Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Cell disruption for microalgae biorefineries
    Günerken, E. ; Hondt, E. d'; Eppink, M.H.M. ; Garcia-Gonzalez, L. ; Elst, K. ; Wijffels, R.H. - \ 2015
    Biotechnology Advances 33 (2015)2. - ISSN 0734-9750 - p. 243 - 260.
    microwave-assisted extraction - fluidized-bed adsorption - electric-field treatment - synechocystis pcc 6803 - life-cycle assessment - chlorella-vulgaris - lipid extraction - microbial-cells - saccharomyces-cerevisiae - biodiesel production
    Microalgae are a potential source for various valuable chemicals for commercial applications ranging from nutraceuticals to fuels. Objective in a biorefinery is to utilize biomass ingredients efficiently similarly to petroleum refineries in which oil is fractionated in fuels and a variety of products with higher value. Downstream processes in microalgae biorefineries consist of different steps whereof cell disruption is the most crucial part. To maintain the functionality of algae biochemicals during cell disruption while obtaining high disruption yields is an important challenge. Despite this need, studies on mild disruption of microalgae cells are limited. This review article focuses on the evaluation of conventional and emerging cell disruption technologies, and a comparison thereof with respect to their potential for the future microalgae biorefineries. The discussed techniques are bead milling, high pressure homogenization, high speed homogenization, ultrasonication, microwave treatment, pulsed electric field treatment, non-mechanical cell disruption and some emerging technologies.
    Analysis of by-product formation and sugar monomerization in sugarcane bagasse pretreated at pilot plant scale: Differences between autohydrolysis, alkaline and acid pretreatment
    Pol, E.C. van der; Bakker, R. ; Zeeland, A.N.T. van; Sanchez Garcia, D. ; Punt, A.M. ; Eggink, G. - \ 2015
    Bioresource Technology 181 (2015). - ISSN 0960-8524 - p. 114 - 123.
    saccharomyces-cerevisiae - degradation-products - wet oxidation - hydrolysis - ethanol - fermentations - cellulose - glucose - biomass
    Sugarcane bagasse is an interesting feedstock for the biobased economy since a large fraction is polymerized sugars. Autohydrolysis, alkaline and acid pretreatment conditions combined with enzyme hydrolysis were used on lignocellulose rich bagasse to acquire monomeric. By-products found after pretreatment included acetic, glycolic and coumaric acid in concentrations up to 40, 21 and 2.5 g/kg dry weight bagasse respectively. Alkaline pretreated material contained up to 45 g/kg bagasse DW of sodium. Acid and autohydrolysis pretreatment results in a furan formation of 14 g/kg and 25 g/kg DW bagasse respectively. Enzyme monomerization efficiencies of pretreated solid material after 72 h were 81% for acid pretreatment, 77% for autohydrolysis and 57% for alkaline pretreatment. Solid material was washed with superheated water to decrease the amount of by-products. Washing decreased organic acid, phenol and furan concentrations in solid material by at least 60%, without a major sugar loss.
    Molecular and metabolic adaptations of Lactococcus lactis at near-zero growth rates
    Ercan, O. ; Wels, M. ; Smid, E.J. ; Kleerebezem, M. - \ 2015
    Applied and Environmental Microbiology 81 (2015)1. - ISSN 0099-2240 - p. 320 - 331.
    acid bacteria - saccharomyces-cerevisiae - quantitative physiology - transcriptome analysis - streptococcus-lactis - maintenance energy - catabolite control - bacillus-subtilis - escherichia-coli - sugar catabolism
    This paper describes the molecular and metabolic adaptations of Lactococcus lactis during the transition from a growing to a near-zero growth state using carbon-limited retentostat cultivation. Transcriptomic analyses revealed that metabolic patterns shifted between lactic- and mixed-acid fermentation during retentostat cultivation, which appeared to be controlled at the transcription level of the corresponding pyruvate-dissipation encoding genes. During retentostat cultivation, cells continued to consume several amino acids, but also produced specific amino acids, which may derive from the conversion of glycolytic intermediates. We identify a novel motif containing CTGTCAG, in the upstream regions of several genes related to amino acid conversion, which we propose to be the target site for CodY in Lactococcus lactis KF147. Finally, under extremely low carbon availability, carbon catabolite repression was progressively relieved and alternative catabolic functions were found to be highly expressed, which was confirmed by enhanced initial acidification rates on various sugars in cells obtained from near-zero growth cultures. The present integrated transcriptome and metabolite (amino acids and previously reported fermentation end-products) study provides molecular understanding of the adaptation of Lactococcus lactis to conditions supporting low-growth rates, and expands our earlier analysis of the quantitative physiology of this bacterium at near-zero growth rates towards gene regulation patterns involved in zero-growth adaptation.
    Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain
    Blombach, F. ; Launay, H. ; Snijders, A.P. ; Zorraquino, V. ; Wu, H. ; Koning, B. de; Brouns, S.J.J. ; Ettema, T.J. ; Camilloni, C. ; Cavalli, A. ; Vendruscolo, M. ; Dickman, M.J. ; Cabrita, L.D. ; Teana, A. La; Benelli, D. ; Londei, P. ; Christodoulou, J. ; Oost, J. van der - \ 2014
    Biochemical Journal 462 (2014)2. - ISSN 0264-6021 - p. 373 - 384.
    frameshift suppressor encodes - glycine transfer rnaccc - nmr chemical-shifts - saccharomyces-cerevisiae - sulfolobus-solfataricus - transcriptional coactivator - translational initiation - gel-electrophoresis - field gradient - protein
    MBF1 (multi-protein bridging factor 1) is a protein containing a conserved HTH (helix–turn–helix) domain in both eukaryotes and archaea. Eukaryotic MBF1 has been reported to function as a transcriptional co-activator that physically bridges transcription regulators with the core transcription initiation machinery of RNA polymerase II. In addition, MBF1 has been found to be associated with polyadenylated mRNA in yeast as well as in mammalian cells. aMBF1 (archaeal MBF1) is very well conserved among most archaeal lineages; however, its function has so far remained elusive. To address this, we have conducted a molecular characterization of this aMBF1. Affinity purification of interacting proteins indicates that aMBF1 binds to ribosomal subunits. On sucrose density gradients, aMBF1 co-fractionates with free 30S ribosomal subunits as well as with 70S ribosomes engaged in translation. Binding of aMBF1 to ribosomes does not inhibit translation. Using NMR spectroscopy, we show that aMBF1 contains a long intrinsically disordered linker connecting the predicted N-terminal zinc-ribbon domain with the C-terminal HTH domain. The HTH domain, which is conserved in all archaeal and eukaryotic MBF1 homologues, is directly involved in the association of aMBF1 with ribosomes. The disordered linker of the ribosome-bound aMBF1 provides the N-terminal domain with high flexibility in the aMBF1–ribosome complex. Overall, our findings suggest a role for aMBF1 in the archaeal translation process.
    By-products resulting from lignocellulose pretreatment and their inhibitory effect on fermentations for (bio)chemicals and fuels
    Pol, E.C. van der; Bakker, R.R. ; Baets, P. ; Eggink, G. - \ 2014
    Applied Microbiology and Biotechnology 98 (2014)23. - ISSN 0175-7598 - p. 9579 - 9593.
    dilute-acid hydrolysis - steam-explosion pretreatment - fiber expansion afex - saccharomyces-cerevisiae - degradation-products - escherichia-coli - ethanol fermentation - wheat-straw - sugarcane bagasse - wet oxidation
    Lignocellulose might become an important feedstock for the future development of the biobased economy. Although up to 75 % of the lignocellulose dry weight consists of sugar, it is present in a polymerized state and cannot be used directly in most fermentation processes for the production of chemicals and fuels. Several methods have been developed to depolymerize the sugars present in lignocellulose, making the sugars available for fermentation. In this review, we describe five different pretreatment methods and their effect on the sugar and non-sugar fraction of lignocellulose. For several pretreatment methods and different types of lignocellulosic biomass, an overview is given of by-products formed. Most unwanted by-products present after pretreatment are dehydrated sugar monomers (furans), degraded lignin polymers (phenols) and small organic acids. Qualitative and quantitative effects of these by-products on fermentation processes have been studied. We conclude this review by giving an overview of techniques and methods to decrease inhibitory effects of unwanted by-products.
    Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes
    Revuelta, M.V. ; Kan, J.A.L. van; Kay, J. ; Have, A. ten - \ 2014
    Genome Biology and Evolution 6 (2014)6. - ISSN 1759-6653 - p. 1480 - 1494.
    botrytis-cinerea secretome - x-ray analyses - candida-albicans - saccharomyces-cerevisiae - phylogenetic trees - unique member - sequence - proteases - prediction - nepenthesin
    The A1 family of eukaryotic aspartic proteinases (APs) forms one of the 16 AP families. Although one of the best characterized families, the recent increase in genome sequence data has revealed many fungal AP homologs with novel sequence characteristics. This study was performed to explore the fungal AP sequence space and to obtain an in-depth understanding of fungal AP evolution. Using a comprehensive phylogeny of approximately 700 AP sequences from the complete proteomes of 87 fungi and 20 nonfungal eukaryotes, 11 major clades of APs were defined of which clade I largely corresponds to the A1A subfamily of pepsin-archetype APs. Clade II largely corresponds to the A1B subfamily of nepenthesin-archetype APs. Remarkably, the nine other clades contain only fungal APs, thus indicating that fungal APs have undergone a large sequence diversification. The topology of the tree indicates that fungal APs have been subject to both “birth and death” evolution and “functional redundancy and diversification.” This is substantiated by coclustering of certain functional sequence characteristics. A meta-analysis toward the identification of Cluster Determining Positions (CDPs) was performed in order to investigate the structural and biochemical basis for diversification. Seven CDPs contribute to the secondary structure of the enzyme. Three other CDPs are found in the vicinity of the substrate binding cleft. Tree topology, the large sequence variation among fungal APs, and the apparent functional diversification suggest that an amendment to update the current A1 AP classification based on a comprehensive phylogenetic clustering might contribute to refinement of the classification in the MEROPS peptidase database.
    Sex or no sex: Evolutionary adaptation occurs regardless
    Seidl, M.F. ; Thomma, B.P.H.J. - \ 2014
    Bioessays 36 (2014)4. - ISSN 0265-9247 - p. 335 - 345.
    horizontal gene-transfer - double-strand breaks - yeast candida-glabrata - genome evolution - transposable elements - saccharomyces-cerevisiae - mitotic recombination - avirulence gene - homologous recombination - cryptococcus-neoformans
    All species continuously evolve to adapt to changing environments. The genetic variation that fosters such adaptation is caused by a plethora of mechanisms, including meiotic recombination that generates novel allelic combinations in the progeny of two parental lineages. However, a considerable number of eukaryotic species, including many fungi, do not have an apparent sexual cycle and are consequently thought to be limited in their evolutionary potential. As such organisms are expected to have reduced capability to eliminate deleterious mutations, they are often considered as evolutionary dead ends. However, inspired by recent reports we argue that such organisms can be as persistent as organisms with conventional sexual cycles through the use of other mechanisms, such as genomic rearrangements, to foster adaptation.
    Pathway transfer in fungi: Transporters are the key to success
    Straat, L. van der; Graaff, L.H. de - \ 2014
    Bioengineered 5 (2014)5. - ISSN 2165-5979 - p. 335 - 339.
    itaconic acid production - saccharomyces-cerevisiae - lactococcus-lactis - aspergillus-niger - cephalosporin production - penicillium-chrysogenum - functional expression - membrane-proteins - ceft gene - overproduction
    Itaconic acid is an important building block for the chemical industry. Currently, Aspergillus terreus is the main organism used for itaconic acid production. Due to the enormous citric acid production capacity of Aspergillus niger, this host is investigated as a potential itaconic acid production host. Several strategies have been tried so far: fermentation optimization, expression of cis-aconitate decarboxylase (cadA) alone and in combination with aconitase targeted to the same compartment, chassis optimization, and the heterologous expression of two transporters flanking the cadA gene. We showed that the heterologous expression of these two transporters were key to improving itaconic acid production in an A. niger strain that was unable to produce oxalic acid and gluconic acid. The expression of transporters has increased the production levels of other industrially relevant processes as well, such as ß-lactam antibiotics and bioethanol. Thus far, the role of transporters in production process optimization is a bit overlooked.
    Effects of inclusion of hydrolyzed yeast on the immune response and performance of piglets after weaning
    Molist, F. ; Eerden, E. van; Parmentier, H.K. ; Vuorenmaa, J. - \ 2014
    Animal Feed Science and Technology 195 (2014). - ISSN 0377-8401 - p. 136 - 141.
    growth-performance - saccharomyces-cerevisiae - natural antibodies - weanling pigs - nutrient digestibility - weaned piglets - supplementation - polysaccharides - challenge - chickens
    The aim of this study was to examine whether yeast derivative (YD) based on brewery yeast hydrolyzate added to a post-weaning diet affected performance and immune responses in weaning pigs. One hundred and twenty pigs were allocated to 20 pens, taking initial body weight into account, and were distributed into two groups as follows: a negative control diet and the same diet supplemented with 2 g YD/kg. The YD used was Progut® (Hankkija Oy/Suomen Rehu, Hyvinkää, Finland). At days 7 and 21 of the experiment, half of the piglets per group were challenged intramuscularly with 1 mL of a solution of 20% sheep red blood cells (SRBC) in sterile phosphate buffered saline (PBS). At days 0, 14, 21 and 28 of the experiment, blood samples from the challenged piglets were obtained and acute-phase proteins (Pig-MAP), natural antibodies of the IgM- and IgG-isotype binding to keyhole limpet hemocyanin (KLH), and agglutinating antibody titers to SRBC were measured. Yeast derivative inclusion improved feed conversion ratio (P=0.025) for the overall period, tended to increase IgG (P=0.087) and IgM (P=0.061) antibodies in serum-binding KLH, and increased (P=0.037) SRBC agglutination titers. Collectively, these data suggest that YD supplementation as 2 g Progut®/kg to weanling pigs triggered the immune system to a more responsive state without penalizing the animal performance which could potentially be beneficial for overcoming disease challenges. Piglets fed with 2 g Progut®/kg for 28 days after weaning also showed an improvement in feed conversion ratio.
    Natural products – learning chemistry from plants
    Staniek, A. ; Bouwmeester, H.J. ; Fraser, P.D. ; Kayser, O. ; Martens, S. ; Tissier, A. ; Krol, A.R. van der; Wessjohann, L. ; Warzecha, H. - \ 2014
    Biotechnology Journal 9 (2014)3. - ISSN 1860-6768 - p. 326 - 336.
    escherichia-coli - benzylisoquinoline alkaloids - saccharomyces-cerevisiae - vanillin production - synthetic biology - organic-synthesis - biosynthesis - biocatalysis - artemisinin - enzymes
    Plant natural products (PNPs) are unique in that they represent a vast array of different structural features, ranging from relatively simple molecules to very complex ones. Given the fact that many plant secondary metabolites exhibit profound biological activity, they are frequently used as fragrances and flavors, medicines, as well as industrial chemicals. As the intricate structures of PNPs often cannot be mimicked by chemical synthesis, the original plant providers constitute the sole source for their industrial, large-scale production. However, sufficient supply is not guaranteed for all molecules of interest, making the development of alternative production systems a priority. Modern techniques, such as genome mining and thorough biochemical analysis, have helped us gain preliminary understanding of the enzymatic formation of the valuable ingredients in planta. Herein, we review recent advances in the application of biocatalytical processes, facilitating generation of complex PNPs through utilization of plant-derived specific enzymes and combinatorial biochemistry. We further evaluate the options of employing heterologous organisms harboring PNP biosynthetic pathways for the production of secondary metabolites of interest.
    Dietary polysaccharide extracts of Agaricus brasiliensis fruiting bodies: chemical characterization and bioactivities at different levels of purifiaction
    Kozarski, M. ; Klaus, A. ; Jakovljevic, D. ; Todorovic, N. ; Niksic, M. ; Vrvic, M.M. ; Griensven, L.J.L.D. van - \ 2014
    Food Research International 64 (2014). - ISSN 0963-9969 - p. 53 - 64.
    pleurotus-sajor-caju - antioxidative activities - edible mushroom - beta-glucan - medicinal mushrooms - antitumor-activity - phellinus-linteus - blazei murill - cell-wall - saccharomyces-cerevisiae
    Polysaccharides of the European strain of A. brasiliensis were obtained by hot water extraction and ethanol precipitation (HWPE I) of fruiting bodies, and further purified by dialysis (HWPE II) and pronase incubation (PPE). These polysaccharides consisted mainly of (1 ¿ 6)-ß-D-glucans. PPE was free of proteins and polyphenols as demonstrated by quantitative assays and NMR profiling. They showed a clear IFN-¿ inducing activity in human PBMCs, which suggests these polysaccharides to have proinflammatory effects. Treatment by ß-glucosidase caused the polysaccharides to be degraded into smaller fragments and at the same time increased their IFN-¿ inducing activity in PBMCs fourfold. In vitro, PPE showed a dose-dependent inhibition of the proliferation of the human leukemia Jurkat cell. At 100 µg/mL the cells’ viabilitywas decreased by appr. 51% compared to the control. EPR spin trapping demonstrated a high antioxidative activity against •OH and •O2- radicals of HWPE I and PPE. Further, the results of the antioxidant assays indicated that antioxidant activity against •OH radicals in the Fenton systemwas achieved through scavenging or through chelating iron mechanisms. The good immunomodulating and antioxidative properties of A. brasiliensis polysaccharide extract obtained by hot water extraction and ethanol precipitation make it suitable for everyday use as an inexpensive dietary supplement.
    Does autophagy mediate age-dependent effect of dietary restriction responses in the filamentous fungus Podospora anserina?
    Diepeningen, A.D. van; Engelmoer, D.J.P. ; Sellem, C.H. ; Huberts, D.H.E.W. ; Slakhorst, S.M. ; Sainsard-Chanet, A. ; Zwaan, B.J. ; Hoekstra, R.F. ; Debets, A.J.M. - \ 2014
    Philosophical Transactions of the Royal Society B. Biological sciences 369 (2014)1646. - ISSN 0962-8436
    life-span extension - calorie restriction - cell-death - saccharomyces-cerevisiae - mitochondrial fission - uth1 gene - senescence - plasmid - yeast - degradation
    Autophagy is a well-conserved catabolic process, involving the degradation of a cell's own components through the lysosomal/vacuolar machinery. Autophagy is typically induced by nutrient starvation and has a role in nutrient recycling, cellular differentiation, degradation and programmed cell death. Another common response in eukaryotes is the extension of lifespan through dietary restriction (DR). We studied a link between DR and autophagy in the filamentous fungus Podospora anserina, a multicellular model organism for ageing studies and mitochondrial deterioration. While both carbon and nitrogen restriction extends lifespan in P. anserina, the size of the effect varied with the amount and type of restricted nutrient. Natural genetic variation for the DR response exists. Whereas a switch to carbon restriction up to halfway through the lifetime resulted in extreme lifespan extension for wild-type P. anserina, all autophagy-deficient strains had a shorter time window in which ageing could be delayed by DR. Under nitrogen limitation, only PaAtg1 and PaAtg8 mediate the effect of lifespan extension; the other autophagy-deficient mutants PaPspA and PaUth1 had a similar response as wild-type. Our results thus show that the ageing process impinges on the DR response and that this at least in part involves the genetic regulation of autophagy
    Effect of Processing on the Quality of Pineapple Juice
    Hounhouigan, M.H. ; Linnemann, A.R. ; Soumanou, M.M. ; Boekel, M.A.J.S. van - \ 2014
    Food Reviews International 30 (2014)2. - ISSN 8755-9129 - p. 112 - 133.
    orange juice - fruit juices - ascorbic-acid - ananas-comosus - food-industry - amino-acids - saccharomyces-cerevisiae - phytochemical properties - neosartorya-fischeri - thermal-degradation
    Pineapple processing plays an important role in juice preservation. Because the quality of the pineapple juice is affected by the processing technology applied, the effects of pasteurization and other preservation methods on the overall juice quality were discussed. During juice processing, microorganisms are destroyed and chemical changes occur. To optimize processing conditions, knowledge of the kinetics of these reactions is needed, but as of yet, data on the degradation of the amino acids and vitamin C and the change in sugar contents during pineapple juice pasteurization are scanty. Furthermore, the kinetics of hydroxymethylfurfural production should be investigated by a precise technique such as high-performance liquid chromatography.
    Pulsed electric field processing of different fruit juices: impac of pH and temperature on inactivation of spoilage and pathogenic micro-organisms
    Timmermans, R.A.H. ; Nierop Groot, M.N. ; Nederhoff, A.L. ; Boekel, M.A.J.S. van; Matser, A.M. ; Mastwijk, H.C. - \ 2014
    International Journal of Food Microbiology 173 (2014). - ISSN 0168-1605 - p. 105 - 111.
    escherichia-coli o157-h7 - listeria-monocytogenes - orange juice - saccharomyces-cerevisiae - apple juice - lactobacillus-plantarum - salmonella-typhimurium - modeling inactivation - thermal inactivation - mild pasteurization
    Pulsed electrical field (PEF) technology can be used for the inactivation of micro-organisms and therefore for preservation of food products. It is a mild technology compared to thermal pasteurization because a lower temperature is used during processing, leading to a better retention of the quality. In this study, pathogenic and spoilage micro-organisms relevant in refrigerated fruit juices were studied to determine the impact of process parameters and juice composition on the effectiveness of the PEF process to inactivate the micro-organisms. Experiments were performed using a continuous-flow PEF system at an electrical field strength of 20kV/cm with variable frequencies to evaluate the inactivation of Salmonella Panama, Escherichia coli, Listeria monocytogenes and Saccharomyces cerevisiae in apple, orange and watermelon juices. Kinetic data showed that under the same conditions, S. cerevisiae was the most sensitive micro-organism, followed by S. Panama and E. coli, which displayed comparable inactivation kinetics. L. monocytogenes was the most resistant micro-organism towards the treatment conditions tested. A synergistic effect between temperature and electric pulses was observed at inlet temperatures above 35°C, hence less energy for inactivation was required at higher temperatures. Different juice matrices resulted in a different degree of inactivation, predominantly determined by pH. The survival curves were nonlinear and could satisfactorily be modeled with the Weibull model.
    Genome-wide analysis of pectate-induced gene expression in Botrytis cinerea: identification and functional analysis of putative D-galacturonic acid transporters
    Zhang, L. ; Hua, C. ; Stassen, J.H.M. ; Chatterjee, S. ; Cornelissen, M. ; Kan, J.A.L. van - \ 2014
    Fungal Genetics and Biology 72 (2014). - ISSN 1087-1845 - p. 182 - 191.
    wall degrading enzymes - saccharomyces-cerevisiae - filamentous fungi - endopolygalacturonase genes - colletotrichum fungi - hexose transporters - confocal microscopy - rna-seq - acid - virulence
    The fungal plant pathogen Botrytis cinerea produces a spectrum of cell wall degrading enzymes for the decomposition of host cell wall polysaccharides and the consumption of the monosaccharides that are released. Especially pectin is an abundant cell wall component, and the decomposition of pectin by B. cinerea has been extensively studied. An effective concerted action of the appropriate pectin depolymerising enzymes, monosaccharide transporters and catabolic enzymes is important for complete d-galacturonic acid utilization by B. cinerea. In this study, we performed RNA sequencing to compare genome-wide transcriptional profiles between B. cinerea cultures grown in media containing pectate or glucose as sole carbon source. Transcript levels of 32 genes that are induced by pectate were further examined in cultures grown on six different monosaccharides, by means of quantitative RT-PCR, leading to the identification of 8 genes that are exclusively induced by d-galacturonic acid. Among these, the hexose transporter encoding genes Bchxt15 and Bchxt19 were functionally characterised. The subcellular location was studied of BcHXT15-GFP and BcHXT19-GFP fusion proteins expressed under control of their native promoter, in a B. cinerea wild-type strain. Both genes are expressed during growth on d-galacturonic acid and the fusion proteins are localized in plasma membranes and intracellular vesicles. Target gene knockout analysis revealed that BcHXT15 contributes to d-galacturonic acid uptake at pH 5~5.6. The virulence of all B. cinerea hexose transporter mutants tested was unaltered on tomato and Nicotiana benthamiana leaves.
    The effect of natamycin on the transcriptome of conidia of Aspergillus niger
    Leeuwen, M.R. van; Krijgsheld, P. ; Wyatt, T.T. ; Golovina, E.A. ; Menke, H. ; Dekker, A. ; Stark, J. ; Stam, H. ; Bleichrodt, R. ; Wosten, H.A.B. ; Dijksterhuis, J. - \ 2013
    Studies in Mycology 74 (2013). - ISSN 0166-0616 - p. 71 - 85.
    plasma-membrane - saccharomyces-cerevisiae - candida-albicans - penicillium-discolor - germinating conidia - gene-expression - protein - ergosterol - fumigatus - metabolism
    The impact of natamycin on Aspergillus niger was analysed during the first 8 h of germination of conidia. Polarisation, germ tube formation, and mitosis were inhibited in the presence of 3 and 10 mu M of the anti-fungal compound, while at 10 mu M also isotropic growth was affected. Natamycin did not have an effect on the decrease of microviscosity during germination and the concomitant reduction in mannitol and trehalose levels. However, it did abolish the increase of intracellular levels of glycerol and glucose during the 8 h period of germination. Natamycin hardly affected the changes that occur in the RNA profile during the first 2 h of germination. During this time period, genes related to transcription, protein synthesis, energy and cell cycle and DNA processing were particularly up-regulated. Differential expression of 280 and 2586 genes was observed when 8 h old germlings were compared with conidia that had been exposed to 3 mu M and 10 mu M natamycin, respectively. For instance, genes involved in ergosterol biosynthesis were down-regulated. On the other hand, genes involved in endocytosis and the metabolism of compatible solutes, and genes encoding protective proteins were up-regulated in natamycin treated conidia.
    Incidence of symbiotic dsRNA 'killer' viruses in wild and domesticated yeast
    Pieczynska, M.D. ; Visser, J.A.G.M. de; Korona, R. - \ 2013
    FEMS Yeast Research 13 (2013)8. - ISSN 1567-1356 - p. 856 - 859.
    saccharomyces-cerevisiae - stranded-rna - toxins
    Viruses are found in almost all organisms and physical habitats. One interesting example is the yeast viral killer system'. The virus provides the host with a toxin directed against strains that do not carry it, while the yeast cell enables its propagation. Although yeast viruses are believed to be common, they have been actually described only for a limited number of yeast isolates. We surveyed 136 Saccharomyces cerevisiae and S.paradoxus strains of known origin and phylogenetic relatedness. Of these, 14 (c. 10%) were infected by killer viruses of one of the three types: K1, K2 or K28. As many as 34 strains (c. 25%) were not sensitive to at least one type of the killer toxin. In most cases, resistance did not disappear after attempts to cure the host strains from their viruses, suggesting that it was encoded in the host's genome. In terms of phylogeny, killer strains appear to be more related to each other than to nonkiller ones. No such tendency is observed for the phenotype of toxin resistance. Our results suggest that even if the killer toxins are not always present, they do play significant role in yeast ecology and evolution.
    Fermentation characteristics of yeasts isolated from traditionally fermented masau (Ziziphus mauritiana) fruits
    Nyanga, L.K. ; Nout, M.J.R. ; Smid, E.J. ; Boekhout, C. ; Zwietering, M.H. - \ 2013
    International Journal of Food Microbiology 166 (2013)3. - ISSN 0168-1605 - p. 426 - 432.
    saccharomyces-cerevisiae - volatile compounds - wine yeasts - immobilized cells - grape varieties - zimbabwe - strains - metabolism - acid - evolution
    Yeast strains were characterized to select potential starter cultures for the production of masau fermented beverages. The yeast species originally isolated from Ziziphus mauritiana (masau) fruits and their traditionally fermented fruit pulp in Zimbabwe were examined for their ability to ferment glucose and fructose using standard broth under aerated and non-aerated conditions. Most Saccharomyces cerevisiae strains were superior to other species in ethanol production. The best ethanol producing S. cerevisiae strains, and strains of the species Pichia kudriavzevii, Pichia fabianii and Saccharomycopsis fibuligera were tested for production of flavor compounds during fermentation of masau fruit juice. Significant differences in the production of ethanol and other volatile compounds during fermentation of masau juice were observed among and within the four tested species. Alcohols and esters were the major volatiles detected in the fermented juice. Trace amounts of organic acids and carbonyl compounds were detected. Ethyl hexanoate and ethyl octanoate were produced in highest amounts as compared to the other volatile compounds. S. cerevisiae strains produced higher amounts of ethanol and flavor compounds as compared to the other species, especially fatty acid ethyl esters that provide the major aroma impact of freshly fermented wines. The developed library of characteristics can help in the design of mixtures of strains to obtain a specific melange of product functionalities. Keywords: Masau juice; Fermentation; Yeast; Volatile compounds; Flavor; Wine
    Gene Coexpression Analysis Reveals Complex Metabolism of the Monoterpene Alcohol Linalool in Arabidopsis FlowersW
    Ginglinger, J.F. ; Boachon, B. ; Hofer, R. ; Paetz, C. ; Kollner, T.G. ; Miesch, L. ; Lugan, R. ; Baltenweck, R. ; Mutterer, J. ; Ullman, P. ; Verstappen, F.W.A. ; Bouwmeester, H.J. - \ 2013
    The Plant Cell 25 (2013)11. - ISSN 1040-4651 - p. 4640 - 4657.
    cytochrome-p450 limonene hydroxylases - avocado persea-americana - functional expression - endoplasmic-reticulum - terpene synthases - mint mentha - saccharomyces-cerevisiae - beta-glucuronidase - essential oil - floral scent
    The cytochrome P450 family encompasses the largest family of enzymes in plant metabolism, and the functions of many of its members in Arabidopsis thaliana are still unknown. Gene coexpression analysis pointed to two P450s that were coexpressed with two monoterpene synthases in flowers and were thus predicted to be involved in monoterpenoid metabolism. We show that all four selected genes, the two terpene synthases (TPS10 and TPS14) and the two cytochrome P450s (CYP71B31 and CYP76C3), are simultaneously expressed at anthesis, mainly in upper anther filaments and in petals. Upon transient expression in Nicotiana benthamiana, the TPS enzymes colocalize in vesicular structures associated with the plastid surface, whereas the P450 proteins were detected in the endoplasmic reticulum. Whether they were expressed in Saccharomyces cerevisiae or in N. benthamiana, the TPS enzymes formed two different enantiomers of linalool: (-)-(R)-linalool for TPS10 and (+)-(S)-linalool for TPS14. Both P450 enzymes metabolize the two linalool enantiomers to form different but overlapping sets of hydroxylated or epoxidized products. These oxygenated products are not emitted into the floral headspace, but accumulate in floral tissues as further converted or conjugated metabolites. This work reveals complex linalool metabolism in Arabidopsis flowers, the ecological role of which remains to be determined.
    The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana
    Wijnker, T.G. ; Velikkakam James, G. ; Ding, J. ; Becker, F.F.M. ; Klasen, J.R. ; Rawat, V. ; Rowan, B.A. ; Jong, de, D.F. ; Snoo, de, C.B. ; Zapata, L. ; Jong, H. de; Ossowski, S. ; Weigel, D. ; Koornneef, M. ; Keurentjes, J.J.B. ; Schneeberger, K. - \ 2013
    eLife 2 (2013). - ISSN 2050-084X
    dna methylation - recombination landscape - saccharomyces-cerevisiae - short reads - yeast - meiosis - reveals - mouse - sex - populations
    Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids. GC detection through short reads has previously been confounded by genomic rearrangements. Rigid filtering for misaligned reads allowed GC identification at high accuracy and revealed an ~80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination. Non-crossover associated GCs were extremely rare most likely due to their short average length of ~25-50 bp, which is significantly shorter than the length of CO-associated GCs. Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs.
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