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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Fetal gut laser microdissection in combination with RNA preamplification enables epithelial-specific transcriptional profiling
Hemmerling, J. ; Jansen, Jenny ; Müller, M. ; Haller, D. - \ 2015
Journal of Immunological Methods 416 (2015). - ISSN 0022-1759 - p. 189 - 192.
Fetal intestinal epithelium - Laser microdissection - Transcriptional profiling - Whole transcriptome preamplification

Laser microdissection (LMD) technology enables highly specific gene expression analyses of biologically relevant questions at cell- or tissue-specific resolution. Nevertheless, specific cell types are often limited in quantity (i.e. fetal tissue), making high quality RNA extraction and subsequent gene expression approaches via common reverse transcriptase-quantitative PCR (RT-q-PCR) challenging. In the case of fetal gut epithelia representing immune modulatory interphases gene expression analysis with common RT-q-PCR is limited to a few genes (2 dissected area of murine fetal intestinal epithelial cells (IEC) from fetal ileum and colon with subsequent RNA isolation, whole transcriptome preamplification (WTA) and gene expression analysis by microarray and quantitative PCR (qPCR). This workflow allows simultaneous analyses of global (microarrays) and targeted gene expression (qPCR) and consequently increases the number of measurable genes up to 25-fold by qPCR. It is suitable for cryosections from many tissues and species in order to evaluate in utero biological effects on specific effector sites.

Maternal high-fat diet accelerates development of Crohn's disease-like ileitis in TNF ΔaRE/WT offspring
Gruber, Lisa ; Hemmerling, Jana ; Schüppel, Valentina ; Müller, Michael ; Boekschoten, M.V. ; Haller, Dirk - \ 2015
Inflammatory Bowel Diseases 21 (2015)9. - ISSN 1078-0998 - p. 2016 - 2025.
High-fat diet - Inflammatory bowel diseases - Maternal imprinting - Obesity - Transcriptomics

Background: Maternal high-fat diet (HFD) and obesity increases the risk of the offspring to develop inflammatory processes in various organs including the gut. We hypothesized that maternal diet-induced obesity programs the fetal gut towards inflammation in a mouse model of genetically-driven Crohn's disease (CD)-like ileitis. Methods: TNF WT/WT (WT) and TNF ΔARE/WT (ARE) dams were fed an experimental control diet (CTRLD; 13 kJ% fat) or HFD (48 kJ%). Offspring mice were fed CTRLD or HFD at 4 weeks of age. Metabolic characteristics and severity of CD-like ileitis was assessed in 8-and 12-week old WT and ARE offspring measuring tissue histopathology and markers of inflammation in the distal ileum as well as plasma cytokine and LPS levels. To study prenatal effects, we laser microdissected fetal intestinal epithelial cells at 17.5 days postconception and performed microarray-based global gene expression analysis. Results: Maternal HFD significantly accelerated the severity of CD-like ileitis in HFD-fed ARE mice at early life stages associated with increased mucosal neutrophil infiltration, Il12p40 expression, and portal vein LPS levels. In contrast to WT mice, metabolic characteristics of ARE offspring were not affected by maternal HFD. Gene expression patterns in fetal intestinal epithelial cells of ARE mice remained largely unchanged under conditions of maternal diet-induced obesity suggesting that the positive association of intestinal inflammation, portal vein endotoxemia, and plasma TNF levels is independent of prenatal conditioning of the gut epithelium. Conclusions: Maternal HFD promotes the early onset of severe CD-like ileitis in genetically susceptible offspring independent of metabolic alterations.

Extension of the GroIMP modelling platform to allow easy specification of differential equations describing biological processes within plant models
Hemmerling, R. ; Evers, J.B. ; Smolenova, K. ; Buck-Sorlin, G.H. ; Kurth, W. - \ 2013
Computers and Electronics in Agriculture 92 (2013). - ISSN 0168-1699 - p. 1 - 8.
l-systems - growth - allocation - grammar
In simulation models of plant development, physiological processes taking place in plants are typically described in terms of ODEs (Ordinary Differential Equations). On the one hand, those processes drive the development of the plant structure and on the other hand, the developed structure again influences these processes (e.g., photosynthesis, hormone synthesis and transport, and allocation of carbon, nitrogen, etc.). To study this dependence, simulation models, termed functional–structural plant models (FSPMs), are developed. Such models usually operate at the organ scale, considering the topology and the geometry of organs, while being validated at the scale of the plant individual. The open source modelling platform GroIMP was designed for the purpose of creating FSPMs. In GroIMP, the structure of a plant is described by the eXtended L-system language (XL) which is an extension of the Java programming language and works on a general graph structure. It is general enough to be used for many biological problems that can be described by graphs. Until now, to specify and solve ODEs, Java code had to be used and there was no general solution for doing this easily and conveniently in XL. Here we propose an extension to the XL language that allows the user to easily specify ODEs in terms of rule applications. Furthermore, their specification is separated from the numerical solution, with the possibility to choose between different integration methods. The new framework is illustrated with examples of auxin transport in Arabidopsis and gibberellic acid signal transduction in barley and compared with the conventional approach in FSPMs (Euler method). We show that besides the user-friendly specification of ODEs within rules by using a special operator, the results are computed faster, are more stable and accurate. The new framework is also compared with the mathematical formalism of differential L-systems (dL-systems).
Modelling of spatial light distribution in the greenhouse: description of the model
Buck-Sorlin, G.H. ; Hemmerling, R. ; Vos, J. ; Visser, P.H.B. de - \ 2010
In: Proceedings of the Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications - PMA09, Beijing, China, 9-13 November 2009. - Beijing, China : IEEE - p. 79 - 86.
In Dutch greenhouse horticulture, use of additional assimilation light in the form of lamps plays an important role. So far, little is known about the effect of lamp positions, types, and spectra, on light distribution per se and on light interception by the crop canopy in relation to the arrangement and architecture of different crops. We present here a new model of a SON-T assimilation lamp, implemented using the interactive modelling platform GroIMP. A set of virtual lamps is positioned in a simulated 3D greenhouse, which latter exhibits main geometric features and semitransparent surface textures imitating glass and construction elements. Here we show results of the simulation of spatial distribution of light. The application of such virtual lamps for the simulation of light interception in static virtual crops of rose and tomato is briefly illustrated and the extension of this model to other lamp types, such as LED, is discussed
Extension of a functional-structural model of barley for modelling of carbon and nitrogen partitioning
Smolenova, K. ; Buck-Sorlin, G.H. ; Hemmerling, R. ; Kurth, W. - \ 2010
In: Proceedings 6th International Workshop on Functional-Structural Plant Models, 12-17 September 2010, Davis, CA, USA. - Davis, USA : University of California - p. 27 - 29.
Easy specification of differential equations describing biological processes, exemplified for plant hormone dynamics
Hemmerling, R. ; Evers, J.B. ; Kurth, W. - \ 2010
In: Proceedings 6th International Workshop on Functional-Structural Plant Models, Davis, California, USA, 12-17 September 2010. - Davis, USA : University of California - p. 143 - 145.
Comparison of two different light models using a virtual tomato crop
Buck-Sorlin, G.H. ; Sarlikioti, V. ; Hemmerling, R. ; Visser, P.H.B. de - \ 2010
In: Proceedings of the 6th International Workshop on Functional-Structural Plant Models, Davis, California, USA, 12-17 September 2010. - Davis, CA, USA : University of California - p. 245 - 245.
The rule-based language XL and the modelling environment GroIMP illustrated with simulated tree competition
Hemmerling, R. ; Kniemeyer, O. ; Lanwert, D. ; Kurth, W. ; Buck-Sorlin, G.H. - \ 2008
Functional Plant Biology 35 (2008)9-10. - ISSN 1445-4408 - p. 739 - 750.
grammar
The programming language XL ('eXtended L-system language') is an extension of Java, which supports the specification and execution of relational growth grammars, a variant of parallel graph grammars. XL is a powerful generalisation of the well-known L-system approach to functional-structural plant modelling. Some features of XL are discussed that are particularly useful for combining structure and function and for querying plant architectural data, and an exemplary functional-structural plant model of young beech trees is presented that is implemented in XL and includes PAR distribution, assimilate allocation and morphological plasticity. Together with a simpler model of spruce trees, this beech model is included in a virtual landscape with a mixed-species forest stand where competition for light occurs. The open-source platform GroIMP was used for the complete model development process and for visualising the results.
A rule-based model of barley morphogenesis, with special respect to shading and gibberellic acid signal transduction
Buck-Sorlin, G.H. ; Hemmerling, R. ; Kniemeyer, O. ; Burema, B.S. ; Kurth, W. - \ 2008
Annals of Botany 101 (2008). - ISSN 0305-7364 - p. 1109 - 1123.
natural-environment - light environment - leaf emergence - main shoot - growth - phytochrome - biosynthesis - population - elongation - avoidance
Background and Aims: Functional¿structural plant models (FSPM) constitute a paradigm in plant modelling that combines 3D structural and graphical modelling with the simulation of plant processes. While structural aspects of plant development could so far be represented using rule-based formalisms such as Lindenmayer systems, process models were traditionally written using a procedural code. The faithful representation of structures interacting with functions across scales, however, requires a new modelling formalism. Therefore relational growth grammars (RGG) were developed on the basis of Lindenmayer systems. Methods: In order to implement and test RGG, a new modelling language, the eXtended L-system language (XL) was created. Models using XL are interpreted by the interactive, Java-based modelling platform GroIMP. Three models, a semi-quantitative gibberellic acid (GA) signal transduction model, and a phytochrome-based shade detection and object avoidance model, both coupled to an existing morphogenetic structural model of barley (Hordeum vulgare L.), serve as examples to demonstrate the versatility and suitability of RGG and XL to represent the interaction of diverse biological processes across hierarchical scales. Key Results: The dynamics of the concentrations in the signal transduction network could be modelled qualitatively and the phenotypes of GA-response mutants faithfully reproduced. The light model used here was simple to use yet effective enough to carry out local measurement of red:far-red ratios. Suppression of tillering at low red:far-red ratios could be simulated. Conclusions: The RGG formalism is suitable for implementation of multi-scaled FSPM of plants interacting with their environment via hormonal control. However, their ensuing complexity requires careful design. On the positive side, such an FSPM displays knowledge gaps better thereby guiding future experimental design.
New rule-based modelling methods for radiation and object avoidance in virtual plant canopies
Buck-Sorlin, G.H. ; Hemmerling, R. ; Kniemeyer, O. ; Burema, B.S. ; Kurth, W. - \ 2007
In: Plant Growth Modeling and Applications: Second International Symposium on Plant Growth Modeling, Simulation, Visualisation and Application, Beijing, China, November 13-17, 2006. - Los Alamitos : IEEE - ISBN 9780769528519 - p. 22 - 25.
As an extension of the L-system formalism, relational growth grammars (RGG) can be expressed in the programming language XL, allowing for a transparent specification of structural botanical rules, dependency on the environment and process-based models, all in the same framework. We demonstrate this at simple models for growth under the constraints of object avoidance and sensitivity to radiation
The rule-based language XL and the modeling environment GroIMP, illustrated with simulated tree competition
Kniemeyer, O. ; Hemmerling, R. ; Buck-Sorlin, G.H. ; Kurth, W. - \ 2007
In: Proceedings of the 5th International Workshop on Functional-Structural Plant Models, Napier, New Zealand, 4¿9 November 2007. - Hawke's Bay : Print Solutions - p. 23.1 - 23.5.
A dynamic 3D model of rape (Brassica napus L.) computing yield components under variable nitrogen fertilization regimes
Groer, C. ; Kniemeyer, O. ; Hemmerling, R. ; Kurth, W. ; Becker, H. ; Buck-Sorlin, G.H. - \ 2007
In: Proceedings of the 5th International Workshop on Functional-Structural Plant Models, Napier, New Zealand, 4¿9 November 2007. - Hawke's Bay : Print Solutions - p. 4.1 - 4.3.
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