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.

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Ecological risk assessment of the antibiotic enrofloxacin applied to Pangasius catfish farms in the Mekong delta, Vietnam
Rico Artero, A. ; Phu, T.M. ; Huong, D.T.T. ; Phuong, N.T. ; Brink, P.J. van den - \ 2015
Chemosphere 119 (2015). - ISSN 0045-6535 - p. 407 - 414.
veterinary antibiotics - ubiquitous occurrence - cell-wall - aquaculture - fate - oxytetracycline - ciprofloxacin - trimethoprim - sulfonamides - microcosms
Antibiotics applied in aquaculture production may be released into the environment and contribute to the deterioration of surrounding aquatic ecosystems. In the present study, we assessed the ecological risks posed by the use of the antibiotic enrofloxacin (ENR), and its main metabolite ciprofloxacin (CIP), in a Pangasius catfish farm in the Mekong Delta region, Vietnam. Water and sediment samples were collected in a stream receiving effluents from a Pangasius catfish farm that had applied ENR. The toxicity of ENR and CIP was assessed on three tropical aquatic species: the green-algae Chlorella sp. (72h - growth inhibition test), the micro-invertebrate Moina macrocopa (48h - immobilization test), and the Nile tilapia (Oreochromis niloticus). The toxic effects on O. niloticus were evaluated by measuring the cholinesterase (ChE) and catalase (CAT) activities in the fish brain and muscles, respectively, and by considering feed exposure and water exposure separately. Ecological risks were assessed by comparing maximum exposure concentrations with predicted no effect concentrations for cyanobacteria, green algae, invertebrates and fish derived with available toxicity data. The results of this study showed that maximum antibiotic concentrations in Pangasius catfish farm effluents were 0.68µgL-1 for ENR and 0.25µgL-1 for CIP (dissolved water concentrations). Antibiotics accumulated in sediments down-stream the effluent discharge point at concentrations up to 2590µgkg-1 d.w. and 592µgkg-1 d.w. for ENR and CIP, respectively. The calculated EC50 values for ENR and CIP were 111000 and 23000µgL-1 for Chlorella sp., and 69000 and 71000µgL-1 for M. macrocopa, respectively. Significant effects on the ChE and CAT enzymatic activities of O. niloticus were observed at 5gkg-1 feed and 400-50000µgL-1, for both antibiotics. The results of the ecological risk assessment performed in this study indicated only minor risks for cyanobacteria communities, suggesting that residual concentrations of ENR and CIP after medication are not likely to result in severe toxic effects on exposed aquatic ecosystems. However, more studies should be performed by considering other antibiotic treatments used in Pangasius catfish production and the potential ecotoxicological effects of relevant antibiotic mixtures on sediment communities.
Interactions between Auxin, Microtubules and XTHs Mediate Green Shade- Induced Petiole Elongation in Arabidopsis
Sasidharan, R. ; Keuskamp, D.H. ; Kooke, R. ; Voesenek, L.A.C.J. ; Pierik, R. - \ 2014
PLoS ONE 9 (2014)3. - ISSN 1932-6203
outer epidermal wall - cortical microtubules - plasma-membrane - cell-wall - maize coleoptiles - differential growth - avoidance responses - abiotic stresses - plant-cells - cellulose
Plants are highly attuned to translating environmental changes to appropriate modifications in growth. Such phenotypic plasticity is observed in dense vegetations, where shading by neighboring plants, triggers rapid unidirectional shoot growth (shade avoidance), such as petiole elongation, which is partly under the control of auxin. This growth is fuelled by cellular expansion requiring cell-wall modification by proteins such as xyloglucan endotransglucosylase/hydrolases (XTHs). Cortical microtubules (cMTs) are highly dynamic cytoskeletal structures that are also implicated in growth regulation. The objective of this study was to investigate the tripartite interaction between auxin, cMTs and XTHs in shade avoidance. Our results indicate a role for cMTs to control rapid petiole elongation in Arabidopsis during shade avoidance. Genetic and pharmacological perturbation of cMTs obliterated shade-induced growth and led to a reduction in XTH activity as well. Furthermore, the cMT disruption repressed the shade-induced expression of a specific set of XTHs. These XTHs were also regulated by the hormone auxin, an important regulator of plant developmental plasticity and also of several shade avoidance responses. Accordingly, the effect of cMT disruption on the shade enhanced XTH expression could be rescued by auxin application. Based on the results we hypothesize that cMTs can mediate petiole elongation during shade avoidance by regulating the expression of cell wall modifying proteins via control of auxin distribution.
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.
Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin
Douillard, F.P. ; Kant, R. ; Ritari, J. ; Paulin, L. ; Palva, A. ; Vos, W.M. de - \ 2013
Microbial Biotechnology 6 (2013)5. - ISSN 1751-7907 - p. 576 - 587.
lactic-acid bacteria - gram-positive bacteria - rhamnosus gg - functional-analysis - cell-wall - surface-proteins - staphylococcus-aureus - controlled-trial - binding-protein - sequence
The members of the Lactobacillus genus are widely used in the food and feed industry and show a remarkable ecological adaptability. Several Lactobacillus strains have been marketed as probiotics as they possess health-promoting properties for the host. In the present study, we used two complementary next-generation sequencing technologies to deduce the genome sequences of two Lactobacillus casei strains LcA and LcY, which were isolated from the products Actimel and Yakult, commercialized as probiotics. The LcA and LcY draft genomes have, respectively, an estimated size of 3067 and 3082 Mb and a G+ C content of 46.3%. Both strains are close to identical to each other and differ by no more than minor chromosomal re-arrangements, substitutions, insertions and deletions, as evident from the verified presence of one insertion-deletion (InDel) and only 29 single-nucleotide polymorphisms (SNPs). In terms of coding capacity, LcA and LcY are predicted to encode a comparable exoproteome, indicating that LcA and LcY are likely to establish similar interactions with human intestinal cells. Moreover, both L. casei LcA and LcY harboured a 59.6 kb plasmid that shared high similarities with plasmids found in other L. casei strains, such as W56 and BD-II. Further analysis revealed that the L. casei plasmids constitute a good evolution marker within the L. casei species. The plasmids of the LcA and LcY strains are almost identical, as testified by the presence of only three verified SNPs, and share a 3.5 kb region encoding a remnant of a lactose PTS system that is absent from the plasmids of W56 and BD-II but conserved in another smaller L. casei plasmid (pLC2W). Our observations imply that the results obtained in animal and human experiments performed with the Actimel and Yakult strains can be compared with each other as these strains share a very recent common ancestor.
A mechanism for reorientation of cortical microtubule arrays driven by microtubule severing
Lindeboom, J.J. ; Nakamura, M. ; Hibbel, A. ; Shundyak, K. ; Gutierrez, R. ; Ketelaar, T. ; Emons, A.M.C. ; Mulder, B.M. - \ 2013
Science 342 (2013)6163. - ISSN 0036-8075
outer epidermal wall - plasma-membrane - arabidopsis hypocotyl - maize coleoptiles - gamma-tubulin - higher-plants - growth-rate - cell-wall - in-vitro - katanin
Environmental and hormonal signals cause reorganization of microtubule arrays in higher plants, but the mechanisms driving these transitions have remained elusive. The organization of these arrays is required to direct morphogenesis. We discovered that microtubule severing by the protein katanin plays a crucial and unexpected role in the reorientation of cortical arrays, as triggered by blue light. Imaging and genetic experiments revealed that phototropin photoreceptors stimulate katanin-mediated severing specifically at microtubule intersections, leading to the generation of new microtubules at these locations. We show how this activity serves as the basis for a mechanism that amplifies microtubules orthogonal to the initial array, thereby driving array reorientation. Our observations show how severing is used constructively to build a new microtubule array.
The structure of an alternative wall teichoic acid produced by a Lactobacillus plantarum WCFS1 mutant contains a 1,5-linked poly(ribitol phosphate) backbone with 2-a-D-glucosyl substitutions
Tomita, S. ; Waard, P. de; Bakx, E.J. ; Schols, H.A. ; Kleerebezem, M. ; Bron, P.A. - \ 2013
Carbohydrate Research : an international journal 370 (2013). - ISSN 0008-6215 - p. 67 - 71.
cell-wall - staphylococcus-aureus - bacillus-subtilis - units
A tagF1-tagF2 deletion mutant of Lactobacillus plantarum lacks poly(glycerol phosphate) polymerase activity required for glycerol-type wall teichoic acid (WTA) biosynthesis. The mutant activates an alternative genetic locus, tarIJKL, encoding the enzymes for nucleotide activation and incorporation of ribitol in the WTA backbone polymer. This alternative ribitol-type WTA backbone and its repeating unit were isolated and characterized by HPAEC, UPLC-MS, NMR spectroscopy, and MALDI-TOF MS, using synthetic molecules as references. The structure was established as 1,5-linked poly(ribitol phosphate) which was substituted at the C-2 hydroxyl group of the ribitol residue with a-D-glucosyl at a frequency of 28%.
Isolation and chemical characterization of a glucogalactomannan of the medicinal mushroom Cordyceps militaris
Smiderle, F.R. ; Sassaki, G.L. ; Griensven, L.J.L.D. van; Iacomini, M. - \ 2013
Carbohydrate Polymers 97 (2013)1. - ISSN 0144-8617 - p. 74 - 80.
alditol acetate standards - beta-d-glucan - structural-characterization - pleurotus-pulmonarius - agaricus-bisporus - nmr-spectroscopy - edible mushroom - rapid synthesis - cell-wall - d-mannan
Cordyceps militaris dried fruiting bodies were extracted with 5% KOH solution. The extract was purified by freeze-thawing treatment, and dialysis (100 kDa), giving rise to a homogeneous polysaccharide (M-w 23,000 Da). Its monosaccharide composition was mannose (56.7%), galactose (34.5%), and glucose (8.8%). The anomeric configurations were determined by their coupling constants. A complex polysaccharide was identified by NMR and methylation analysis. The HSQC spectrum showed signals at delta 107.7/5.06 and 106.1/5.14; 105.9/5.12 relative to beta-D-Galf, and O-2-substituted beta-D-Galf units, respectively. The sign at delta 104.4/5.21 corresponded to alpha-D-Galf. Other signals corresponded to alpha-D-Manp O-6- and O-2-substituted (delta 100.2/4.94; 100.5/5.27; 100.6/5.23; 100.7/5.16), and alpha-D-Manp 2,6-di-O-substituted (from delta 99.3 to 99.9). The main linkages, confirmed by methylation analysis, showed the derivatives: 2,3,4-Me-3-Manp (11.9%) and 3,4,6-Me-3-Manp (28.6%). The branches were (1 -> 6)-linked-alpha-D-Manp or (1 -> 2)-linked-beta-D-Galf, terminating with beta-D-Galf, alpha-D-Galf, alpha-D-Galp, or alpha-D-Manp. 42.7% of the partially hydrolyzed product consisted of 3,4,6-Me-3-Manp, suggesting a (1 -> 2)-linked backbone. (C) 2013 Elsevier Ltd. All rights reserved.
The potential of C4 grasses for cellulosic biofuel production
Weijde, R.T. van der; Alvim Kamei, C.L. ; Torres Salvador, A.F. ; Vermerris, W. ; Dolstra, O. ; Visser, R.G.F. ; Trindade, L.M. - \ 2013
Frontiers in Plant Science 4 (2013). - ISSN 1664-462X
miscanthus-x-giganteus - bicolor-l. moench - leading pretreatment technologies - switchgrass panicum-virgatum - water-use efficiency - 1st 2 years - sorghum-bicolor - biomass production - corn stover - cell-wall
With the advent of biorefinery technologies enabling plant biomass to be processed into biofuel, many researchers set out to study and improve candidate biomass crops. Many of these candidates are C4 grasses, characterized by a high productivity and resource use efficiency. In this review the potential of five C4 grasses as lignocellulosic feedstock for biofuel production is discussed. These include three important field crops-maize, sugarcane and sorghum-and two undomesticated perennial energy grasses-miscanthus and switchgrass. Although all these grasses are high yielding, they produce different products. While miscanthus and switchgrass are exploited exclusively for lignocellulosic biomass, maize, sorghum, and sugarcane are dual-purpose crops. It is unlikely that all the prerequisites for the sustainable and economic production of biomass for a global cellulosic biofuel industry will be fulfilled by a single crop. High and stable yields of lignocellulose are required in diverse environments worldwide, to sustain a year-round production of biofuel. A high resource use efficiency is indispensable to allow cultivation with minimal inputs of nutrients and water and the exploitation of marginal soils for biomass production. Finally, the lignocellulose composition of the feedstock should be optimized to allow its efficient conversion into biofuel and other by-products. Breeding for these objectives should encompass diverse crops, to meet the demands of local biorefineries and provide adaptability to different environments. Collectively, these C4 grasses are likely to play a central role in the supply of lignocellulose for the cellulosic ethanol industry. Moreover, as these species are evolutionary closely related, advances in each of these crops will expedite improvements in the other crops. This review aims to provide an overview of their potential, prospects and research needs as lignocellulose feedstocks for the commercial production of biofuel.
Impact of Lactobacillus plantarum sortase on target-protein sorting, gastrointestinal persistence, and host immune response modulation
Remus, D.M. ; Bongers, R.S. ; Meijerink, M. ; Fusetti, F. ; Poolman, B. ; Vos, P. de; Wells, J. ; Kleerebezem, M. ; Bron, P.A. - \ 2013
Journal of Bacteriology 195 (2013)3. - ISSN 0021-9193 - p. 502 - 509.
surface-associated proteins - gene-expression omnibus - cell-wall - staphylococcus-aureus - srta gene - streptococcus-gordonii - listeria-monocytogenes - functional-analysis - lipoteichoic acid - binding-protein
Sortases are transpeptidases that couple surface proteins to the peptidoglycan of Gram-positive bacteria, and several sortase-dependent proteins (SDPs) have been demonstrated to be crucial for the interactions of pathogenic and nonpathogenic bacteria with their hosts. Here, we studied the role of sortase A (SrtA) in Lactobacillus plantarum WCFS1, a model Lactobacillus for probiotic organisms. An isogenic srtA deletion derivative was constructed which did not show residual SrtA activity. DNA microarray-based transcriptome analysis revealed that the srtA deletion had only minor impact on the full-genome transcriptome of L. plantarum, while the expression of SDP-encoding genes remained completely unaffected. Mass spectrometry analysis of the bacterial cell surface proteome, which was assessed by trypsinization of intact bacterial cells and by LiCl protein extraction, revealed that SrtA is required for the appropriate subcellular location of specific SDPs and for their covalent coupling to the cell envelope, respectively. We further found that SrtA deficiency did not affect the persistence and/or survival of L. plantarum in the gastrointestinal tract of mice. In addition, an in vitro immature dendritic cell (iDC) assay revealed that the removal of surface proteins by LiCl strongly affected the proinflammatory signaling properties of the SrtA-deficient strain but not of the wild type, which suggests a role of SDPs in host immune response modulation.
The quest for probiotic effector molecules - Unraveling strain specificity at the molecular level
Lee, I.C. ; Tomita, S. ; Kleerebezem, M. ; Bron, P.A. - \ 2013
Pharmacological Research 69 (2013)1. - ISSN 1043-6618 - p. 61 - 74.
wall teichoic-acid - lactobacillus-rhamnosus gg - alanyl-lipoteichoic acid - complete genome sequence - gram-positive bacteria - antibiotic-associated diarrhea - bacillus-subtilis w23 - cell-wall - staphylococcus-aureus - dendritic-cell
Pharmaceutical agents are widely applied for the treatment of gastrointestinal (and systemic) disorders and their role as modulators of host cell responses is relatively well characterized. By contrast, we are only beginning to understand the molecular mechanisms by which health-promoting, probiotic bacteria act as host cell modulators. The last decade has seen a rapid development of the genomics field for the widely applied probiotic genus Lactobacillus, and nowadays dozens of full genome sequences are available, as well as sophisticated post genomic and genetic engineering tools. This development has enabled comparative (functional) genomics approaches to identify the bacterial effector molecules involved in molecular communication with the host system that may underlie the probiotic effects observed. These efforts can also be complemented with dedicated mutagenesis approaches to eliminate or alter these effector molecules, followed by assessment of the host interaction consequences thereof, allowing the elucidation of the molecular mechanisms involved in probiotic health effects. Many of these approaches have pinpointed that the Lactobacillus cell envelope contains several effector molecules that are pivotal in the direct signaling capacity of these bacteria that underlies their immunomodulatory effects, including lipoteichoic acid, peptidoglycan, and (glyco)proteins. Moreover, the cell envelope contains several compounds such as wall teichoic acid and capsular polysaccharides that may not be involved in direct signaling to the host cell, but still affect signaling through shielding of other bacterial effector molecules. Initial structural studies revealed subtle strain- and species-specific biochemical differences in the canonical cell envelope compounds that are involved in these host interactions. These biochemical variations include the degree and positioning of d-alanyl and glycosyl substitution in lipoteichoic acids, and acetylation of peptidoglycan. Furthermore, specific peptides derived from peptidoglycan and envelope associated (glyco)proteins were recently identified as potent immunomodulators. The latter findings are exciting in the light of the possibility of more pharmacological application of these bioactive probiotic molecules, and especially cost-effective production and targeted delivery of bioactive peptides seems to emerge as a feasible strategy to harness this knowledge.
Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching
Bron, P.A. ; Tomita, S. ; Swam, I. van; Remus, D.M. ; Meijerink, M. ; Wels, M. ; Okada, S. ; Wells, J. ; Kleerebezem, M. - \ 2012
Microbial Cell Factories 11 (2012). - ISSN 1475-2859
aureus nasal colonization - complete genome sequence - toll-like receptor-2 - staphylococcus-aureus - bacillus-subtilis - lipoteichoic acid - cell-wall - peptidoglycan - biosynthesis - glycerol
Background - Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA) in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. Results - Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-¿B reporter cells expressing Toll like receptor (TLR)-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-a after stimulation with the WTA mutants as compared to the wild-type. Conclusions - The study presented here correlates structural differences in WTA to their functional characteristics, thereby providing important information aiding to improve our understanding of molecular host-microbe interactions and probiotic functionality
Identification of key peptidoglycan hydrolases for morphogenesis, autolysis, and peptidoglycan composition of Lactobacillus plantarum WCFS1.
Rolain, T. ; Bernard, E. ; Courtin, P. ; Bron, P.A. ; Kleerebezem, M. ; Chapot-Chartier, M.P. ; Hols, P. - \ 2012
Microbial Cell Factories 11 (2012). - ISSN 1475-2859
lactic-acid bacteria - lactococcus-lactis - n-acetylglucosaminidase - cell-wall - staphylococcus-aureus - bacillus-subtilis - murein hydrolase - gene - genome - electroporation
Background - Lactobacillus plantarum is commonly used in industrial fermentation processes. Selected strains are also marketed as probiotics for their health beneficial effects. Although the functional role of peptidoglycan-degrading enzymes is increasingly documented to be important for a range of bacterial processes and host-microbe interactions, little is known about their functional roles in lactobacilli. This knowledge holds important potential for developing more robust strains resistant to autolysis under stress conditions as well as peptidoglycan engineering for a better understanding of the contribution of released muramyl-peptides as probiotic immunomodulators. Results - Here, we explored the functional role of the predicted peptidoglycan hydrolase (PGH) complement encoded in the genome of L. plantarum by systematic gene deletion. From twelve predicted PGH-encoding genes, nine could be individually inactivated and their corresponding mutant strains were characterized regarding their cell morphology, growth, and autolysis under various conditions. From this analysis, we identified two PGHs, the predicted N-acetylglucosaminidase Acm2 and NplC/P60 D,L-endopeptidase LytA, as key determinants in the morphology of L. plantarum. Acm2 was demonstrated to be required for the ultimate step of cell separation of daughter cells, whereas LytA appeared to be required for cell shape maintenance and cell-wall integrity. We also showed by autolysis experiments that both PGHs are involved in the global autolytic process with a dominant role for Acm2 in all tested conditions, identifying Acm2 as the major autolysin of L. plantarum WCFS1. In addition, Acm2 and the putative N-acetylmuramidase Lys2 were shown to play redundant roles in both cell separation and autolysis under stress conditions. Finally, the analysis of the peptidoglycan composition of Acm2- and LytA-deficient derivatives revealed their potential hydrolytic activities by the disappearance of specific cleavage products. Conclusion - In this study, we showed that two PGHs of L. plantarum have a predominant physiological role in a range of growth conditions. We demonstrate that the N-acetylglucosaminidase Acm2 is the major autolysin whereas the D,L-endopeptidase LytA is a key morphogenic determinant. In addition, both PGHs have a direct impact on PG structure by generating a higher diversity of cleavage products that could be of importance for interaction with the innate immune system.
The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry
Wit, P.J.G.M. de; Burgt, I.A. van der; Ökman, B. ; Stergiopoulos, I. ; Abd-Elsalam, K.A. ; Aerts, A.L. ; Bahkali, A.H. ; Beenen, H.G. ; Chettri, P. ; Cox, M.P. ; Datema, E. ; Vries, R.P. de; Dhillon, B. ; Ganley, A.R. ; Griffiths, S.A. ; Guo, Y. ; Hamelin, R.C. ; Henrissat, B. ; Karimi Jashni, M. ; Kema, G.H.J. ; Klaubauf, S. ; Lapidus, A. ; Levasseur, A. ; Lindquist, E. ; Mehrabi, R. ; Ohm, R.A. ; Owen, T.J. ; Salamov, A. ; Schwelm, A. ; Burg, H.A. van den; Ham, R.C.H.J. van; Zhang, S. ; Goodwin, S.B. ; Collemare, J. - \ 2012
Plos Genetics 8 (2012)11. - ISSN 1553-7404
induced point mutation - fusiform rust disease - avirulence gene avr9 - mating-type genes - aspergillus-nidulans - needle blight - leptosphaeria-maculans - forest pathogen - leaf mold - cell-wall
We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an a-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation
Mechanism and control of Genipa americana seed germination
Queiroz, S.E.E. ; Silva, E.A.A. da; Davide, A.C. ; Jose, A.C. ; Silva, A.T. ; Fraiz, A.C.R. ; Faria, J.M.R. ; Hilhorst, H.W.M. - \ 2012
Physiologia Plantarum 144 (2012)3. - ISSN 0031-9317 - p. 263 - 276.
endo-beta-mannanase - tomato lycopersicon-esculentum - endosperm cap - abscisic-acid - cell-wall - micropylar endosperm - radicle emergence - molecular-cloning - embryo - gene
Genipa americana (Rubiaceae) is important for restoration of riparian forest in the Brazilian Cerrado. The objective was to characterize the mechanism and control of germination of G. americana to support uniform seedling production. Morphology and morphometrics of seeds, embryo and endosperm were assessed by light and scanning electron microscopy during germination. Imbibition and germination curves were generated and over the same time interval endosperm digestion and resistance were measured by puncture force analysis and activity assay of endo-ß-mannanase in water and in abscisic acid. The gene encoding for endo-ß-mannanase was partially cloned and its expression monitored by qRT-PCR. Embryos displayed growth prior to radicle protrusion. A two-phase increase in endo-ß-mannanase activity coincided with the two stages of weakening of the micropylar endosperm. The second stage also coincided with growth of the embryo prior to radicle protrusion. Enzyme activity was initiated in the micropylar endosperm but spread to the lateral endosperm. ABA
Fluorescence and Atomic Force Microscopy Imaging of Wall Teichoic Acids in Lactobacillus plantarum
Andre, G. ; Deghorain, M. ; Bron, P.A. ; Swam, I.I. van; Kleerebezem, M. ; Hols, P. ; Dufrene, Y.F. - \ 2011
Acs Chemical Biology 6 (2011)4. - ISSN 1554-8929 - p. 366 - 376.
gram-positive bacteria - staphylococcus-aureus - cell-wall - lipoteichoic acid - bacillus-subtilis - growth - localization - peptidoglycan - biosynthesis - spectroscopy
Although teichoic acids are major constituents of bacterial cell walls, little is known about the relationships between their spatial localization and their functional roles. Here, we used single-molecule atomic force microscopy (AFM) combined with fluorescence microscopy to image the distribution of wall teichoic acids (WTAs) in. Lactobacillus plantarum, in relation with their physiological roles. Phenotype analysis of the wild-type strain and of mutant strains deficient for the synthesis of WTAs (Delta tagO) or cell wall polysaccharides (Delta cps1-4) revealed that WTAs are required for proper cell elongation and cell division. Nanoscale imaging by AFM showed that strains expressing WTAs have a highly polarized surface morphology, the poles being much smoother than the side walls. AFM and fluorescence imaging with specific lectin probes demonstrated that the polarized surface structure correlates with a heterogeneous distribution of WTAs, the latter being absent from the surface of the poles. These observations indicate that the polarized distribution of WTAs in L. plantarum plays a key role in controlling cell morphogenesis (surface roughness, cell shape, elongation, and division).
The Nutritive value of mulberry leaves (Morus Alba) and partial replacement of cotton seed in rations on the performance of growing Vietnamese cattle
Vu, C.C. ; Verstegen, M.W.A. ; Hendriks, W.H. ; Pham, K.T. - \ 2011
Asian-Australasian Journal of Animal Sciences 24 (2011)9. - ISSN 1011-2367 - p. 1233 - 1242.
grass hay - cell-wall - digestibility - sheep - digestion - matter - goats
The in vivo digestibility of mulberry leaves (Morus alba) and the effects of the partial replacement of cotton seed with fresh mulberry leaf in rations on the performance of growing Vietnamese cattle was investigated. For the in vivo digestibility trial, twenty castrated rams of Phanrang breed (a local prolific breed) with an initial weight of 23-25 kg, were first assigned to four groups according to weight and then randomly assigned to one of four dietary treatments to determine digestibility of nutrients in mulberry leaves (M. alba), natural Bermuda grass (Cynodon dactylon), elephant grass (Pennisetum purpureum) and buffalo grass (Panicum maximum cv. TD 58). All forages were cut and chopped daily before being offered (at 120% maintenance) to the sheep. In the feeding trial, 20 Laisind (Vietnam yellow cows×Red Sindhy bulls) crossbred bulls averaged 18 month old and 184 kg were used to investigate the effect of partial replacement of cottonseed in the diet by mulberry leaves on live weight gain and feed conversion rate. The experiment was a randomized complete block design with four levels of fresh mulberry leaves which varied from 0 to 15% of total dietary dry mater and five animals per treatment over an 84 day period. The in vivo digestion trial showed the superior quality of mulberry leaves compared with the grasses. Chemical analysis indicated that mulberry leaves had the highest CP and the lowest NDF contents (22.3 and 31.1% DM, respectively) among the four forages tested. Digestibility of DM and OM of the mulberry leaf (66.4 and 71.8%, respectively) was also the highest but that of CP (58.2%) and NDF (58.4%) was the lowest of the four forages evaluated (p
Aiming for the complete utilization of sugar-beet pulp: Examination of the effects of mild acid and hydrothermal pretreatment followed by enzymatic digestion
Kuhnel, S. ; Schols, H.A. ; Gruppen, H. - \ 2011
Biotechnology for Biofuels 4 (2011). - ISSN 1754-6834 - 14 p.
severity parameter - side-chains - cell-wall - degradation - fermentation - pectins - inhibition - hydrolysis - cellulose - lignocellulosics
Background - Biomass use for the production of bioethanol or platform chemicals requires efficient breakdown of biomass to fermentable monosaccharides. Lignocellulosic feedstocks often require physicochemical pretreatment before enzymatic hydrolysis can begin. The optimal pretreatment can be different for different feedstocks, and should not lead to biomass destruction or formation of toxic products. Methods - We examined the influence of six mild sulfuric acid or water pretreatments at different temperatures on the enzymatic degradability of sugar-beet pulp (SBP). Results - We found that optimal pretreatment at 140°C of 15 minutes in water was able to solubilize 60% w/w of the total carbohydrates present, mainly pectins. More severe treatments led to the destruction of the solubilized sugars, and the subsequent production of the sugar-degradation products furfural, hydroxymethylfurfural, acetic acid and formic acid. The pretreated samples were successfully degraded enzymatically with an experimental cellulase preparation. Conclusions - In this study, we found that pretreatment of SBP greatly facilitated the subsequent enzymatic degradation within economically feasible time ranges and enzyme levels. In addition, pretreatment of SBP can be useful to fractionate functional ingredients such as arabinans and pectins from cellulose. We found that the optimal combined severity factor to enhance the enzymatic degradation of SBP was between log R'0 = -2.0 and log R'0 = -1.5. The optimal pretreatment and enzyme treatment solubilized up to 80% of all sugars present in the SBP, including =90% of the cellulose.
Distribution of callose synthase, cellulose synthase, and sucrose synthase in tobacco pollen tube is controlled in dissimilar ways by actin filaments and microtubules
Cai, G. ; Faleri, C. ; Casino, C. ; Emons, A.M.C. ; Cresti, M. - \ 2011
Plant Physiology 155 (2011)3. - ISSN 0032-0889 - p. 1169 - 1190.
arabidopsis root hairs - nicotiana-alata link - cell-wall - plasma-membrane - f-actin - cortical microtubules - vegetative nucleus - polarized growth - genetic-evidence - generative cell
Callose and cellulose are fundamental components of the cell wall of pollen tubes and are probably synthesized by distinct enzymes, callose synthase and cellulose synthase, respectively. We examined the distribution of callose synthase and cellulose synthase in tobacco (Nicotiana tabacum) pollen tubes in relation to the dynamics of actin filaments, microtubules, and the endomembrane system using specific antibodies to highly conserved peptide sequences. The role of the cytoskeleton and membrane flow was investigated using specific inhibitors (latrunculin B, 2,3-butanedione monoxime, taxol, oryzalin, and brefeldin A). Both enzymes are associated with the plasma membrane, but cellulose synthase is present along the entire length of pollen tubes (with a higher concentration at the apex) while callose synthase is located in the apex and in distal regions. In longer pollen tubes, callose synthase accumulates consistently around callose plugs, indicating its involvement in plug synthesis. Actin filaments and endomembrane dynamics are critical for the distribution of callose synthase and cellulose synthase, showing that enzymes are transported through Golgi bodies and/or vesicles moving along actin filaments. Conversely, microtubules appear to be critical in the positioning of callose synthase in distal regions and around callose plugs. In contrast, cellulose synthases are only partially coaligned with cortical microtubules and unrelated to callose plugs. Callose synthase also comigrates with tubulin by Blue Native-polyacrylamide gel electrophoresis. Membrane sucrose synthase, which expectedly provides UDP-glucose to callose synthase and cellulose synthase, binds to actin filaments depending on sucrose concentration; its distribution is dependent on the actin cytoskeleton and the endomembrane system but not on microtubules.
Biochemical Characterization and Relative Expression Levels of Multiple Carbohydrate Esterases of the Xylanolytic Rumen Bacterium Prevotella ruminicola 23 Grown on an Ester-Enriched Substrate
Kabel, M.A. ; Yeoman, C.J. ; Han, Y. ; Dodd, D. ; Abbas, C.A. ; Bont, J.A.M. de; Morrison, M. ; Cann, I.K.O. ; Mackie, R.I. - \ 2011
Applied and Environmental Microbiology 77 (2011)16. - ISSN 0099-2240 - p. 5671 - 5681.
predicting subcellular-localization - eucalyptus-globulus labill - xylo-oligosaccharides - acetyl xylan - cell-wall - structural features - ferulic acid - maize bran - specificity - hydrolysis
We measured expression and used biochemical characterization of multiple carbohydrate esterases by the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate to gain insight into the carbohydrate esterase activities of this hemicellulolytic rumen bacterium. The P. ruminicola 23 genome contains 16 genes predicted to encode carbohydrate esterase activity, and based on microarray data, four of these were upregulated >2-fold at the transcriptional level during growth on an ester-enriched oligosaccharide (XOSFA,Ac) from corn relative to a nonesterified fraction of corn oligosaccharides (AXOS). Four of the 16 esterases (Xyn10D-Fae1A, Axe1-6A, AxeA1, and Axe7A), including the two most highly induced esterases (Xyn10D-Fae1A and Axe1-6A), were heterologously expressed in Escherichia coli, purified, and biochemically characterized. All four enzymes showed the highest activity at physiologically relevant pH (6 to 7) and temperature (30 to 40°C) ranges. The P. ruminicola 23 Xyn10D-Fae1A (a carbohydrate esterase [CE] family 1 enzyme) released ferulic acid from methylferulate, wheat bran, corn fiber, and XOSFA,Ac, a corn fiber-derived substrate enriched in O-acetyl and ferulic acid esters, but exhibited negligible activity on sugar acetates. As expected, the P. ruminicola Axe1-6A enzyme, which was predicted to possess two distinct esterase family domains (CE1 and CE6), released ferulic acid from the same substrates as Xyn10D-Fae1 and was also able to cleave O-acetyl ester bonds from various acetylated oligosaccharides (AcXOS). The P. ruminicola 23 AxeA1, which is not assigned to a CE family, and Axe7A (CE7) were found to be acetyl esterases that had activity toward a broad range of mostly nonpolymeric acetylated substrates along with AcXOS. All enzymes were inhibited by the proximal location of other side groups like 4-O-methylglucuronic acid, ferulic acid, or acetyl groups. The unique diversity of carbohydrate esterases in P. ruminicola 23 likely gives it the ability to hydrolyze substituents on the xylan backbone and enhances its capacity to efficiently degrade hemicellulose.
Organic modification and subsequent biofunctionalization of porous anodic alumina using terminal alkynes
Maat, J. ter; Regeling, R. ; Ingham, C.J. ; Weijers, C.A.G.M. ; Giesbers, M. ; Vos, W.M. de; Zuilhof, H. - \ 2011
Langmuir 27 (2011)22. - ISSN 0743-7463 - p. 13606 - 13617.
ultraviolet difference spectroscopy - normal-alkanoic acids - coated glass slides - candida-albicans - cell-wall - molecular assemblies - peanut agglutinin - carbohydrate interactions - carbon nanotubes - oxide membranes
Porous anodic alumina (PAA) is a well-defined material that has found many applications. The range of applications toward sensing and recognition can be greatly expanded if the alumina surface is covalently modified with an organic monolayer. Here, we present a new method for the organic modification of PAA based on the reaction of terminal alkynes with the alumina surface. The reaction results in the the formation of a monolayer within several hours at 80 °C and is dependent on both oxygen and light. Characterization with X-ray photoelectron spectroscopy and infrared spectroscopy indicates formation of a well-defined monolayer in which the adsorbed species is an oxidation product of the 1-alkyne, namely, its a-hydroxy carboxylate. The obtained monolayers are fairly stable in water and at elevated temperatures, as was shown by monitoring the water contact angle. Modification with 1,15-hexadecadiyne resulted in a surface that has alkyne end groups available for further reaction, as was demonstrated by the subsequent reaction of N-(11-azido-3,6,9-trioxaundecyl)trifluoroacetamide with the modified surface. Biofunctionalization was explored by coupling 11-azidoundecyl lactoside to the surface and studying the subsequent adsorption of the lectin peanut agglutinin (PNA) and the yeast Candida albicans , respectively. Selective and reversible binding of PNA to the lactosylated surfaces was demonstrated. Moreover, PNA adsorption was higher on surfaces that exposed the ß-lactoside than on those that displayed the a anomer, which was attributed to surface-associated steric hindrance. Likewise, the lactosylated surfaces showed increased colonization of C. albicans compared to unmodified surfaces, presumably due to interactions involving the cell wall ß-glucan. Thus, this study provides a new modification method for PAA surfaces and shows that it can be used to induce selective adsorption of proteins and microorganisms
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