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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Requirements for the domain model of environmental computational spreadsheets
Top, J.L. ; Vos, M. de; Wielemaker, J. ; Schreiber, M. - \ 2015
A methodology for constructing the calculation model of scientific spreadsheets
Vos, M. de; Wielemaker, J. ; Schreiber, G. ; Wielinga, B. ; Top, J.L. - \ 2015
- p. 1 - 8.
Spreadsheets models are frequently used by scientists to analyze research data. These models are typically described in a paper or a report, which serves as single source of information on the underlying research project. As the calculation workflow in these models is not made explicit, readers are not able to fully understand how the research results are calculated, and trace them back to the underlying spreadsheets. This paper proposes a methodology for semi-automatically deriving the calculation workflow underlying a set of spreadsheets. The starting point of our methodology is the cell dependency graph, representing all spreadsheet cells and connections. We automatically aggregate all cells in the graph that represent instances and duplicates of the same quantities, based on analysis of the formula syntax. Subsequently, we use a set of heuristics, incorporating knowledge on spreadsheet design, computational procedures and domain knowledge, to select those quantities, that are relevant for understanding the calculation workflow. We explain and illustrate our methodology by actually applying it on three sets of spreadsheets from existing research projects in the domains of environmental and life science. Results from these case studies show that our constructed calculation models approximate the ground truth calculation workflows, both in terms of content and size, but are not a perfect match.
Impact of Matric Potential and Pore Size Distribution on Growth Dynamics of Filamentous and Non-Filamentous Soil Bacteria
Wolf, A.B. ; Vos, M. de; Boer, W. de; Kowalchuk, G.A. - \ 2013
PLoS ONE 8 (2013)12. - ISSN 1932-6203 - 8 p.
organic-matter - fungi - respiration - diversity
The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.
Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack
Vos, M. de; Oosten, V.R. van; Poecke, R.M.P. van; Pelt, J.A. van; Pozo, M.J. ; Mueller, M.J. ; Buchala, A.J. ; Métraux, J.P. ; Loon, L.C. van; Dicke, M. ; Pieterse, C.M.J. - \ 2005
Molecular Plant-Microbe Interactions 18 (2005)9. - ISSN 0894-0282 - p. 923 - 937.
induced systemic resistance - parasitoid cotesia-rubecula - plant-disease resistance - western flower thrips - egyptian cotton worm - salicylic-acid - gene-expression - pseudomonas-syringae - defense responses - jasmonic acid
Plant defenses against pathogens and insects are regulated differentially by cross-communicating signaling pathways in which salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) play key roles. To understand how plants integrate pathogen- and insect-induced signals into specific defense responses, we monitored the dynamics of SA, JA, and ET signaling in Arabidopsis after attack by a set of microbial pathogens and herbivorous insects with different modes of attack. Arabidopsis plants were exposed to a pathogenic leaf bacterium (Pseudomonas syringae pv. tomato), a pathogenic leaf fungus (Alternaria brassicicola), tissue-chewing caterpillars (Pieris rapae), cell-content-feeding thrips (Frankliniella occidentalis), or phloem-feeding aphids (Myzus persicae). Monitoring the signal signature in each plant-attacker combination showed that the kinetics of SA, JA, and ET production varies greatly in both quantity and timing. Analysis of global gene expression profiles demonstrated that the signal signature characteristic of each Arabidopsis-attacker combination is orchestrated into a surprisingly complex set of transcriptional alterations in which, in all cases, stress-related genes are overrepresented. Comparison of the transcript profiles revealed that consistent changes induced by pathogens and insects with very different modes of attack can show considerable overlap. Of all consistent changes induced by A. brassicicola, Pieris rapae, and F occidentalis, more than 50% also were induced consistently by R syringae. Notably, although these four attackers all stimulated JA biosynthesis, the majority of the changes in JA-responsive gene expression were attacker specific. All together, our study shows that SA, JA, and ET play a primary role in the orchestration of the plant's defense response, but other regulatory mechanisms, such as pathway cross-talk or additional attacker-induced signals, eventually shape the highly complex attacker-specific defense response.
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