)

Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging environments for life in continental sites due to the combination of extremely high pH, low salinity and lack of obvious electron acceptors and carbon sources. Nevertheless, certain Betaproteobacteria have been frequently observed in such environments. Here...

journal article 2014

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Characterization of the RnfB and RnfG Subunits of the Rnf Complex from the Archaeon Methanosarcina acetivorans

Suharti, S. (author), Wang, M. (author), De Vries, S. (author), Ferry, J.G. (author)

Rnf complexes are redox-driven ion pumps identified in diverse species from the domains Bacteria and Archaea, biochemical characterizations of which are reported for two species from the domain Bacteria. Here, we present characterizations of the redox-active subunits RnfG and RnfB from the Rnf complex of Methanosarcina acetivorans, an acetate...

journal article 2014

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Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae

Suarez-Mendez, C.A. (author), Sousa, A. (author), Heijnen, J.J. (author), Wahl, S.A. (author)

Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes...

journal article 2014

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Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles

Hebly, M. (author), De Ridder, D. (author), De Hulster, E.A. (author), De la Torre Cortes, P. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)

Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures...

journal article 2014