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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    Similarities among FARA-led IAR4D innovation platforms
    Sagary Nokoe, K. ; Rijn, F.C. van; Adekunle, A.A. ; Ayanwale, A.B. ; Nyikahadzoi, K. - \ 2013
    ESJ European Scientific Journal 9 (2013)36. - ISSN 1857-7881
    Multi-stakeholder partnerships network which is typified by the FARA-led Integrated Agriculture Research for Development (IAR4D) of the SSA-Challenge Program is an innovation platform (IP) composed of stakeholders bound together by their individual interests in a shared commodity or outcome. The result from such innovation platforms is largely influenced by the strength of the network. In this paper, similarities within and across platforms are assessed using the simple matching procedure. Results indicate consistency in conduct of Innovation Platform activities. Minor differences in IPs across various regions are consistent with impact outcome observed in the operation of the IPs.
    Identification of modules in Aspergillus niger by gene co-expression network analysis
    Berg, R.A. van den; Braaksma, M. ; Veen, D. van der; Werf, M.J. van der; Punt, P.J. ; Oost, J. van der; Graaff, L.H. de - \ 2010
    Fungal Genetics and Biology 47 (2010)6. - ISSN 1087-1845 - p. 539 - 550.
    filamentous fungi - regulatory networks - expression analysis - analysis reveals - microarray data - scale - yeast - cell - conservation - encyclopedia
    The fungus Aspergillus niger has been studied in considerable detail with respect to various industrial applications. Although its central metabolic pathways are established relatively well, the mechanisms that control the adaptation of its metabolism are understood rather poorly. In this study, clustering of co-expressed genes has been performed on the basis of DNA microarray data sets from two experimental approaches. In one approach, low amounts of inducer caused a relatively mild perturbation, while in the other approach the imposed environmental conditions including carbon source starvation caused severe perturbed stress. A set of conserved genes was used to construct gene co-expression networks for both the individual and combined data sets. Comparative analysis revealed the existence of modules, some of which are present in all three networks. In addition, experimental condition-specific modules were identified. Module-derived consensus expression profiles enabled the integration of all protein-coding A. niger genes to the co-expression analysis, including hypothetical and poorly conserved genes. Conserved sequence motifs were detected in the upstream region of genes that cluster in some modules, e.g., the binding site for the amino acid metabolism-related transcription factor CpcA as well as for the fatty acid metabolism-related transcription factors, FarA and FarB. Moreover, not previously described putative transcription factor binding sites were discovered for two modules: the motif 5'-CGACAA is overrepresented in the module containing genes encoding cytosolic ribosomal proteins, while the motif 5'-GGCCGCG is overrepresented in genes related to 'gene expression', such as RNA helicases and translation initiation factors
    Disinfection and the prevention of infectious disease
    Bloomfield, S.F. ; Beumer, R.R. ; Exner, M. ; Fara, G.M. ; Scott, E. ; Nath, K.J. - \ 2004
    American Journal of Infection Control 32 (2004)5. - ISSN 0196-6553 - p. 311 - 313.
    domestic kitchen - hygiene - contamination
    Guidelines for prevention of infection and cross infection in the domestic environment
    Beumer, R.R. ; Bloomfield, S. ; Exner, M. ; Fara, G.M. ; Scott, E. ; Kumar Jyoti Nath, - \ 2002
    Unknown Publisher (Intramed Communications ) - 44 p.
    Listeria monocytogenes in domestic environments: recommendations of the international forum on home hygiene
    Beumer, R.R. ; Bloomfield, S.F. ; Exner, M. ; Fara, G.M. ; Nath, K.J. ; Scott, E. - \ 2001
    In: Proceedings of ISOPOL XIV, Mannheim, 2001 Mannheim : ISOPOL - p. 182 - 182.
    Development of guidelines for prevention of infection and cross infection in the domestic setting
    Beumer, R. ; Bloomfield, S.F. ; Exner, M. ; Fara, G.M. ; Nath, K.J. ; Scott, E. - \ 2001
    In: SAM Summer Conference, Swansea, UK, 2001. - Swansea : Society for Applied Microbiology, 2001 - p. 26 - 26.
    Microbial resistance and biocides : A review by the International Forum on Home Hygiene (IFH)
    Beumer, R.R. ; Bloomfield, S.F. ; Exner, M. ; Fara, G.M. ; Nath, K.J. ; Scott, E. - \ 2000
    International Scientific Forum on Home Hygiene - 42 p.
    Recommendations for selection of suitable hygiene procedures for use in the domestic environment
    Beumer, R. ; Bloomfield, S. ; Exner, M. ; Fara, G.M. ; Nath, K.J. ; Scott, E. - \ 2000
    Milan, Italy : Intramed Communications s.r.l. - 36 p.
    The need for a home hygiene policy and guidelines on home hygiene
    Beumer, R. ; Bloomfield, S. ; Exner, M. ; Fara, G.M. ; Scott, E. - \ 1999
    Annali di Igiene (1999)11. - p. 11 - 26.
    Glucuronoarabinoxylans from sorghum grain
    Verbruggen, M.A. - \ 1996
    Agricultural University. Promotor(en): A.G.J. Voragen; G. Beldman. - S.l. : Verbruggen - ISBN 9789054855026 - 131
    sorghum bicolor - polysacchariden - structuur - chemische reacties - sorghum - sorghum bicolor - polysaccharides - structure - chemical reactions - sorghum

    Water-unextractable cell wall materials (WUS) were prepared from raw, polished, and malted sorghum ( Sorghum vulgare cv. Fara Fara). Except for the amounts, hardly any difference could be observed between the WUS of these three raw materials. This means that cell wall materials of the endosperm cell walls are basically the same as those of the outer endosperm and pericarp layers, and that the cell walls largely persist, during malting. These preparations were further fractionated by a sequential extraction procedure using aqueous solutions of saturated Ba(OH) 2 , 1M KOH and 4M KOH. The WUS preparations were composed of glucuronoarabinoxylans (GAX), (1→3),(1→4)-β-D-glucans, cellulose, and some protein. GAX was primarily extracted by Ba(OH) 2 solutions. All GAX fractions were composed of a highly substituted (1→4)-β-D-xylan backbone, substituted by arabinose and uronic acid. It was concluded that sorghum GAX populations were characterized by a reasonable homogeneity, since they could not be separated further by several chromatographic and precipitation techniques.

    Degradation studies using purified xylanases, arabinofuranosidases and a glucuronidase alone or in combination, showed that the GAX populations were hardly broken down. Some oligomers were formed by digesting Ba(OH) 2 extracted GAX with a combination of endoxylanase I and (1→4)-β-D-arabinoxylan arabinofuranohydrolase, both purified from Aspergillus awamori . These oligomers were found to have a main chain of three or four xylose units, and to contain α-glucuronic acid linked to O -2 of the non-reducing terminal xylose unit. Two oligomers were found to have a dimeric (1→2)-linked arabinose side, chain linked at O -3 of an internal xylose unit. Also single arabinose substitution occured at O -3 of an internal xylose unit. There are strong indications that these side groups can also be linked at O -2 of an internal xylose residue. The reducing xylose units were unsubstituted. A model for the GAX populations from sorghum was proposed combining the results of the degradation studies, the identification of the oligomers, and knowledge about the mode of action of the enzymes used.

    Finally, the developed techniques to investigate GAX in particular, were used to study the behaviour of GAX in the brewing process. Worts and spent grains of mashes, supplemented with commercial enzyme preparations containing xylanases among others were studied. Except for the amount of solubilized GAX, the GAX hardly changed with respect to the sugar composition and molecular weight distribution. A direct relationship between GAX, xylanases, and filtration behaviour of worts prepared from malted sorghum, could therefore not be established.

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